//#define myNoSave //do not save images to disk
#ifdef _MSC_VER
#include <direct.h>
#define getcwd _getcwd
#define chdir _chrdir
#include "io.h"
//#include <math.h>
#define MiniZ
#else
#include <unistd.h>
#ifdef myDisableMiniZ
#undef MiniZ
#else
#define MiniZ
#endif
#endif

#if defined(__APPLE__) && defined(__MACH__)
#endif
#ifndef myDisableZLib
#ifdef MiniZ
#include "miniz.c" //single file clone of libz
#else
#include <zlib.h>
#endif
#else
#undef MiniZ
#endif
#include "tinydir.h"
#include "print.h"
#include "nifti1_io_core.h"
#ifndef USING_R
#include "nifti1.h"
#endif
#include "nii_dicom_batch.h"
#ifndef USING_R
#include "nii_foreign.h"
#endif
#include "nii_dicom.h"
#include "nii_ortho.h"
#ifdef myEnableJNIFTI
 #include "base64.h"
 #include "cJSON.h"
#endif
#include <ctype.h> //toupper
#include <float.h>
#include <math.h>
#include <stdbool.h> //requires VS 2015 or later
#include <stddef.h>
#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/stat.h>
#include <time.h> // clock_t, clock, CLOCKS_PER_SEC
#if defined(_WIN64) || defined(_WIN32)
#include <windows.h> //write to registry
#endif
#ifndef M_PI
#define M_PI 3.14159265358979323846
#endif
#define kSliceTolerance 0.2

#if defined(_WIN64) || defined(_WIN32)
const char kPathSeparator = '\\';
const char kFileSep[2] = "\\";
#else
const char kPathSeparator = '/';
const char kFileSep[2] = "/";
#endif

#ifdef USING_R
#include "ImageList.h"

#undef isnan
#define isnan ISNAN

#undef isfinite
#define isfinite R_FINITE
#endif

#define newTilt

#ifdef USING_R

#ifndef max
#define max(a, b) (a > b ? a : b)
#endif

#ifndef min
#define min(a, b) (a < b ? a : b)
#endif

#else

#ifndef max
#define max(a, b) \
	({ __typeof__ (a) _a = (a); \
		__typeof__ (b) _b = (b); \
	_a > _b ? _a : _b; })
#endif

#ifndef min
#define min(a, b) \
	({ __typeof__ (a) _a = (a); \
		__typeof__ (b) _b = (b); \
	_a < _b ? _a : _b; })
#endif

#endif

#ifdef USING_DCM2NIIXFSWRAPPER
// create the struct to save nifti header, image data, TDICOMdata, & TDTI information.
// no .nii, .bval, .bvec are created.
MRIFSSTRUCT mrifsStruct;
std::vector<MRIFSSTRUCT> mrifsStruct_vector;

// retrieve the struct
MRIFSSTRUCT* nii_getMrifsStruct()
{
	return &mrifsStruct;
}

// free the memory used for the image and dti
void nii_clrMrifsStruct()
{
	free(mrifsStruct.imgM);
	free(mrifsStruct.tdti);
	
	for (int n = 0; n < mrifsStruct.nDcm; n++)
	  free(mrifsStruct.dicomlst[n]);
	
	if (mrifsStruct.dicomlst != NULL)
	  free(mrifsStruct.dicomlst);
		 
}

// retrieve the struct
std::vector<MRIFSSTRUCT>* nii_getMrifsStructVector()
{
  return &mrifsStruct_vector;
}

// free the memory used for the image and dti
void nii_clrMrifsStructVector()
{
  int nitem = mrifsStruct_vector.size();
  for (int n = 0; n < nitem; n++)
  {
    free(mrifsStruct_vector[n].imgM);
    free(mrifsStruct_vector[n].tdti);

    for (int n = 0; n < mrifsStruct.nDcm; n++)
        free(mrifsStruct_vector[n].dicomlst[n]);
    
    if (mrifsStruct_vector[n].dicomlst != NULL)
	free(mrifsStruct_vector[n].dicomlst);
  }
}
#endif

bool isADCnotDTI(TDTI bvec) { //returns true if bval!=0 but all bvecs == 0 (Philips code for derived ADC image)
	return ((!isSameFloat(bvec.V[0], 0.0f)) && //not a B-0 image
			((isSameFloat(bvec.V[1], 0.0f)) && (isSameFloat(bvec.V[2], 0.0f)) && (isSameFloat(bvec.V[3], 0.0f))));
}

struct TDCMsort {
	uint64_t indx, img;
	uint32_t dimensionIndexValues[MAX_NUMBER_OF_DIMENSIONS];
};

struct TSearchList {
	unsigned long numItems, maxItems;
	char **str;
};

#ifndef PATH_MAX
#define PATH_MAX 4096
#endif

void dropFilenameFromPath(char *path) {
	const char *dirPath = strrchr(path, '/'); //UNIX
	if (dirPath == 0)
		dirPath = strrchr(path, '\\'); //Windows
	if (dirPath == NULL) {
		strcpy(path, "");
	} else
		path[dirPath - path] = 0; // please make sure there is enough space in TargetDirectory
	if (strlen(path) == 0) { //file name did not specify path, assume relative path and return current working directory
		//strcat (path,"."); //relative path - use cwd <- not sure if this works on Windows!
		char cwd[PATH_MAX];
		char *ok = getcwd(cwd, sizeof(cwd));
		if (ok != NULL)
			strcat(path, cwd);
	}
}

void dropTrailingFileSep(char *path) { //
	size_t len = strlen(path) - 1;
	if (len <= 0)
		return;
	if (path[len] == '/')
		path[len] = '\0';
	else if (path[len] == '\\')
		path[len] = '\0';
}

bool is_fileexists(const char *filename) {
	FILE *fp = NULL;
	if ((fp = fopen(filename, "r"))) {
		fclose(fp);
		return true;
	}
	return false;
}

#ifndef S_ISDIR
#define S_ISDIR(mode) (((mode)&S_IFMT) == S_IFDIR)
#endif

#ifndef S_ISREG
#define S_ISREG(mode) (((mode)&S_IFMT) == S_IFREG)
#endif

bool is_fileNotDir(const char *path) { //returns false if path is a folder; requires #include <sys/stat.h>
	struct stat buf;
	stat(path, &buf);
	return S_ISREG(buf.st_mode);
} //is_file()

bool is_exe(const char *path) { //requires #include <sys/stat.h>
	struct stat buf;
	if (stat(path, &buf) != 0)
		return false; //file does not eist
	if (!S_ISREG(buf.st_mode))
		return false; //not regular file, e.g. '..'
	return (buf.st_mode & 0111);
	//return (S_ISREG(buf.st_mode) && (buf.st_mode & 0111) );
} //is_exe()

#if defined(_WIN64) || defined(_WIN32)
//Windows does not support lstat
int is_dir(const char *pathname, int follow_link) {
	struct stat s;
	if ((NULL == pathname) || (0 == strlen(pathname)))
		return 0;
	int err = stat(pathname, &s);
	if (-1 == err)
		return 0; // does not exist
	else {
		if (S_ISDIR(s.st_mode)) {
			return 1; // it's a dir
		} else {
			return 0; // exists but is no dir
		}
	}
} // is_dir()
#else //if windows else Unix
int is_dir(const char *pathname, int follow_link) {
	struct stat s;
	int retval;
	if ((NULL == pathname) || (0 == strlen(pathname)))
		return 0; // does not exist
	retval = follow_link ? stat(pathname, &s) : lstat(pathname, &s);
	if ((-1 != retval) && (S_ISDIR(s.st_mode)))
		return 1; // it's a dir
	return 0; // exists but is no dir
} // is_dir()
#endif

void opts2Prefs(struct TDCMopts *opts, struct TDCMprefs *prefs) {
	setDefaultPrefs(prefs);
	prefs->isVerbose = opts->isVerbose;
	prefs->compressFlag = opts->compressFlag;
	prefs->isIgnoreTriggerTimes = opts->isIgnoreTriggerTimes;
}

void geCorrectBvecs(struct TDICOMdata *d, int sliceDir, struct TDTI *vx, int isVerbose) {
	//0018,1312 phase encoding is either in row or column direction
	//0043,1039 (or 0043,a039). b value (as the first number in the string).
	//0019,10bb (or 0019,a0bb). phase diffusion direction
	//0019,10bc (or 0019,a0bc). frequency diffusion direction
	//0019,10bd (or 0019,a0bd). slice diffusion direction
	//These directions are relative to freq,phase,slice, so although no
	//transformations are required, you need to check the direction of the
	//phase encoding. This is in DICOM message 0018,1312. If this has value
	//COL then if swap the x and y value and reverse the sign on the z value.
	//If the phase encoding is not COL, then just reverse the sign on the x value.
	if ((d->manufacturer != kMANUFACTURER_GE) && (d->manufacturer != kMANUFACTURER_CANON))
		return;
	if (d->isBVecWorldCoordinates)
		return; //Canon classic DICOMs use image space, enhanced use world space!
	if ((!d->isEPI) && (d->CSA.numDti == 1))
		d->CSA.numDti = 0; //issue449
	if (d->CSA.numDti < 1)
		return;
	if ((toupper(d->patientOrient[0]) == 'H') && (toupper(d->patientOrient[1]) == 'F') && (toupper(d->patientOrient[2]) == 'S'))
		; //participant was head first supine
	else {
		printWarning("Limited validation for non-HFS (Head first supine) GE DTI: confirm gradient vector transformation\n");
	}
	bool col = false;
	if (d->phaseEncodingRC == 'C')
		col = true;
	else if (d->phaseEncodingRC != 'R') {
		printWarning("Unable to determine DTI gradients, 0018,1312 should be either R or C");
		return;
	}
	if (abs(sliceDir) != 3)
		printWarning("Limited validation for non-Axial DTI: confirm gradient vector transformation.\n");
	//GE vectors from Xiangrui Li' dicm2nii, validated with datasets from https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging
	ivec3 flp;
	if (abs(sliceDir) == 1)
		flp = setiVec3(1, 1, 0); //SAGITTAL
	else if (abs(sliceDir) == 2)
		flp = setiVec3(0, 1, 1); //CORONAL
	else if (abs(sliceDir) == 3)
		flp = setiVec3(0, 0, 1); //AXIAL
	else {
		printMessage("Impossible GE slice orientation!");
		flp = setiVec3(0, 0, 1); //AXIAL???
	}
	if (sliceDir < 0)
		flp.v[2] = 1 - flp.v[2];
	if ((isVerbose) || (!col)) {
		printMessage("Saving %d DTI gradients. GE Reorienting %s : please validate. isCol=%d sliceDir=%d flp=%d %d %d\n", d->CSA.numDti, d->protocolName, col, sliceDir, flp.v[0], flp.v[1], flp.v[2]);
		if (!col)
			printWarning("Reorienting for ROW phase-encoding untested.\n");
	}
	bool scaledBValWarning = false;
	for (int i = 0; i < d->CSA.numDti; i++) {
		float vLen = sqrt((vx[i].V[1] * vx[i].V[1]) + (vx[i].V[2] * vx[i].V[2]) + (vx[i].V[3] * vx[i].V[3]));
		if ((vx[i].V[0] <= FLT_EPSILON) || (vLen <= FLT_EPSILON)) { //bvalue=0
			for (int v = 1; v < 4; v++)
				vx[i].V[v] = 0.0f;
			continue; //do not normalize or reorient 0 vectors
		}
		if ((vLen > 0.03) && (vLen < 0.97)) {
			//bVal scaled by norm(g)^2 issue163,245
			float bValtemp = 0, bVal = 0, bVecScale = 0;
			// rounding by 5 with minimum of 5 if b-value > 0
			bValtemp = vx[i].V[0] * (vLen * vLen);
			if (bValtemp > 0 && bValtemp < 5) {
				bVal = 5;
			} else {
				bVal = (int)((bValtemp + 2.5f) / 5) * 5;
			}
			if (bVal == 0)
				bVecScale = 0;
			else {
				bVecScale = sqrt((float)vx[i].V[0] / bVal);
			}
			if (!scaledBValWarning) {
				printMessage("GE BVal scaling (e.g. %g -> %g s/mm^2)\n", vx[i].V[0], bVal);
				scaledBValWarning = true;
			}
			vx[i].V[0] = bVal;
			vx[i].V[1] = vx[i].V[1] * bVecScale;
			vx[i].V[2] = vx[i].V[2] * bVecScale;
			vx[i].V[3] = vx[i].V[3] * bVecScale;
		}
		if (!col) { //rows need to be swizzled
					//see Stanford dataset Ax_DWI_Tetrahedral_7 unable to resolve between possible solutions
					// http://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging
			float swap = vx[i].V[1];
			vx[i].V[1] = vx[i].V[2];
			vx[i].V[2] = swap;
			vx[i].V[2] = -vx[i].V[2]; //because of transpose?
		}
		for (int v = 0; v < 3; v++)
			if (flp.v[v] == 1)
				vx[i].V[v + 1] = -vx[i].V[v + 1];
		vx[i].V[2] = -vx[i].V[2]; //we read out Y-direction opposite order as dicm2nii, see also opts.isFlipY
	}
	//These next lines are only so files appear identical to old versions of dcm2niix:
	// dicm2nii and dcm2niix generate polar opposite gradient directions.
	// this does not matter, since intensity is the normal of the gradient vector.
	for (int i = 0; i < d->CSA.numDti; i++)
		for (int v = 1; v < 4; v++)
			vx[i].V[v] = -vx[i].V[v];
	//These next lines convert any "-0" values to "0"
	for (int i = 0; i < d->CSA.numDti; i++)
		for (int v = 1; v < 4; v++)
			if (isSameFloat(vx[i].V[v], -0))
				vx[i].V[v] = 0.0f;
} // geCorrectBvecs()

void siemensPhilipsCorrectBvecs(struct TDICOMdata *d, int sliceDir, struct TDTI *vx, int isVerbose) {
	//see Matthew Robson's http://users.fmrib.ox.ac.uk/~robson/internal/Dicom2Nifti111.m
	//convert DTI vectors from scanner coordinates to image frame of reference
	//Uses 6 orient values from ImageOrientationPatient (0020,0037)
	// requires PatientPosition 0018,5100 is HFS (head first supine)
	if ((!d->isBVecWorldCoordinates) && (d->manufacturer != kMANUFACTURER_MEDISO) && (d->manufacturer != kMANUFACTURER_BRUKER) && (d->manufacturer != kMANUFACTURER_TOSHIBA) && (d->manufacturer != kMANUFACTURER_HITACHI) && (d->manufacturer != kMANUFACTURER_UIH) && (d->manufacturer != kMANUFACTURER_SIEMENS) && (d->manufacturer != kMANUFACTURER_PHILIPS))
		return;
	if (d->CSA.numDti < 1)
		return;
	if (d->manufacturer == kMANUFACTURER_UIH) {
		for (int i = 0; i < d->CSA.numDti; i++) {
			vx[i].V[2] = -vx[i].V[2];
			for (int v = 0; v < 4; v++)
				if (vx[i].V[v] == -0.0f)
					vx[i].V[v] = 0.0f; //remove sign from values that are virtually zero
		}
		//simple diagnostics for data prior to realignment: useful as first direction is the same for al Philips sequences
		//for (int i = 0; i < 3; i++)
		//	printf("%g = %g %g %g\n", vx[i].V[0], vx[i].V[1], vx[i].V[2], vx[i].V[3]);
		return;
	} //https://github.com/rordenlab/dcm2niix/issues/225
	if ((toupper(d->patientOrient[0]) == 'H') && (toupper(d->patientOrient[1]) == 'F') && (toupper(d->patientOrient[2]) == 'S'))
		; //participant was head first supine
	else {
		printMessage("Check bvecs: expected Patient Position (0018,5100) to be 'HFS' not '%s'\n", d->patientOrient);
		//return; //see https://github.com/rordenlab/dcm2niix/issues/238
	}
	vec3 read_vector = setVec3(d->orient[1], d->orient[2], d->orient[3]);
	vec3 phase_vector = setVec3(d->orient[4], d->orient[5], d->orient[6]);
	vec3 slice_vector = crossProduct(read_vector, phase_vector);
	read_vector = nifti_vect33_norm(read_vector);
	phase_vector = nifti_vect33_norm(phase_vector);
	slice_vector = nifti_vect33_norm(slice_vector);
	for (int i = 0; i < d->CSA.numDti; i++) {
		float vLen = sqrt((vx[i].V[1] * vx[i].V[1]) + (vx[i].V[2] * vx[i].V[2]) + (vx[i].V[3] * vx[i].V[3]));
		if ((vx[i].V[0] <= FLT_EPSILON) || (vLen <= FLT_EPSILON)) { //bvalue=0
			if ((vx[i].V[0] > 50.0) && (!d->isDerived))	//Philip stores n.b. UIH B=1.25126 Vec=0,0,0 while Philips stored isotropic images
				printWarning("Volume %d appears to be derived image ADC/Isotropic (non-zero b-value with zero vector length)\n", i);
			continue; //do not normalize or reorient b0 vectors
		} //if bvalue=0
		vec3 bvecs_old = setVec3(vx[i].V[1], vx[i].V[2], vx[i].V[3]);
		vec3 bvecs_new = setVec3(dotProduct(bvecs_old, read_vector), dotProduct(bvecs_old, phase_vector), dotProduct(bvecs_old, slice_vector));
		bvecs_new = nifti_vect33_norm(bvecs_new);
		vx[i].V[1] = bvecs_new.v[0];
		vx[i].V[2] = -bvecs_new.v[1];
		vx[i].V[3] = bvecs_new.v[2];
		if (abs(sliceDir) == kSliceOrientMosaicNegativeDeterminant)
			vx[i].V[2] = -vx[i].V[2];
		for (int v = 0; v < 4; v++)
			if (vx[i].V[v] == -0.0f)
				vx[i].V[v] = 0.0f; //remove sign from values that are virtually zero
	} //for each direction
	if (d->isVectorFromBMatrix) {
		printWarning("Saving %d DTI gradients. Eddy users: B-matrix does not encode b-vector polarity (issue 265).\n", d->CSA.numDti);
	} else if (abs(sliceDir) == kSliceOrientMosaicNegativeDeterminant) {
		printWarning("Saving %d DTI gradients. Validate vectors (matrix had a negative determinant).\n", d->CSA.numDti); //perhaps Siemens sagittal
	} else if ((d->sliceOrient == kSliceOrientTra) || (d->manufacturer != kMANUFACTURER_PHILIPS)) {
		if (isVerbose)
			printMessage("Saving %d DTI gradients. Validate vectors.\n", d->CSA.numDti);
	} else if (d->sliceOrient == kSliceOrientUnknown)
		printWarning("Saving %d DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).\n", d->CSA.numDti);
	if (d->manufacturer == kMANUFACTURER_BRUKER)
		printWarning("Bruker DTI support experimental (issue 265).\n");
} // siemensPhilipsCorrectBvecs()

bool isNanPosition(struct TDICOMdata d) { //in 2007 some Siemens RGB DICOMs did not include the PatientPosition 0020,0032 tag
	if (isnan(d.patientPosition[1]))
		return true;
	if (isnan(d.patientPosition[2]))
		return true;
	if (isnan(d.patientPosition[3]))
		return true;
	return false;
} // isNanPosition()

bool isSamePosition(struct TDICOMdata d, struct TDICOMdata d2) {
	if (isNanPosition(d) || isNanPosition(d2))
		return false;
	if (!isSameFloat(d.patientPosition[1], d2.patientPosition[1]))
		return false;
	if (!isSameFloat(d.patientPosition[2], d2.patientPosition[2]))
		return false;
	if (!isSameFloat(d.patientPosition[3], d2.patientPosition[3]))
		return false;
	return true;
} // isSamePosition()

void nii_saveText(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts, struct nifti_1_header *h, char *dcmname) {
	if (!opts.isCreateText)
		return;
	char txtname[2048] = {""};
	strcpy(txtname, pathoutname);
	strcat(txtname, ".txt");
	//printMessage("Saving text %s\n",txtname);
	FILE *fp = fopen(txtname, "w");
	fprintf(fp, "%s\tField Strength:\t%g\tProtocolName:\t%s\tScanningSequence00180020:\t%s\tTE:\t%g\tTR:\t%g\tSeriesNum:\t%ld\tAcquNum:\t%d\tImageNum:\t%d\tImageComments:\t%s\tDateTime:\t%f\tName:\t%s\tConvVers:\t%s\tDoB:\t%s\tGender:\t%c\tAge:\t%s\tDimXYZT:\t%d\t%d\t%d\t%d\tCoil:\t%d\tEchoNum:\t%d\tOrient(6)\t%g\t%g\t%g\t%g\t%g\t%g\tbitsAllocated\t%d\tInputName\t%s\n",
			pathoutname, d.fieldStrength, d.protocolName, d.scanningSequence, d.TE, d.TR, d.seriesNum, d.acquNum, d.imageNum, d.imageComments,
			d.dateTime, d.patientName, kDCMvers, d.patientBirthDate, d.patientSex, d.patientAge, h->dim[1], h->dim[2], h->dim[3], h->dim[4],
			d.coilCrc, d.echoNum, d.orient[1], d.orient[2], d.orient[3], d.orient[4], d.orient[5], d.orient[6],
			d.bitsAllocated, dcmname);
	fclose(fp);
} // nii_saveText()

#define myReadAsciiCsa

#ifdef myReadAsciiCsa
//read from the ASCII portion of the Siemens CSA series header
// this is not recommended: poorly documented
// it is better to stick to the binary portion of the Siemens CSA image header

#if defined(_WIN64) || defined(_WIN32) || defined(__sun) || (defined(__APPLE__) && defined(__POWERPC__))
//https://opensource.apple.com/source/Libc/Libc-1044.1.2/string/FreeBSD/memmem.c
/*-
 * Copyright (c) 2005 Pascal Gloor <pascal.gloor@spale.com>
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions
 * are met:
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the distribution.
 * 3. The name of the author may not be used to endorse or promote
 *    products derived from this software without specific prior written
 *    permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
 * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
 * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
 * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
 * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
 * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
 * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
 * SUCH DAMAGE.
 */
const void *memmem(const char *l, size_t l_len, const char *s, size_t s_len) {
	char *cur, *last;
	const char *cl = (const char *)l;
	const char *cs = (const char *)s;
	/* we need something to compare */
	if (l_len == 0 || s_len == 0)
		return NULL;
	/* "s" must be smaller or equal to "l" */
	if (l_len < s_len)
		return NULL;
	/* special case where s_len == 1 */
	if (s_len == 1)
		return memchr(l, (int)*cs, l_len);
	/* the last position where its possible to find "s" in "l" */
	last = (char *)cl + l_len - s_len;
	for (cur = (char *)cl; cur <= last; cur++)
		if (cur[0] == cs[0] && memcmp(cur, cs, s_len) == 0)
			return cur;
	return NULL;
}
//n.b. memchr returns "const void *" not "void *" for Windows C++ https://msdn.microsoft.com/en-us/library/d7zdhf37.aspx
#endif //for systems without memmem

int readKeyN1(const char *key, char *buffer, int remLength) { //look for text key in binary data stream, return subsequent integer value
	char *keyPos = (char *)memmem(buffer, remLength, key, strlen(key));
	if (!keyPos)
		return -1;
	int ret = 0;
	int i = (int)strlen(key);
	while ((i < remLength) && (keyPos[i] != 0x0A)) {
		if (keyPos[i] >= '0' && keyPos[i] <= '9')
			ret = (10 * ret) + keyPos[i] - '0';
		i++;
	}
	return ret;
} //readKeyN1() //return -1 if key not found

int readKey(const char *key, char *buffer, int remLength) { //look for text key in binary data stream, return subsequent integer value
	int ret = 0;
	char *keyPos = (char *)memmem(buffer, remLength, key, strlen(key));
	if (!keyPos)
		return ret;
	int i = (int)strlen(key);
	while ((i < remLength) && (keyPos[i] != 0x0A)) {
		if (keyPos[i] >= '0' && keyPos[i] <= '9')
			ret = (10 * ret) + keyPos[i] - '0';
		i++;
	}
	return ret;
} //readKey() //return 0 if key not found

float readKeyFloatNan(const char *key, char *buffer, int remLength) { //look for text key in binary data stream, return subsequent integer value
	char *keyPos = (char *)memmem(buffer, remLength, key, strlen(key));
	if (!keyPos)
		return NAN;
	char str[kDICOMStr];
	strcpy(str, "");
	char tmpstr[2];
	tmpstr[1] = 0;
	int i = (int)strlen(key);
	while ((i < remLength) && (keyPos[i] != 0x0A)) {
		if ((keyPos[i] >= '0' && keyPos[i] <= '9') || (keyPos[i] == '.') || (keyPos[i] == '-')) {
			tmpstr[0] = keyPos[i];
			strcat(str, tmpstr);
		}
		i++;
	}
	if (strlen(str) < 1)
		return NAN;
	return atof(str);
} //readKeyFloatNan()

float readKeyFloat(const char *key, char *buffer, int remLength) { //look for text key in binary data stream, return subsequent integer value
	char *keyPos = (char *)memmem(buffer, remLength, key, strlen(key));
	if (!keyPos)
		return 0.0;
	char str[kDICOMStr];
	strcpy(str, "");
	char tmpstr[2];
	tmpstr[1] = 0;
	int i = (int)strlen(key);
	while ((i < remLength) && (keyPos[i] != 0x0A)) {
		if ((keyPos[i] >= '0' && keyPos[i] <= '9') || (keyPos[i] == '.') || (keyPos[i] == '-')) {
			tmpstr[0] = keyPos[i];
			strcat(str, tmpstr);
		}
		i++;
	}
	if (strlen(str) < 1)
		return 0.0;
	return atof(str);
} //readKeyFloat()

void readKeyStrLen(const char *key, char *buffer, int remLength, char *outStr, int outStrLen) {
	//if key is CoilElementID.tCoilID the string 'CoilElementID.tCoilID = 	""Head_32""' returns 'Head32'
	strcpy(outStr, "");
	char *keyPos = (char *)memmem(buffer, remLength, key, strlen(key));
	if (!keyPos)
		return;
	int i = (int)strlen(key);
	int outLen = 0;
	char tmpstr[2];
	tmpstr[1] = 0;
	bool isQuote = false;
	while ((i < remLength) && (keyPos[i] != 0x0A)) {
		if ((isQuote) && (keyPos[i] != '"') && (outLen < outStrLen)) {
			tmpstr[0] = keyPos[i];
			strcat(outStr, tmpstr);
			outLen++;
		}
		if (keyPos[i] == '"') {
			if (outLen > 0)
				break;
			isQuote = true;
		}
		i++;
	}
} //readKeyStr()

void readKeyStr(const char *key, char *buffer, int remLength, char *outStr) {
    readKeyStrLen(key, buffer, remLength, outStr, kDICOMStrLarge);
} //readKeyStr()

int phoenixOffsetCSASeriesHeader(unsigned char *buff, int lLength) {
	//returns offset to ASCII Phoenix data
	if (lLength < 36)
		return 0;
	if ((buff[0] != 'S') || (buff[1] != 'V') || (buff[2] != '1') || (buff[3] != '0'))
		return EXIT_FAILURE;
	int lPos = 8; //skip 8 bytes of data, 'SV10' plus 2 32-bit values unused1 and unused2
	int lnTag = buff[lPos] + (buff[lPos + 1] << 8) + (buff[lPos + 2] << 16) + (buff[lPos + 3] << 24);
	if ((buff[lPos + 4] != 77) || (lnTag < 1))
		return 0;
	lPos += 8; //skip 8 bytes of data, 32-bit lnTag plus 77 00 00 0
	TCSAtag tagCSA;
	TCSAitem itemCSA;
	for (int lT = 1; lT <= lnTag; lT++) {
		memcpy(&tagCSA, &buff[lPos], sizeof(tagCSA)); //read tag
		if (!littleEndianPlatform())
			nifti_swap_4bytes(1, &tagCSA.nitems);
		if (tagCSA.nitems > 128) {
			printError("%d n_tags CSA Series Header corrupted (0029,1020 ) see issue 633.\n", tagCSA.nitems);
			return EXIT_FAILURE;
		}
		//printf("%d CSA of %s %d\n",lPos, tagCSA.name, tagCSA.nitems);
		lPos += sizeof(tagCSA);
		if (strcmp(tagCSA.name, "MrPhoenixProtocol") == 0)
			return lPos;
		for (int lI = 1; lI <= tagCSA.nitems; lI++) {
			memcpy(&itemCSA, &buff[lPos], sizeof(itemCSA));
			lPos += sizeof(itemCSA);
			if (!littleEndianPlatform())
				nifti_swap_4bytes(1, &itemCSA.xx2_Len);
			lPos += ((itemCSA.xx2_Len + 3) / 4) * 4;
		}
	}
	return 0;
} //phoenixOffsetCSASeriesHeader()

#define kMaxWipFree 64
#define freeDiffusionMaxN 512
typedef struct {
	float TE0, TE1, delayTimeInTR, phaseOversampling, phaseResolution, txRefAmp, accelFactTotal;
	int lInvContrasts, lContrasts ,phaseEncodingLines, existUcImageNumb, ucMode, baseResolution, interp, partialFourier, echoSpacing,
		difBipolar, parallelReductionFactorInPlane, refLinesPE, combineMode, patMode, ucMTC, accelFact3D, freeDiffusionN;
	float alFree[kMaxWipFree];
	float adFree[kMaxWipFree];
	float alTI[kMaxWipFree];
	float sPostLabelingDelay, ulLabelingDuration, dAveragesDouble, dThickness, ulShape, sPositionDTra, sNormalDTra;
	vec3 freeDiffusionVec[freeDiffusionMaxN];
} TCsaAscii;

void siemensCsaAscii(const char *filename, TCsaAscii *csaAscii, int csaOffset, int csaLength, float *shimSetting, char *coilID, char *consistencyInfo, char *coilElements, char *pulseSequenceDetails, char *fmriExternalInfo, char *protocolName, char *wipMemBlock) {
	//reads ASCII portion of CSASeriesHeaderInfo and returns lEchoTrainDuration or lEchoSpacing value
	// returns 0 if no value found
	csaAscii->sPostLabelingDelay = 0.0;
	csaAscii->ulLabelingDuration = 0.0;
	csaAscii->TE0 = 0.0;
	csaAscii->TE1 = 0.0;
	csaAscii->delayTimeInTR = -0.001;
	csaAscii->phaseOversampling = 0.0;
	csaAscii->phaseResolution = 0.0;
	csaAscii->txRefAmp = 0.0;
	csaAscii->phaseEncodingLines = 0;
	csaAscii->existUcImageNumb = 0;
	csaAscii->ucMode = -1;
	csaAscii->baseResolution = 0;
	csaAscii->interp = 0;
	csaAscii->partialFourier = 0;
	csaAscii->echoSpacing = 0;
	csaAscii->lInvContrasts = 0;
	csaAscii->lContrasts = 0;
	csaAscii->difBipolar = 0; //0=not assigned,1=bipolar,2=monopolar
	csaAscii->parallelReductionFactorInPlane = 0;
	csaAscii->accelFact3D = 0;//lAccelFact3D
	csaAscii->accelFactTotal = 0.0;
	csaAscii->refLinesPE = 0;
	csaAscii->combineMode = 0;
	csaAscii->patMode = 0;
	csaAscii->ucMTC = 0;
	csaAscii->freeDiffusionN = 0;
	for (int i = 0; i < 8; i++)
		shimSetting[i] = 0.0;
	strcpy(coilID, "");
	strcpy(consistencyInfo, "");
	strcpy(coilElements, "");
	strcpy(pulseSequenceDetails, "");
	strcpy(fmriExternalInfo, "");
	strcpy(wipMemBlock, "");
	strcpy(protocolName, "");
	if ((csaOffset < 0) || (csaLength < 8))
		return;
	FILE *pFile = fopen(filename, "rb");
	if (pFile == NULL)
		return;
	fseek(pFile, 0, SEEK_END);
	long lSize = ftell(pFile);
	if (lSize < (csaOffset + csaLength)) {
		fclose(pFile);
		return;
	}
	fseek(pFile, csaOffset, SEEK_SET);
	char *buffer = (char *)malloc(csaLength);
	if (buffer == NULL)
		return;
	size_t result = fread(buffer, 1, csaLength, pFile);
	if ((int)result != csaLength)
		return;
	fclose(pFile);
	//next bit complicated: restrict to ASCII portion to avoid buffer overflow errors in BINARY portion
	int startAscii = phoenixOffsetCSASeriesHeader((unsigned char *)buffer, csaLength);
	//n.b. previous function parses binary V* "SV10" portion of header
	// it will return "EXIT_FAILURE for text based X* "<XProtocol>"
	int csaLengthTrim = csaLength;
	char *bufferTrim = buffer;
	if ((startAscii > 0) && (startAscii < csaLengthTrim)) { //ignore binary data at start
		bufferTrim += startAscii;
		csaLengthTrim -= startAscii;
	}
	char keyStr[] = "### ASCCONV BEGIN"; //skip to start of ASCII often "### ASCCONV BEGIN ###" but also "### ASCCONV BEGIN object=MrProtDataImpl@MrProtocolData"
	char *keyPos = (char *)memmem(bufferTrim, csaLengthTrim, keyStr, strlen(keyStr));
	if (keyPos) {
		//We can detect multi-echo MPRAGE here, e.g. "lContrasts = 4"- but ideally we want an earlier detection
		csaLengthTrim -= (keyPos - bufferTrim);
//FmriExternalInfo listed AFTER AscConvEnd and uses different delimiter ||
// char keyStrExt[] = "FmriExternalInfo";
// readKeyStr(keyStrExt, keyPos, csaLengthTrim, fmriExternalInfo);
#define myCropAtAscConvEnd
#ifdef myCropAtAscConvEnd
		char keyStrEnd[] = "### ASCCONV END";
		char *keyPosEnd = (char *)memmem(keyPos, csaLengthTrim, keyStrEnd, strlen(keyStrEnd));
		if ((keyPosEnd) && ((keyPosEnd - keyPos) < csaLengthTrim)) //ignore binary data at end
			csaLengthTrim = (int)(keyPosEnd - keyPos);
#endif
		char keyStrLns[] = "sKSpace.lPhaseEncodingLines";
		csaAscii->phaseEncodingLines = readKey(keyStrLns, keyPos, csaLengthTrim);
		char keyStrUcImg[] = "sSliceArray.ucImageNumb"; //some non-mosaics like ToF include "sSliceArray.ucImageNumbSag"
		csaAscii->existUcImageNumb = readKey(keyStrUcImg, keyPos, csaLengthTrim);
		char keyStrUcMode[] = "sSliceArray.ucMode";
		csaAscii->ucMode = readKeyN1(keyStrUcMode, keyPos, csaLengthTrim);
		char keyStrBase[] = "sKSpace.lBaseResolution";
		csaAscii->baseResolution = readKey(keyStrBase, keyPos, csaLengthTrim);
		char keyStrInterp[] = "sKSpace.uc2DInterpolation";
		csaAscii->interp = readKey(keyStrInterp, keyPos, csaLengthTrim);
		char keyStrPF[] = "sKSpace.ucPhasePartialFourier";
		csaAscii->partialFourier = readKey(keyStrPF, keyPos, csaLengthTrim);
		char keyStrES[] = "sFastImaging.lEchoSpacing";
		csaAscii->echoSpacing = readKey(keyStrES, keyPos, csaLengthTrim);
		char keyStrNumInv[] = "lInvContrasts";
		csaAscii->lInvContrasts = readKey(keyStrNumInv, keyPos, csaLengthTrim);
		char keyStrNumEcho[] = "lContrasts";
		csaAscii->lContrasts = readKey(keyStrNumEcho, keyPos, csaLengthTrim);
		char keyStrDS[] = "sDiffusion.dsScheme";
		csaAscii->difBipolar = readKey(keyStrDS, keyPos, csaLengthTrim);
		if (csaAscii->difBipolar == 0) {
			char keyStrROM[] = "ucReadOutMode";
			csaAscii->difBipolar = readKey(keyStrROM, keyPos, csaLengthTrim);
			if ((csaAscii->difBipolar >= 1) && (csaAscii->difBipolar <= 2)) { //E11C Siemens/CMRR dsScheme: 1=bipolar, 2=unipolar, B17 CMRR ucReadOutMode 0x1=monopolar, 0x2=bipolar
				csaAscii->difBipolar = 3 - csaAscii->difBipolar;
			} //https://github.com/poldracklab/fmriprep/pull/1359#issuecomment-448379329
		}
		char keyStrAF[] = "sPat.lAccelFactPE";
		csaAscii->parallelReductionFactorInPlane = readKey(keyStrAF, keyPos, csaLengthTrim);
		char keyStrAF3D[] = "sPat.lAccelFact3D";
		csaAscii->accelFact3D = readKey(keyStrAF3D, keyPos, csaLengthTrim);
		char keyStrAFTotal[] = "sPat.dTotalAccelFact";
		csaAscii->accelFactTotal = readKeyFloat(keyStrAFTotal, keyPos, csaLengthTrim);
		//issue 672: the tag "sSliceAcceleration.lMultiBandFactor" is not reliable:
		//  series 7 dcm_qa_xa30 has x3 multiband, but this tag reports "1" (perhaps cmrr sequences)
		//char keyStrMB[] = "sSliceAcceleration.lMultiBandFactor";
		//csaAscii->multiBandFactor = readKey(keyStrMB, keyPos, csaLengthTrim);
		char keyStrRef[] = "sPat.lRefLinesPE";
		csaAscii->refLinesPE = readKey(keyStrRef, keyPos, csaLengthTrim);
		char keyStrCombineMode[] = "ucCoilCombineMode";
		csaAscii->combineMode = readKeyN1(keyStrCombineMode, keyPos, csaLengthTrim);
		//BIDS CoilCombinationMethod <- Siemens 'Coil Combine Mode' CSA ucCoilCombineMode 1 = Sum of Squares, 2 = Adaptive Combine,
		//printf("CoilCombineMode %d\n", csaAscii->combineMode);
		char keyStrPATMode[] = "sPat.ucPATMode"; //n.b. field set even if PAT not enabled, e.g. will list SENSE for a R-factor of 1
		csaAscii->patMode = readKeyN1(keyStrPATMode, keyPos, csaLengthTrim);
		char keyStrucMTC[] = "sPrepPulses.ucMTC"; //n.b. field set even if PAT not enabled, e.g. will list SENSE for a R-factor of 1
		csaAscii->ucMTC = readKeyN1(keyStrucMTC, keyPos, csaLengthTrim);
		//printf("PATMODE %d\n", csaAscii->patMode);
		//char keyStrETD[] = "sFastImaging.lEchoTrainDuration";
		//*echoTrainDuration = readKey(keyStrETD, keyPos, csaLengthTrim);
		//char keyStrEF[] = "sFastImaging.lEPIFactor";
		//ret = readKey(keyStrEF, keyPos, csaLengthTrim);
		char keyStrCoil[] = "sCoilElementID.tCoilID";
		readKeyStr(keyStrCoil, keyPos, csaLengthTrim, coilID);
		char keyStrCI[] = "sProtConsistencyInfo.tMeasuredBaselineString";
		readKeyStr(keyStrCI, keyPos, csaLengthTrim, consistencyInfo);
		char keyStrCS[] = "sCoilSelectMeas.sCoilStringForConversion";
		readKeyStr(keyStrCS, keyPos, csaLengthTrim, coilElements);
		char keyStrSeq[] = "tSequenceFileName";
		readKeyStr(keyStrSeq, keyPos, csaLengthTrim, pulseSequenceDetails);
		char keyStrWipMemBlock[] = "sWipMemBlock.tFree";
		readKeyStrLen(keyStrWipMemBlock, keyPos, csaLengthTrim, wipMemBlock, kDICOMStrExtraLarge);
		char keyStrPn[] = "tProtocolName";
		readKeyStr(keyStrPn, keyPos, csaLengthTrim, protocolName);
		char keyStrTE0[] = "alTE[0]";
		csaAscii->TE0 = readKeyFloatNan(keyStrTE0, keyPos, csaLengthTrim);
		char keyStrTE1[] = "alTE[1]";
		csaAscii->TE1 = readKeyFloatNan(keyStrTE1, keyPos, csaLengthTrim);
		char keyStrPLD[] = "sAsl.sPostLabelingDelay[0]";
		csaAscii->sPostLabelingDelay = readKeyFloatNan(keyStrPLD, keyPos, csaLengthTrim);
		char keyStrLD[] = "sAsl.ulLabelingDuration";
		csaAscii->ulLabelingDuration = readKeyFloatNan(keyStrLD, keyPos, csaLengthTrim);
		//read ALL alTI[*] values
		for (int k = 0; k < kMaxWipFree; k++)
			csaAscii->alTI[k] = NAN;
		char keyStrTiFree[] = "alTI[";
		//check if ANY csaAscii.alFree tags exist
		char *keyPosTi = (char *)memmem(keyPos, csaLengthTrim, keyStrTiFree, strlen(keyStrTiFree));
		if (keyPosTi) {
			for (int k = 0; k < kMaxWipFree; k++) {
				char txt[1024] = {""};
				snprintf(txt, 1024, "%s%d]", keyStrTiFree, k);
				csaAscii->alTI[k] = readKeyFloatNan(txt, keyPos, csaLengthTrim);
			}
		}
		//read ALL csaAscii.alFree[*] values
		for (int k = 0; k < kMaxWipFree; k++)
			csaAscii->alFree[k] = 0.0;
		char keyStrAlFree[] = "sWipMemBlock.alFree[";
		//check if ANY csaAscii.alFree tags exist
		char *keyPosFree = (char *)memmem(keyPos, csaLengthTrim, keyStrAlFree, strlen(keyStrAlFree));
		if (keyPosFree) {
			for (int k = 0; k < kMaxWipFree; k++) {
				char txt[1024] = {""};
				snprintf(txt, 1024, "%s%d]", keyStrAlFree, k);
				csaAscii->alFree[k] = readKeyFloat(txt, keyPos, csaLengthTrim);
			}
		}
		//read ALL csaAscii.adFree[*] values
		for (int k = 0; k < kMaxWipFree; k++)
			csaAscii->adFree[k] = NAN;
		char keyStrAdFree[50];
		strcpy(keyStrAdFree, "sWipMemBlock.adFree[");
		//char keyStrAdFree[] = "sWipMemBlock.adFree[";
		//check if ANY csaAscii.adFree tags exist
		keyPosFree = (char *)memmem(keyPos, csaLengthTrim, keyStrAdFree, strlen(keyStrAdFree));
		if (!keyPosFree) { //"Wip" -> "WiP", modern -> old Siemens
			strcpy(keyStrAdFree, "sWiPMemBlock.adFree[");
			keyPosFree = (char *)memmem(keyPos, csaLengthTrim, keyStrAdFree, strlen(keyStrAdFree));
		}
		if (keyPosFree) {
			for (int k = 0; k < kMaxWipFree; k++) {
				char txt[1024] = {""};
				snprintf(txt, 1024, "%s%d]", keyStrAdFree, k);
				csaAscii->adFree[k] = readKeyFloatNan(txt, keyPos, csaLengthTrim);
			}
		}
		//read labelling plane
		char keyStrDThickness[] = "sRSatArray.asElm[1].dThickness";
		csaAscii->dThickness = readKeyFloat(keyStrDThickness, keyPos, csaLengthTrim);
		if (csaAscii->dThickness > 0.0) {
			char keyStrUlShape[] = "sRSatArray.asElm[1].ulShape";
			csaAscii->ulShape = readKeyFloat(keyStrUlShape, keyPos, csaLengthTrim);
			char keyStrSPositionDTra[] = "sRSatArray.asElm[1].sPosition.dTra";
			csaAscii->sPositionDTra = readKeyFloat(keyStrSPositionDTra, keyPos, csaLengthTrim);
			char keyStrSNormalDTra[] = "sRSatArray.asElm[1].sNormal.dTra";
			csaAscii->sNormalDTra = readKeyFloat(keyStrSNormalDTra, keyPos, csaLengthTrim);
		}
		//Read NEX number of averages
		char keyStrDAveragesDouble[] = "dAveragesDouble";
		csaAscii->dAveragesDouble = readKeyFloat(keyStrDAveragesDouble, keyPos, csaLengthTrim);
		//read delay time
		char keyStrDelay[] = "lDelayTimeInTR";
		csaAscii->delayTimeInTR = readKeyFloat(keyStrDelay, keyPos, csaLengthTrim);
		char keyStrOver[] = "sKSpace.dPhaseOversamplingForDialog";
		csaAscii->phaseOversampling = readKeyFloat(keyStrOver, keyPos, csaLengthTrim);
		char keyStrPhase[] = "sKSpace.dPhaseResolution";
		csaAscii->phaseResolution = readKeyFloat(keyStrPhase, keyPos, csaLengthTrim);
		char keyStrAmp[] = "sTXSPEC.asNucleusInfo[0].flReferenceAmplitude";
		csaAscii->txRefAmp = readKeyFloat(keyStrAmp, keyPos, csaLengthTrim);
		//lower order shims: newer sequences
		char keyStrSh0[] = "sGRADSPEC.asGPAData[0].lOffsetX";
		shimSetting[0] = readKeyFloat(keyStrSh0, keyPos, csaLengthTrim);
		char keyStrSh1[] = "sGRADSPEC.asGPAData[0].lOffsetY";
		shimSetting[1] = readKeyFloat(keyStrSh1, keyPos, csaLengthTrim);
		char keyStrSh2[] = "sGRADSPEC.asGPAData[0].lOffsetZ";
		shimSetting[2] = readKeyFloat(keyStrSh2, keyPos, csaLengthTrim);
		//lower order shims: older sequences
		char keyStrSh0s[] = "sGRADSPEC.lOffsetX";
		if (shimSetting[0] == 0.0)
			shimSetting[0] = readKeyFloat(keyStrSh0s, keyPos, csaLengthTrim);
		char keyStrSh1s[] = "sGRADSPEC.lOffsetY";
		if (shimSetting[1] == 0.0)
			shimSetting[1] = readKeyFloat(keyStrSh1s, keyPos, csaLengthTrim);
		char keyStrSh2s[] = "sGRADSPEC.lOffsetZ";
		if (shimSetting[2] == 0.0)
			shimSetting[2] = readKeyFloat(keyStrSh2s, keyPos, csaLengthTrim);
		//higher order shims: older sequences
		char keyStrSh3[] = "sGRADSPEC.alShimCurrent[0]";
		shimSetting[3] = readKeyFloat(keyStrSh3, keyPos, csaLengthTrim);
		char keyStrSh4[] = "sGRADSPEC.alShimCurrent[1]";
		shimSetting[4] = readKeyFloat(keyStrSh4, keyPos, csaLengthTrim);
		char keyStrSh5[] = "sGRADSPEC.alShimCurrent[2]";
		shimSetting[5] = readKeyFloat(keyStrSh5, keyPos, csaLengthTrim);
		char keyStrSh6[] = "sGRADSPEC.alShimCurrent[3]";
		shimSetting[6] = readKeyFloat(keyStrSh6, keyPos, csaLengthTrim);
		char keyStrSh7[] = "sGRADSPEC.alShimCurrent[4]";
		shimSetting[7] = readKeyFloat(keyStrSh7, keyPos, csaLengthTrim);
        // pull out the directions in the DVI
        char keyStrDVIn[] = "sDiffusion.sFreeDiffusionData.lDiffDirections";
        int nDiffDir = readKey(keyStrDVIn, keyPos, csaLengthTrim);
        csaAscii->freeDiffusionN = min(nDiffDir, freeDiffusionMaxN);

        //printMessage("Free diffusion: %i\n", csaAscii->freeDiffusionN);

        for (int k = 0; k < csaAscii->freeDiffusionN; k++) {
            char txt[128];

            snprintf(txt, 128, "sDiffusion.sFreeDiffusionData.asDiffDirVector[%i].dSag", k);
            float x = readKeyFloat(txt, keyPos, csaLengthTrim);

            snprintf(txt, 128, "sDiffusion.sFreeDiffusionData.asDiffDirVector[%i].dCor", k);
            float y = readKeyFloat(txt, keyPos, csaLengthTrim);

            snprintf(txt, 128, "sDiffusion.sFreeDiffusionData.asDiffDirVector[%i].dTra", k);
            float z = readKeyFloat(txt, keyPos, csaLengthTrim);

            csaAscii->freeDiffusionVec[k].v[0] = x;
            csaAscii->freeDiffusionVec[k].v[1] = y;
            csaAscii->freeDiffusionVec[k].v[2] = z;
        }
	}
	free(buffer);
	return;
} // siemensCsaAscii()

#endif //myReadAsciiCsa()

#ifndef myDisableZLib
//Uncomment next line to decode GE Protocol Data Block, for caveats see https://github.com/rordenlab/dcm2niix/issues/163
#define myReadGeProtocolBlock
#endif
#ifdef myReadGeProtocolBlock
int geProtocolBlock(const char *filename, int geOffset, int geLength, int isVerbose, int *sliceOrder, int *viewOrder, int *mbAccel, int *nSlices, float *groupDelay, char ioptGE[], char seqStr[]) {
	*sliceOrder = -1;
	*viewOrder = 0;
	*mbAccel = 0;
	*nSlices = 0;
	*groupDelay = 0.0;
	int ret = EXIT_FAILURE;
	if ((geOffset < 0) || (geLength < 20))
		return ret;
	FILE *pFile = fopen(filename, "rb");
	if (pFile == NULL)
		return ret;
	fseek(pFile, 0, SEEK_END);
	long lSize = ftell(pFile);
	if (lSize < (geOffset + geLength)) {
		fclose(pFile);
		return ret;
	}
	fseek(pFile, geOffset, SEEK_SET);
	uint8_t *pCmp = (uint8_t *)malloc(geLength); //uint8_t -> mz_uint8
	if (pCmp == NULL)
		return ret;
	size_t result = fread(pCmp, 1, geLength, pFile);
	if ((int)result != geLength)
		return ret;
	int cmpSz = geLength;
	//http://www.forensicswiki.org/wiki/Gzip
	// always little endia! http://www.onicos.com/staff/iz/formats/gzip.html
	if (cmpSz < 20)
		return ret;
	if ((pCmp[0] != 31) || (pCmp[1] != 139) || (pCmp[2] != 8))
		return ret; //check signature and deflate algorithm
	uint8_t flags = pCmp[3];
	bool isFNAME = ((flags & 0x08) == 0x08);
	bool isFCOMMENT = ((flags & 0x10) == 0x10);
	int hdrSz = 10;
	if (isFNAME) { //skip null-terminated string FNAME
		for (; hdrSz < cmpSz; hdrSz++)
			if (pCmp[hdrSz] == 0)
				break;
		hdrSz++;
	}
	if (isFCOMMENT) { //skip null-terminated string COMMENT
		for (; hdrSz < cmpSz; hdrSz++)
			if (pCmp[hdrSz] == 0)
				break;
		hdrSz++;
	}
	uint32_t unCmpSz = ((uint32_t)pCmp[cmpSz - 4]) + ((uint32_t)pCmp[cmpSz - 3] << 8) + ((uint32_t)pCmp[cmpSz - 2] << 16) + ((uint32_t)pCmp[cmpSz - 1] << 24);
	//printf(">> %d %d %zu %zu %zu\n", isFNAME, isFCOMMENT, cmpSz, unCmpSz, hdrSz);
	z_stream s;
	memset(&s, 0, sizeof(z_stream));
#ifdef myDisableMiniZ
#define MZ_DEFAULT_WINDOW_BITS 15 // Window bits
#endif
	inflateInit2(&s, -MZ_DEFAULT_WINDOW_BITS);
	uint8_t *pUnCmp = (uint8_t *)malloc((size_t)unCmpSz);
	s.avail_out = unCmpSz;
	s.next_in = pCmp + hdrSz;
	s.avail_in = cmpSz - hdrSz - 8;
	s.next_out = (uint8_t *)pUnCmp;
#ifdef myDisableMiniZ
	ret = inflate(&s, Z_SYNC_FLUSH);
	if (ret != Z_STREAM_END) {
		free(pUnCmp);
		return EXIT_FAILURE;
	}
#else
	ret = mz_inflate(&s, MZ_SYNC_FLUSH);
	if (ret != MZ_STREAM_END) {
		free(pUnCmp);
		return EXIT_FAILURE;
	}
#endif
	//https://groups.google.com/forum/#!msg/comp.protocols.dicom/mxnCkv8A-i4/W_uc6SxLwHQJ
	// DISCOVERY MR750 / 24\MX\MR Software release:DV24.0_R01_1344.a) are now storing an XML file
	// <?xml version="1.0" encoding="UTF-8"?>
	if ((pUnCmp[0] == '<') && (pUnCmp[1] == '?'))
		printWarning("New XML-based GE Protocol Block is not yet supported: please report issue on dcm2niix Github page\n");
	char keyStrSO[] = "\nSLICEORDER";
	*sliceOrder = readKeyN1(keyStrSO, (char *)pUnCmp, unCmpSz);
	char keyStrVO[] = "VIEWORDER";
	*viewOrder = readKey(keyStrVO, (char *)pUnCmp, unCmpSz);
	char keyStrMB[] = "MBACCEL";
	*mbAccel = readKey(keyStrMB, (char *)pUnCmp, unCmpSz);
	char keyStrNS[] = "NOSLC";
	*nSlices = readKey(keyStrNS, (char *)pUnCmp, unCmpSz);
	char keyStrDELACQ[] = "DELACQ";
	char DELACQ[100];
	readKeyStr(keyStrDELACQ, (char *)pUnCmp, unCmpSz, DELACQ);
	char keyStrGD[] = "DELACQNOAV";
	*groupDelay = readKeyFloat(keyStrGD, (char *)pUnCmp, unCmpSz);

	char keyStrPSEQ[] = "PSEQ";
	readKeyStr(keyStrPSEQ, (char *)pUnCmp, unCmpSz, seqStr);
	char keyStrIOPT[] = "IOPT";
	readKeyStr(keyStrIOPT, (char *)pUnCmp, unCmpSz, ioptGE);
	char PHASEDELAYS1[10000];
	char keyStrPHASEDELAYS1[] = "PHASEDELAYS1";
	readKeyStr(keyStrPHASEDELAYS1, (char *)pUnCmp, unCmpSz, PHASEDELAYS1);
	if (strstr(ioptGE, "MPh") != NULL) {
		if (strcmp(DELACQ, "Minimum") == 0) {
			*groupDelay = 0;
		}
		if (strstr(ioptGE, "MPhVar") != NULL) {
			*groupDelay = -1;
			// Multiphase EPI with Variable Delays
			// TO-DO
			// NEED TO rescue ALL_PHASES case (=Group delay)
			// IF values in PHASEDELAYS1 are all same except 1st value (0), this case should be same as Group Delay
		}
	}
	if (isVerbose > 1) {
		printMessage("GE Protocol Block %s bytes %d compressed, %d uncompressed @ %d\n", filename, geLength, unCmpSz, geOffset);
		printMessage(" ViewOrder %d SliceOrder %d\n", *viewOrder, *sliceOrder);
		printMessage("%s\n", pUnCmp);
	}
	free(pUnCmp);
	return EXIT_SUCCESS;
}
#endif //myReadGeProtocolBlock()

void json_Str(FILE *fp, const char *sLabel, char *sVal) { // issue131,425
	if (strlen(sVal) < 1)
		return;
	unsigned char sValEsc[2048] = {""};
	unsigned char *iVal = (unsigned char *)sVal;
	int o = 0;
	for (int i = 0; i < (int)strlen(sVal); i++) {
		//escape double quote (") and Backslash
		//if ((sVal[i] == '"') || (sVal[i] == '\\') || (sVal[i] == '/')) { //issue640: escape double quotes, back slash, or slash
		if ((sVal[i] == '"') || (sVal[i] == '\\')) { //escape double quotes and back slash
			sValEsc[o] = '\\';
			o++;
		}
		if ((sVal[i] >= 0x01) && (sVal[i] <= 0x07))
			continue; //control characters like "bell"
		//http://dicom.nema.org/medical/dicom/current/output/html/part05.html
		//0x08 Backspace is replaced with \b
		//0x09 Tab is replaced with \t
		//0x0A Newline is replaced with \n
		//0x0B Escape ??
		//0x0C Form feed is replaced with \f
		//0x0D Carriage return is replaced with \r
		if ((sVal[i] >= 0x08) && (sVal[i] <= 0x0D)) {
			sValEsc[o] = '\\';
			o++;
			if (sVal[i] == 0x08)
				sValEsc[o] = 'b';
			if (sVal[i] == 0x09)
				sValEsc[o] = '9';
			if (sVal[i] == 0x0A)
				sValEsc[o] = 'n';
			if (sVal[i] == 0x0B)
				sValEsc[o] = '\\';
			if (sVal[i] == 0x0C)
				sValEsc[o] = 'f';
			if (sVal[i] == 0x0D)
				sValEsc[o] = 'r';
			o++;
			continue;
		}
		//https://stackoverflow.com/questions/4059775/convert-iso-8859-1-strings-to-utf-8-in-c-c
		if (iVal[i] >= 128) {
			sValEsc[o] = 0xc2 + (iVal[i] > 0xbf);
			o++;
			sValEsc[o] = (iVal[i] & 0x3f) + 0x80;
		} else {
			sValEsc[o] = sVal[i];
		}
		o++;
	}
	sValEsc[o] = '\0';
	fprintf(fp, sLabel, sValEsc);
} //json_Str

void json_FloatNotNan(FILE *fp, const char *sLabel, float sVal) {
	if (isnan(sVal))
		return;
	fprintf(fp, sLabel, sVal);
} //json_Float

void print_FloatNotNan(const char *sLabel, int iVal, float sVal) {
	if (isnan(sVal))
		return;
	printMessage(sLabel, iVal, sVal);
} //json_Float

void json_Float(FILE *fp, const char *sLabel, float sVal) {
	if (!isfinite(sVal)) { //isfinite() defined in C99
		// https://github.com/bids-standard/bids-2-devel/issues/12
		printWarning(sLabel, sVal);
		return;
	}
	if (sVal <= 0.0)
		return;
	fprintf(fp, sLabel, sVal);
} //json_Float

void json_Bool(FILE *fp, const char *sLabel, int sVal) {
	// json_Str(fp, "\t\"MTState\"", d.mtState);
	//n.b. in JSON, true and false are lower case, whereas in Python they are capitalized
	// only print 0 and >=1 for false and true, ignore negative values
	if (sVal == 0)
		fprintf(fp, sLabel, "false");
	if (sVal > 0)
		fprintf(fp, sLabel, "true");
} //json_Bool

void rescueProtocolName(struct TDICOMdata *d, const char *filename) {
	//tools like gdcmanon strip protocol name (0018,1030) but for Siemens we can recover it from CSASeriesHeaderInfo (0029,1020)
	if ((d->manufacturer != kMANUFACTURER_SIEMENS) || (d->CSA.SeriesHeader_offset < 1) || (d->CSA.SeriesHeader_length < 1))
		return;
	if (strlen(d->protocolName) > 0)
		return;
#ifdef myReadAsciiCsa
	float shimSetting[8];
	char protocolName[kDICOMStrLarge], fmriExternalInfo[kDICOMStrLarge], coilID[kDICOMStrLarge], consistencyInfo[kDICOMStrLarge], coilElements[kDICOMStrLarge], pulseSequenceDetails[kDICOMStrLarge], wipMemBlock[kDICOMStrExtraLarge];
	TCsaAscii csaAscii;
	siemensCsaAscii(filename, &csaAscii, d->CSA.SeriesHeader_offset, d->CSA.SeriesHeader_length, shimSetting, coilID, consistencyInfo, coilElements, pulseSequenceDetails, fmriExternalInfo, protocolName, wipMemBlock);
	if (strlen(protocolName) >= kDICOMStr)
		protocolName[kDICOMStr - 1] = 0;
	strcpy(d->protocolName, protocolName);
#endif
}

void nii_SaveBIDSX(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts, struct nifti_1_header *h, const char *filename, struct TDTI4D *dti4D) {
	//https://docs.google.com/document/d/1HFUkAEE-pB-angVcYe6pf_-fVf4sCpOHKesUvfb8Grc/edit#
	// Generate Brain Imaging Data Structure (BIDS) info
	// sidecar JSON file (with the same filename as the .nii.gz file, but with .json extension).
	// we will use %g for floats since exponents are allowed
	// we will not set the locale, so decimal separator is always a period, as required
	// https://www.ietf.org/rfc/rfc4627.txt
	if ((!opts.isCreateBIDS) && (opts.isOnlyBIDS))
		printMessage("Input-only mode: no BIDS/NIfTI output generated for '%s'\n", pathoutname);
	if (!opts.isCreateBIDS)
		return;
	char txtname[2048] = {""};
	strcpy(txtname, pathoutname);
	strcat(txtname, ".json");
#ifdef USING_R
	FILE *fp = NULL;
	if (opts.isImageInMemory)
	{
		ImageList *images = (ImageList *)opts.imageList;
		fp = images->jsonHandle();
	}
	if (fp == NULL)
		fp = fopen(txtname, "w");
#else
	FILE *fp = fopen(txtname, "w");
#endif
	fprintf(fp, "{\n");
	switch (d.modality) {
	case kMODALITY_CR:
		fprintf(fp, "\t\"Modality\": \"CR\",\n");
		break;
	case kMODALITY_CT:
		fprintf(fp, "\t\"Modality\": \"CT\",\n");
		break;
	case kMODALITY_MR:
		fprintf(fp, "\t\"Modality\": \"MR\",\n");
		break;
	case kMODALITY_PT:
		fprintf(fp, "\t\"Modality\": \"PT\",\n");
		break;
	case kMODALITY_US:
		fprintf(fp, "\t\"Modality\": \"US\",\n");
		break;
	};
	//attempt to determine BIDS sequence type
	/*(0018,0024) SequenceName
ep_b: dwi
epfid2d: perf
epfid2d: bold
epfid3d1_15: swi
epse2d: dwi (when b-vals specified)
epse2d: fmap (spin echo, e.g. TOPUP, nb could also be extra B=0 for DWI sequence)
fl2d: localizer
fl3d1r_t: angio
fl3d1r_tm: angio
fl3d1r: angio
fl3d1r: swi
fl3d1r: ToF
fm2d: fmap (gradient echo, e.g. FUGUE)
spc3d: T2
spcir: flair (dark fluid)
spcR: PD
tfl3d: T1
tfl_me3d5_16ns: T1 (ME-MPRAGE)
tir2d: flair
tse2d: PD
tse2d: T2
tse3d: T2*/
	/*
	if (d.manufacturer == kMANUFACTURER_SIEMENS) {
		#define kLabel_UNKNOWN 0
		#define kLabel_T1w 1
		#define kLabel_T2w 2
		#define kLabel_bold 3
		#define kLabel_perf 4
		#define kLabel_dwi 5
		#define kLabel_fieldmap 6
		int iLabel = kLabel_UNKNOWN;
		if (d.CSA.numDti > 1) iLabel = kLabel_dwi;
		//if ((iLabel == kLabel_UNKNOWN) && (d.is2DAcq))
		//if ((iLabel == kLabel_UNKNOWN) && (d.is3DAcq))
		if (iLabel != kLabel_UNKNOWN) {
			char tLabel[20] = {""};
			if (iLabel == kLabel_dwi) strcat (tLabel,"dwi");
			json_Str(fp, "\t\"ModalityLabel\": \"%s\",\n", tLabel);
		}
	}*/
	//report vendor
	if (d.fieldStrength > 0.0)
		fprintf(fp, "\t\"MagneticFieldStrength\": %g,\n", d.fieldStrength);
	//Imaging Frequency (0018,0084) can be useful https://support.brainvoyager.com/brainvoyager/functional-analysis-preparation/29-pre-processing/78-epi-distortion-correction-echo-spacing-and-bandwidth
	// however, UIH stores 128176031 not 128.176031 https://github.com/rordenlab/dcm2niix/issues/225
	if ((d.imagingFrequency < 9000000.0) && (d.imagingFrequency > 0.0))
		fprintf(fp, "\t\"ImagingFrequency\": %.10g,\n", d.imagingFrequency);
	switch (d.manufacturer) {
	case kMANUFACTURER_BRUKER:
		fprintf(fp, "\t\"Manufacturer\": \"Bruker\",\n");
		break;
	case kMANUFACTURER_SIEMENS:
		fprintf(fp, "\t\"Manufacturer\": \"Siemens\",\n");
		break;
	case kMANUFACTURER_GE:
		fprintf(fp, "\t\"Manufacturer\": \"GE\",\n");
		break;
	case kMANUFACTURER_PHILIPS:
		fprintf(fp, "\t\"Manufacturer\": \"Philips\",\n");
		break;
	case kMANUFACTURER_TOSHIBA:
		fprintf(fp, "\t\"Manufacturer\": \"Toshiba\",\n");
		break;
	case kMANUFACTURER_CANON:
		fprintf(fp, "\t\"Manufacturer\": \"Canon\",\n");
		break;
	case kMANUFACTURER_MEDISO:
		fprintf(fp, "\t\"Manufacturer\": \"Mediso\",\n");
		break;
	case kMANUFACTURER_HITACHI:
		fprintf(fp, "\t\"Manufacturer\": \"Hitachi\",\n");
		break;
	case kMANUFACTURER_UIH:
		fprintf(fp, "\t\"Manufacturer\": \"UIH\",\n");
		break;
	case kMANUFACTURER_MRSOLUTIONS:
		fprintf(fp, "\t\"Manufacturer\": \"MRSolutions\",\n");
		break;
	case kMANUFACTURER_HYPERFINE:
		fprintf(fp, "\t\"Manufacturer\": \"Hyperfine\",\n");
		break;
	};
	//if (d.epiVersionGE == 0)
	//	fprintf(fp, "\t\"PulseSequenceName\": \"epi\",\n");
	//if (d.epiVersionGE == 1)
	//	fprintf(fp, "\t\"PulseSequenceName\": \"epiRT\",\n");
	if (d.internalepiVersionGE == 1)
		fprintf(fp, "\t\"InternalPulseSequenceName\": \"EPI\",\n");
	if (d.internalepiVersionGE == 2)
		fprintf(fp, "\t\"InternalPulseSequenceName\": \"EPI2\",\n");
	//GE pepolar with phase encoding direction reversed within a series
	//if (d.epiVersionGE >= kGE_EPI_PEPOLAR_FWD)
	//	printWarning("Validate results for custom ABCD GE pepolar sequence\n");
	json_Str(fp, "\t\"ManufacturersModelName\": \"%s\",\n", d.manufacturersModelName);
	json_Str(fp, "\t\"InstitutionName\": \"%s\",\n", d.institutionName);
	json_Str(fp, "\t\"InstitutionalDepartmentName\": \"%s\",\n", d.institutionalDepartmentName);
	json_Str(fp, "\t\"InstitutionAddress\": \"%s\",\n", d.institutionAddress);
	json_Str(fp, "\t\"DeviceSerialNumber\": \"%s\",\n", d.deviceSerialNumber);
	json_Str(fp, "\t\"StationName\": \"%s\",\n", d.stationName);
	if (!opts.isAnonymizeBIDS) {
		json_Str(fp, "\t\"SeriesInstanceUID\": \"%s\",\n", d.seriesInstanceUID);
		json_Str(fp, "\t\"StudyInstanceUID\": \"%s\",\n", d.studyInstanceUID);
		json_Str(fp, "\t\"ReferringPhysicianName\": \"%s\",\n", d.referringPhysicianName);
		json_Str(fp, "\t\"StudyID\": \"%s\",\n", d.studyID);
		//Next lines directly reveal patient identity
		json_Str(fp, "\t\"PatientName\": \"%s\",\n", d.patientName);
		json_Str(fp, "\t\"PatientID\": \"%s\",\n", d.patientID);
		json_Str(fp, "\t\"AccessionNumber\": \"%s\",\n", d.accessionNumber);
		if (strlen(d.patientBirthDate) == 8) { //DICOM DA YYYYMMDD -> ISO 8601 "YYYY-MM-DD"
			int ayear, amonth, aday;
			sscanf(d.patientBirthDate, "%4d%2d%2d", &ayear, &amonth, &aday);
			fprintf(fp, "\t\"PatientBirthDate\": ");
			fprintf(fp, (ayear >= 0 && ayear <= 9999) ? "\"%4d" : "\"%+4d", ayear);
			fprintf(fp, "-%02d-%02d\",\n", amonth, aday);
		}
		if (d.patientSex != '?')
			fprintf(fp, "\t\"PatientSex\": \"%c\",\n", d.patientSex);
		json_Float(fp, "\t\"PatientWeight\": %g,\n", d.patientWeight);
		//d.patientBirthDate //convert from DICOM YYYYMMDD to JSON
		//d.patientAge //4-digit Age String: nnnD, nnnW, nnnM, nnnY;
		//issue 763 following BIDS standard, unit for Age is YEARS
		int ageLen = strlen(d.patientAge);
		if ((ageLen > 1) && (d.patientAge[ageLen-1] == 'Y')) {
			char ageStr[kDICOMStr];
			strcpy(ageStr, d.patientAge);
			ageStr[ageLen -1] = '\0';
			fprintf(fp, "\t\"PatientAge\": %d,\n", atoi(ageStr));
		}
	}
	if (d.isQuadruped)
		json_Bool(fp, "\t\"Quadruped\": %s,\n", true); // BIDS suggests 0018,9020 but Siemens V-series do not populate this, alternatives are CSA or (0018,0021) CS [SK\MTC\SP]
	json_Str(fp, "\t\"BodyPartExamined\": \"%s\",\n", d.bodyPartExamined);
	json_Str(fp, "\t\"PatientPosition\": \"%s\",\n", d.patientOrient); // 0018,5100 = PatientPosition in DICOM
	json_Str(fp, "\t\"ProcedureStepDescription\": \"%s\",\n", d.procedureStepDescription);
	json_Str(fp, "\t\"SoftwareVersions\": \"%s\",\n", d.softwareVersions);
	//json_Str(fp, "\t\"MRAcquisitionType\": \"%s\",\n", d.mrAcquisitionType);
	if (d.is2DAcq)
		fprintf(fp, "\t\"MRAcquisitionType\": \"2D\",\n");
	if (d.is3DAcq)
		fprintf(fp, "\t\"MRAcquisitionType\": \"3D\",\n");
	json_Str(fp, "\t\"SeriesDescription\": \"%s\",\n", d.seriesDescription);
	json_Str(fp, "\t\"ProtocolName\": \"%s\",\n", d.protocolName);
	json_Str(fp, "\t\"ScanningSequence\": \"%s\",\n", d.scanningSequence);
	json_Str(fp, "\t\"SequenceVariant\": \"%s\",\n", d.sequenceVariant);
	json_Str(fp, "\t\"ScanOptions\": \"%s\",\n", d.scanOptions);
	json_Str(fp, "\t\"SequenceName\": \"%s\",\n", d.sequenceName);
	json_Str(fp, "\t\"PulseSequenceName\": \"%s\",\n", d.pulseSequenceName);
	if (strlen(d.imageType) > 0) {
		fprintf(fp, "\t\"ImageType\": [\"");
		bool isSep = false;
		for (size_t i = 0; i < strlen(d.imageType); i++) {
			if (d.imageType[i] != '_') {
				if (isSep)
					fprintf(fp, "\", \"");
				isSep = false;
				fprintf(fp, "%c", d.imageType[i]);
			} else
				isSep = true;
		}
		if ((d.isHasPhase) && ((d.manufacturer == kMANUFACTURER_GE) || (strstr(d.imageType, "_PHASE_") == NULL)))
			fprintf(fp, "\", \"PHASE"); //"_IMAGINARY_"
		if ((d.isHasReal) && ((d.manufacturer == kMANUFACTURER_GE) || (strstr(d.imageType, "_REAL_") == NULL)))
			fprintf(fp, "\", \"REAL");
		if ((d.isHasImaginary) && ((d.manufacturer == kMANUFACTURER_GE) || (strstr(d.imageType, "_IMAGINARY_") == NULL)))
			fprintf(fp, "\", \"IMAGINARY");
		if ((d.isRealIsPhaseMapHz)) // && ((d.manufacturer == kMANUFACTURER_GE) || (strstr(d.imageType, "_IMAGINARY_") == NULL)) )
			fprintf(fp, "\", \"FIELDMAPHZ");
		fprintf(fp, "\"],\n");
	}
	if (strlen(d.imageTypeText) > 0) {
		fprintf(fp, "\t\"ImageTypeText\": [\"");
		bool isSep = false;
		for (size_t i = 0; i < strlen(d.imageTypeText); i++) {
			if (d.imageTypeText[i] != '_') {
				if (isSep)
					fprintf(fp, "\", \"");
				isSep = false;
				fprintf(fp, "%c", d.imageTypeText[i]);
			} else
				isSep = true;
		}
		fprintf(fp, "\"],\n");
	}
	if ((strstr(d.imageTypeText, "_DIS2D") != NULL) || (strstr(d.imageType, "_DIS2D") != NULL) ||
		(strstr(d.imageTypeText, "_DIS3D") != NULL) || (strstr(d.imageType, "_DIS3D") != NULL))
			fprintf(fp, "\t\"NonlinearGradientCorrection\": true,\n");
	if ((strstr(d.imageTypeText, "_ND") != NULL) || (strstr(d.imageType, "_ND") != NULL) ||
		(strstr(d.imageTypeText, "_ND") != NULL) || (strstr(d.imageType, "_ND") != NULL))
			fprintf(fp, "\t\"NonlinearGradientCorrection\": false,\n");
	if (d.isDerived) //DICOM is derived image or non-spatial file (sounds, etc)
		fprintf(fp, "\t\"RawImage\": false,\n");
	if (d.seriesNum > 0)
		fprintf(fp, "\t\"SeriesNumber\": %ld,\n", d.seriesNum);
	//Chris Gorgolewski: BIDS standard specifies ISO8601 date-time format (Example: 2016-07-06T12:49:15.679688)
	//Lines below directly save DICOM values
	if (d.acquisitionTime > 0.0 && d.acquisitionDate > 0.0) {
		long acquisitionDate = d.acquisitionDate;
		double acquisitionTime = d.acquisitionTime;
		char acqDateTimeBuf[64];
		//snprintf(acqDateTimeBuf, sizeof acqDateTimeBuf, "%+08ld%+08f", acquisitionDate, acquisitionTime);
		snprintf(acqDateTimeBuf, sizeof acqDateTimeBuf, "%+08ld%+013.5f", acquisitionDate, acquisitionTime); //CR 20170404 add zero pad so 1:23am appears as +012300.00000 not +12300.00000
		//printMessage("acquisitionDateTime %s\n",acqDateTimeBuf);
		int ayear, amonth, aday, ahour, amin;
		double asec;
		int count = 0;
		sscanf(acqDateTimeBuf, "%5d%2d%2d%3d%2d%lf%n", &ayear, &amonth, &aday, &ahour, &amin, &asec, &count); //CR 20170404 %lf not %f for double precision
		//printf("-%02d-%02dT%02d:%02d:%02.6f\",\n", amonth, aday, ahour, amin, asec);
		if (count) { // ISO 8601 specifies a sign must exist for distant years.
			//report time of the day only format, https://www.cs.tut.fi/~jkorpela/iso8601.html
			fprintf(fp, "\t\"AcquisitionTime\": \"%02d:%02d:%02.6f\",\n", ahour, amin, asec);
			//report date and time together
			if (!opts.isAnonymizeBIDS) {
				fprintf(fp, "\t\"AcquisitionDateTime\": ");
				fprintf(fp, (ayear >= 0 && ayear <= 9999) ? "\"%4d" : "\"%+4d", ayear);
				fprintf(fp, "-%02d-%02dT%02d:%02d:%02.6f\",\n", amonth, aday, ahour, amin, asec);
			}
		} //if (count)
	} //if acquisitionTime and acquisitionDate recorded
	// if (d.acquisitionTime > 0.0) fprintf(fp, "\t\"AcquisitionTime\": %f,\n", d.acquisitionTime );
	// if (d.acquisitionDate > 0.0) fprintf(fp, "\t\"AcquisitionDate\": %8.0f,\n", d.acquisitionDate );
	if (d.acquNum > 0)
		fprintf(fp, "\t\"AcquisitionNumber\": %d,\n", d.acquNum);
	bool maskComments =  (strlen(opts.imageComments) == 1) && (opts.imageComments[0] == '\t');
	if (!maskComments) {
		json_Str(fp, "\t\"ImageComments\": \"%s\",\n", d.imageComments);
		json_Str(fp, "\t\"ConversionComments\": \"%s\",\n", opts.imageComments);
	}
	//if conditionals: the following values are required for DICOM MRI, but not available for CT
	json_Float(fp, "\t\"TriggerDelayTime\": %g,\n", d.triggerDelayTime);
	if (d.RWVScale != 0) {
		fprintf(fp, "\t\"PhilipsRWVSlope\": %g,\n", d.RWVScale);
		fprintf(fp, "\t\"PhilipsRWVIntercept\": %g,\n", d.RWVIntercept);
	}
	if ((!d.isScaleVariesEnh) && (d.intenScalePhilips != 0) && (d.manufacturer == kMANUFACTURER_PHILIPS)) { //for details, see PhilipsPrecise()
		fprintf(fp, "\t\"PhilipsRescaleSlope\": %g,\n", d.intenScale);
		fprintf(fp, "\t\"PhilipsRescaleIntercept\": %g,\n", d.intenIntercept);
		fprintf(fp, "\t\"PhilipsScaleSlope\": %g,\n", d.intenScalePhilips);
		fprintf(fp, "\t\"UsePhilipsFloatNotDisplayScaling\": %d,\n", opts.isPhilipsFloatNotDisplayScaling);
	}
	//https://bids-specification--622.org.readthedocs.build/en/622/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#case-3-direct-field-mapping
	if ((d.isRealIsPhaseMapHz) && ((d.manufacturer == kMANUFACTURER_GE) || (d.isHasReal)))
		fprintf(fp, "\t\"Units\": \"Hz\",\n"); //
	//PET ISOTOPE MODULE ATTRIBUTES
	json_Str(fp, "\t\"Radiopharmaceutical\": \"%s\",\n", d.radiopharmaceutical);
	json_Float(fp, "\t\"RadionuclidePositronFraction\": %g,\n", d.radionuclidePositronFraction);
	json_Float(fp, "\t\"RadionuclideTotalDose\": %g,\n", d.radionuclideTotalDose);
	json_Float(fp, "\t\"RadionuclideHalfLife\": %g,\n", d.radionuclideHalfLife);
	json_Float(fp, "\t\"DoseCalibrationFactor\": %g,\n", d.doseCalibrationFactor);
	json_Float(fp, "\t\"IsotopeHalfLife\": %g,\n", d.ecat_isotope_halflife);
	json_Float(fp, "\t\"Dosage\": %g,\n", d.ecat_dosage);
	json_Str(fp, "\t\"ConvolutionKernel\": \"%s\",\n", d.convolutionKernel);
	json_Str(fp, "\t\"Units\": \"%s\",\n", d.unitsPT); //https://github.com/bids-standard/bids-specification/pull/773
	json_Str(fp, "\t\"DecayCorrection\": \"%s\",\n", d.decayCorrection);
	json_Str(fp, "\t\"AttenuationCorrectionMethod\": \"%s\",\n", d.attenuationCorrectionMethod);
	json_Str(fp, "\t\"ReconstructionMethod\": \"%s\",\n", d.reconstructionMethod);
	//json_Float(fp, "\t\"DecayFactor\": %g,\n", d.decayFactor);
	if (dti4D->decayFactor[0] >= 0.0) { //see BEP009 PET https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0
		fprintf(fp, "\t\"DecayFactor\": [\n");
		for (int i = 0; i < h->dim[4]; i++) {
			if (i != 0)
				fprintf(fp, ",\n");
			if (dti4D->decayFactor[i] < 0)
				break;
			fprintf(fp, "\t\t%g", dti4D->decayFactor[i]);
		}
		fprintf(fp, "\t],\n");
	}
	if ((h->dim[4] > 1) && (dti4D->volumeOnsetTime[0] >= 0.0)) { //see BEP009 PET https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0
		fprintf(fp, "\t\"FrameTimesStart\": [\n");
		for (int i = 0; i < h->dim[4]; i++) {
			if (i != 0)
				fprintf(fp, ",\n");
			if (dti4D->volumeOnsetTime[i] < 0)
				break;
			fprintf(fp, "\t\t%g", dti4D->volumeOnsetTime[i]);
		}
		fprintf(fp, "\t],\n");
	}
	if ((h->dim[4] > 1) && (dti4D->frameDuration[0] >= 0.0)) { //see BEP009 PET https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0
		fprintf(fp, "\t\"FrameDuration\": [\n");
		for (int i = 0; i < h->dim[4]; i++) {
			if (i != 0)
				fprintf(fp, ",\n");
			if (dti4D->frameDuration[i] < 0)
				break;
			if ((isSameFloatGE(dti4D->frameDuration[i], 0.0)) && (d.TR > 0.0))
				fprintf(fp, "\t\t%g", d.TR / 1000.0); // from 0018,1242 ms -> sec
			else
				fprintf(fp, "\t\t%g", dti4D->frameDuration[i] / 1000.0); // from 0018,1242 ms -> sec
		}
		fprintf(fp, "\t],\n");
	}
	if ((dti4D->frameReferenceTime[0] >= 0.0) && (h->dim[4] > 1)) { //see BEP009 PET https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0
		bool varies = false;
		for (int i = 0; i < h->dim[4]; i++)
			if (dti4D->frameReferenceTime[i] != dti4D->frameReferenceTime[0])
				varies = true;
		if (varies) {
			fprintf(fp, "\t\"FrameReferenceTime\": [\n");
			for (int i = 0; i < h->dim[4]; i++) {
				if (i != 0)
					fprintf(fp, ",\n");
				if (dti4D->frameReferenceTime[i] < 0)
					break;
				fprintf(fp, "\t\t%g", dti4D->frameReferenceTime[i] / 1000.0); // from 0018,1242 ms -> sec
			}
			fprintf(fp, "\t],\n");
		}
	}
	//CT parameters
	json_Float(fp, "\t\"ExposureTime\": %g,\n", d.exposureTimeMs / 1000.0);
	json_Float(fp, "\t\"XRayTubeCurrent\": %g,\n", d.xRayTubeCurrent);
	if ((d.TE > 0.0) && (d.isXRay))
		fprintf(fp, "\t\"XRayExposure\": %g,\n", d.TE);
	//MRI parameters
	if (!d.isXRay) { //with CT scans, slice thickness often varies
		//beware, not used correctly by all vendors https://public.kitware.com/pipermail/insight-users/2005-September/014711.html
		json_Float(fp, "\t\"SliceThickness\": %g,\n", d.zThick);
		json_Float(fp, "\t\"SpacingBetweenSlices\": %g,\n", d.zSpacing);
	}
	//if (!opts.isAnonymizeBIDS) //issue668 is SAR identifiable??
	json_Float(fp, "\t\"SAR\": %g,\n", d.SAR);
	if (d.numberOfAverages > 1.0)
		json_Float(fp, "\t\"NumberOfAverages\": %g,\n", d.numberOfAverages);
	if ((d.echoNum > 1) || ((d.isMultiEcho) && (d.echoNum > 0)))
		fprintf(fp, "\t\"EchoNumber\": %d,\n", d.echoNum);
	if ((d.TE > 0.0) && (!d.isXRay)) {
		if ((d.manufacturer == kMANUFACTURER_GE) && (d.isRealIsPhaseMapHz) && (d.velocityEncodeScaleGE < 0))  { //issue617, only set for GE fieldmaphz
			json_Float(fp, "\t\"EchoTime1\": %g,\n", d.TE / 1000.0 );
			json_Float(fp, "\t\"EchoTime2\": %g,\n", d.TE / 1000.0 - 1.0/(2.0 * M_PI * d.velocityEncodeScaleGE));
			// delta TE = -1/(2 * pi * velocityEncodeScaleGE)
		}
		else
			fprintf(fp, "\t\"EchoTime\": %g,\n", d.TE / 1000.0);
	}	
	//if ((d.TE2 > 0.0) && (!d.isXRay)) fprintf(fp, "\t\"EchoTime2\": %g,\n", d.TE2 / 1000.0 );
	if (dti4D->frameDuration[0] < 0.0) //e.g. PET scans can have variable TR
		json_Float(fp, "\t\"RepetitionTime\": %g,\n", d.TR / 1000.0);
	json_Float(fp, "\t\"RepetitionTimeExcitation\": %g,\n", dti4D->repetitionTimeExcitation);
	json_Float(fp, "\t\"RepetitionTimeInversion\": %g,\n", dti4D->repetitionTimeInversion);
	json_Bool(fp, "\t\"MTState\": %s,\n", d.mtState); // BIDS suggests 0018,9020 but Siemens V-series do not populate this, alternatives are CSA or (0018,0021) CS [SK\MTC\SP]
	//SpoilingState
	bool isSpoiled = (d.spoiling > kSPOILING_NONE);
	if ((d.spoiling == kSPOILING_UNKOWN) && (strstr(d.sequenceVariant, "\\SP") != NULL)) //BIDS suggests 0018,9016 Siemens V-series do not populate this, (0018,0021) CS [SK\MTC\SP]
		isSpoiled = true;
	if (isSpoiled)
		json_Bool(fp, "\t\"SpoilingState\": %s,\n", true); //Siemens reports SpoilingState but not SpoilingType
	if (d.spoiling == kSPOILING_RF)
		fprintf(fp, "\t\"SpoilingType\": \"RF\",\n");
	if (d.spoiling == kSPOILING_GRADIENT)
		fprintf(fp, "\t\"SpoilingType\": \"GRADIENT\",\n");
	if (d.spoiling == kSPOILING_RF_AND_GRADIENT)
		fprintf(fp, "\t\"SpoilingType\": \"COMBINED\",\n");
	json_Float(fp, "\t\"InversionTime\": %g,\n", d.TI / 1000.0);
	json_Float(fp, "\t\"FlipAngle\": %g,\n", d.flipAngle);
	if (d.isVariableFlipAngle)
		json_Bool(fp, "\t\"VariableFlipAngleFlag\": %s,\n", true); // BIDS suggests 0018,9020 but Siemens V-series do not populate this, alternatives are CSA or (0018,0021) CS [SK\MTC\SP]
	bool interp = false; //2D interpolation
	float phaseOversampling = 0.0;
	//n.b. https://neurostars.org/t/getting-missing-ge-information-required-by-bids-for-common-preprocessing/1357/7
	if (d.manufacturer == kMANUFACTURER_UIH)
		json_Str(fp, "\t\"PhaseEncodingDirectionDisplayed\": \"%s\",\n", d.phaseEncodingDirectionDisplayedUIH);
	if ((d.manufacturer == kMANUFACTURER_GE) && (d.phaseEncodingGE != kGE_PHASE_ENCODING_POLARITY_UNKNOWN)) { //only set for GE
		if (d.phaseEncodingGE == kGE_PHASE_ENCODING_POLARITY_UNFLIPPED)
			fprintf(fp, "\t\"PhaseEncodingPolarityGE\": \"Unflipped\",\n");
		if (d.phaseEncodingGE == kGE_PHASE_ENCODING_POLARITY_FLIPPED)
			fprintf(fp, "\t\"PhaseEncodingPolarityGE\": \"Flipped\",\n");
	}
	//GE specific fields
	if (d.shimGradientX > -33333)
		fprintf(fp, "\t\"ShimSetting\": [\n\t\t%d,\n\t\t%d,\n\t\t%d\t],\n", d.shimGradientX, d.shimGradientY, d.shimGradientZ);
	json_Str(fp, "\t\"PrescanReuseString\": \"%s\",\n", d.prescanReuseString);
	float delayTimeInTR = -0.01;
	float repetitionTimePreparation = 0.0;
	// GE Diffusion specific fields
	if ((d.epiVersionGE == kGE_EPI_EPI2) || (d.internalepiVersionGE == 2)) {
		if (d.numberOfDiffusionDirectionGE > 0)
			fprintf(fp, "\t\"NumberOfDiffusionDirectionGE\": %d,\n", d.numberOfDiffusionDirectionGE);
		if (d.numberOfDiffusionT2GE > 0)
			fprintf(fp, "\t\"NumberOfDiffusionT2GE\": %d,\n", d.numberOfDiffusionT2GE);
		if (d.tensorFileGE > 0)
			fprintf(fp, "\t\"TensorFileNumberGE\": %d,\n", d.tensorFileGE);
		if (opts.diffCyclingModeGE >= 0) {
			fprintf(fp, "\t\"DiffGradientCyclingGE\": \"OVERRIDE\",\n"); // see issue 635
			d.diffCyclingModeGE = opts.diffCyclingModeGE;
		}
		if (d.diffCyclingModeGE > 0) {
			if (d.diffCyclingModeGE == kGE_DIFF_CYCLING_OFF)
				fprintf(fp, "\t\"DiffGradientCyclingGE\": \"OFF\",\n");
			if (d.diffCyclingModeGE == kGE_DIFF_CYCLING_ALLTR)
				fprintf(fp, "\t\"DiffGradientCyclingGE\": \"ALLTR\",\n");
			if (d.diffCyclingModeGE == kGE_DIFF_CYCLING_2TR)
				fprintf(fp, "\t\"DiffGradientCyclingGE\": \"2TR\",\n");
			if (d.diffCyclingModeGE == kGE_DIFF_CYCLING_3TR)
				fprintf(fp, "\t\"DiffGradientCyclingGE\": \"3TR\",\n");
			if (d.diffCyclingModeGE == kGE_DIFF_CYCLING_SPOFF)
				fprintf(fp, "\t\"DiffGradientCyclingGE\": \"SPOFF\",\n");
		}
	}
#ifdef myReadAsciiCsa
	if ((d.manufacturer == kMANUFACTURER_SIEMENS) && (d.CSA.SeriesHeader_offset > 0) && (d.CSA.SeriesHeader_length > 0)) {
		float pf = 1.0f; //partial fourier
		float shimSetting[8];
		char protocolName[kDICOMStrLarge], fmriExternalInfo[kDICOMStrLarge], coilID[kDICOMStrLarge], consistencyInfo[kDICOMStrLarge], coilElements[kDICOMStrLarge], pulseSequenceDetails[kDICOMStrLarge], wipMemBlock[kDICOMStrExtraLarge];
		TCsaAscii csaAscii;
		siemensCsaAscii(filename, &csaAscii, d.CSA.SeriesHeader_offset, d.CSA.SeriesHeader_length, shimSetting, coilID, consistencyInfo, coilElements, pulseSequenceDetails, fmriExternalInfo, protocolName, wipMemBlock);
		if ((d.phaseEncodingLines < 1) && (csaAscii.phaseEncodingLines > 0))
			d.phaseEncodingLines = csaAscii.phaseEncodingLines;
		//if (d.phaseEncodingLines != csaAscii.phaseEncodingLines) //e.g. phaseOversampling
		//	printWarning("PhaseEncodingLines reported in DICOM (%d) header does not match value CSA-ASCII (%d) %s\n", d.phaseEncodingLines, csaAscii.phaseEncodingLines, pathoutname);
		delayTimeInTR = csaAscii.delayTimeInTR;
		if ((d.isHasPhase) && (csaAscii.TE0 > 0.0) && (csaAscii.TE1 > 0.0)) { //issue400
			//https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html
			json_Float(fp, "\t\"EchoTime1\": %g,\n", csaAscii.TE0 / 1000000.0);
			json_Float(fp, "\t\"EchoTime2\": %g,\n", csaAscii.TE1 / 1000000.0);
		}
		if (csaAscii.dAveragesDouble > 1.0) //*spcR_44ns fractional and independent of (0018,0083) DS NumberOfAverages, e.g. 0018,0083=2, dAveragesDouble = 1.4?
			json_Float(fp, "\t\"AveragesDouble\": %g,\n", csaAscii.dAveragesDouble);
		phaseOversampling = csaAscii.phaseOversampling;
		if ((d.CSA.mosaicSlices > 1) && (csaAscii.existUcImageNumb > 0)) {
			if (d.CSA.protocolSliceNumber1 < 2) {
				printWarning("Assuming mosaics saved in reverse order due to 'sSliceArray.ucImageNumb'\n");
				//never seen such an image in the wild.... sliceDir may need to be reversed
			}
			d.CSA.protocolSliceNumber1 = 2;
		}
		//ultra-verbose output for deciphering adFree/alFree/alTI values:
		/*
		if (opts.isVerbose > 1) {
			for (int i = 0; i < kMaxWipFree; i++)
				print_FloatNotNan("adFree[%d]=\t%g\n",i, csaAscii.adFree[i]);
			for (int i = 0; i < kMaxWipFree; i++)
				print_FloatNotNan("alFree[%d]=\t%g\n",i, csaAscii.alFree[i]);
			for (int i = 0; i < kMaxWipFree; i++)
				print_FloatNotNan("alTI[%d]=\t%g\n",i, csaAscii.alTI[i]);
		} //verbose
		*/
		bool isPCASL = false;
		bool isPASL = false;
		//ASL specific tags - 2D pCASL Danny J.J. Wang http://www.loft-lab.org
		//ASL specific tags - 2D PASL Siemens Product XA30, n.b pasl/casl/pcasl set using 0018,9250
		if (strstr(pulseSequenceDetails, "ep2d_asl")) {
			json_FloatNotNan(fp, "\t\"LabelingDuration\": %g,\n", csaAscii.ulLabelingDuration * (1.0 / 1000000.0)); //usec->sec
			json_FloatNotNan(fp, "\t\"PostLabelingDelay\": %g,\n", csaAscii.sPostLabelingDelay * (1.0 / 1000000.0)); //usec -> sec
		}
		//ASL specific tags - 2D pCASL Danny J.J. Wang http://www.loft-lab.org
		if ((strstr(pulseSequenceDetails, "ep2d_pcasl")) || (strstr(pulseSequenceDetails, "ep2d_pcasl_UI_PHC"))) {
			isPCASL = true;
			repetitionTimePreparation = d.TR;
			json_FloatNotNan(fp, "\t\"LabelOffset\": %g,\n", csaAscii.adFree[1]); //mm
			json_FloatNotNan(fp, "\t\"PostLabelingDelay\": %g,\n", csaAscii.adFree[2] * (1.0 / 1000000.0)); //usec -> sec
			float num_RF_Block = csaAscii.adFree[3];
			json_FloatNotNan(fp, "\t\"NumRFBlocks\": %g,\n", num_RF_Block);
			// Sep 5, 2023, at 7:56 PM, Danny JJ Wang the labeling duration is (0.92*20*Num_RF_Block) ms
			json_FloatNotNan(fp, "\t\"LabelingDuration\": %g,\n", (0.92 *20.0 *num_RF_Block)/1000.0); //in seconds
			json_FloatNotNan(fp, "\t\"RFGap\": %g,\n", csaAscii.adFree[4] * (1.0 / 1000000.0)); //usec -> sec
			json_FloatNotNan(fp, "\t\"MeanGzx10\": %g,\n", csaAscii.adFree[10]);
			json_FloatNotNan(fp, "\t\"PhiAdjust\": %g,\n", csaAscii.adFree[11]);				// percent
		}
		//ASL specific tags - 3D pCASL Danny J.J. Wang http://www.loft-lab.org
		if (strstr(pulseSequenceDetails, "tgse_pcasl")) {
			isPCASL = true;
			repetitionTimePreparation = d.TR;
			json_FloatNotNan(fp, "\t\"RFGap\": %g,\n", csaAscii.adFree[4] * (1.0 / 1000000.0)); //usec -> sec
			json_FloatNotNan(fp, "\t\"MeanGzx10\": %g,\n", csaAscii.adFree[10]);				// mT/m
			json_FloatNotNan(fp, "\t\"T1\": %g,\n", csaAscii.adFree[12] * (1.0 / 1000000.0));	//usec -> sec
			float num_RF_Block = csaAscii.adFree[3];
			json_FloatNotNan(fp, "\t\"NumRFBlocks\": %g,\n", num_RF_Block);
			// Sep 5, 2023, at 7:56 PM, Danny JJ Wang the labeling duration is (0.92*20*Num_RF_Block) ms
			json_FloatNotNan(fp, "\t\"LabelingDuration\": %g,\n", (0.92 *20.0 *num_RF_Block)/1000.0); //in seconds
		}
		//ASL specific tags - 2D PASL Siemens Product
		if (strstr(pulseSequenceDetails, "ep2d_pasl")) {
			isPASL = true;
			json_FloatNotNan(fp, "\t\"BolusDuration\": %g,\n", csaAscii.alTI[0] * (1.0 / 1000000.0)); //usec->sec
			json_FloatNotNan(fp, "\t\"InversionTime\": %g,\n", csaAscii.alTI[2] * (1.0 / 1000000.0)); //usec -> sec
		}
		//ASL specific tags - 3D PASL Siemens Product http://adni.loni.usc.edu/wp-content/uploads/2010/05/ADNI3_Basic_Siemens_Skyra_E11.pdf
		if (strstr(pulseSequenceDetails, "tgse_pasl")) {
			isPASL = true;
			json_FloatNotNan(fp, "\t\"BolusDuration\": %g,\n", csaAscii.alTI[0] * (1.0 / 1000000.0)); //usec->sec
			json_FloatNotNan(fp, "\t\"InversionTime\": %g,\n", csaAscii.alTI[2] * (1.0 / 1000000.0)); //usec -> sec
			//json_FloatNotNan(fp, "\t\"SaturationStopTime\": %g,\n", csaAscii.alTI[2] * (1.0/1000.0));
		}
		//PASL http://www.pubmed.com/11746944 http://www.pubmed.com/21606572
		if (strstr(pulseSequenceDetails, "ep2d_fairest")) {
			isPASL = true;
			json_FloatNotNan(fp, "\t\"PostInversionDelay\": %g,\n", csaAscii.adFree[2] * (1.0 / 1000.0)); //usec->sec
			json_FloatNotNan(fp, "\t\"PostLabelingDelay\": %g,\n", csaAscii.adFree[4] * (1.0 / 1000.0)); //usec -> sec
		}
		//ASL specific tags - Oxford (Thomas OKell)
		bool isOxfordASL = false;
		if (strstr(pulseSequenceDetails, "to_ep2d_VEPCASL")) { //Oxford 2D pCASL
			isOxfordASL = true;
			isPCASL = true;
			repetitionTimePreparation = d.TR;
			json_FloatNotNan(fp, "\t\"InversionTime\": %g,\n", csaAscii.alTI[2] * (1.0 / 1000000.0)); //ms->sec
			json_FloatNotNan(fp, "\t\"BolusDuration\": %g,\n", csaAscii.alTI[0] * (1.0 / 1000000.0)); //usec -> sec
			json_Float(fp, "\t\"TagRFFlipAngle\": %g,\n", csaAscii.alFree[4]);
			json_Float(fp, "\t\"TagRFDuration\": %g,\n", csaAscii.alFree[5] / 1000000.0);	//usec -> sec
			json_Float(fp, "\t\"TagRFSeparation\": %g,\n", csaAscii.alFree[6] / 1000000.0); //usec -> sec
			json_FloatNotNan(fp, "\t\"MeanTagGradient\": %g,\n", csaAscii.adFree[0]);		//mTm
			json_FloatNotNan(fp, "\t\"TagGradientAmplitude\": %g,\n", csaAscii.adFree[1]);	//mTm
			json_Float(fp, "\t\"TagDuration\": %g,\n", csaAscii.alFree[9] / 1000.0);		//ms -> sec
			json_Float(fp, "\t\"MaximumT1Opt\": %g,\n", csaAscii.alFree[10] / 1000.0);		//ms -> sec
			//report post label delay
			int nPLD = 0;
			bool isValid = true; //detect gaps in PLD array: If user sets PLD1=250, PLD2=0 PLD3=375 only PLD1 was acquired
			for (int k = 11; k < 31; k++) {
				if ((isnan(csaAscii.alFree[k])) || (csaAscii.alFree[k] <= 0.0))
					isValid = false;
				if (isValid)
					nPLD++;
			} //for k
			if (nPLD > 0) { // record PostLabelDelays, these are listed as "PLD0","PLD1",etc in PDF
				fprintf(fp, "\t\"InitialPostLabelDelay\": [\n"); //https://docs.google.com/document/d/15tnn5F10KpgHypaQJNNGiNKsni9035GtDqJzWqkkP6c/edit#
				for (int i = 0; i < nPLD; i++) {
					if (i != 0)
						fprintf(fp, ",\n");
					fprintf(fp, "\t\t%g", csaAscii.alFree[i + 11] / 1000.0); //ms -> sec
				}
				fprintf(fp, "\t],\n");
			}
			/*isValid = true; //detect gaps in PLD array: If user sets PLD1=250, PLD2=0 PLD3=375 only PLD1 was acquired
			for (int k = 11; k < 31; k++) {
				if (isValid) {
					char newstr[256];
					snprintf(newstr, 256, "\t\"PLD%d\": %%g,\n", k-11);
					json_Float(fp, newstr, csaAscii.alFree[k]/ 1000.0); //ms -> sec
					if (csaAscii.alFree[k] <= 0.0) isValid = false;
				}//isValid
			} //for k */
			for (int k = 3; k < 11; k++) { //vessel locations
				char newstr[256];
				snprintf(newstr, 256, "\t\"sWipMemBlockAdFree%d\": %%g,\n", k); //issue483: sWipMemBlock.AdFree -> sWipMemBlockAdFree
				json_FloatNotNan(fp, newstr, csaAscii.adFree[k]);
			}
		}
		if (strstr(pulseSequenceDetails, "jw_tgse_VEPCASL")) { //Oxford 3D pCASL
			isPCASL = true;
			isOxfordASL = true;
			json_Float(fp, "\t\"TagRFFlipAngle\": %g,\n", csaAscii.alFree[6]);
			json_Float(fp, "\t\"TagRFDuration\": %g,\n", csaAscii.alFree[7] / 1000000.0);	//usec -> sec
			json_Float(fp, "\t\"TagRFSeparation\": %g,\n", csaAscii.alFree[8] / 1000000.0); //usec -> sec
			json_Float(fp, "\t\"MaximumT1Opt\": %g,\n", csaAscii.alFree[9] / 1000.0);		//ms -> sec
			json_Float(fp, "\t\"Tag0\": %g,\n", csaAscii.alFree[10] / 1000.0);				//DelayTimeInTR usec -> sec
			json_Float(fp, "\t\"Tag1\": %g,\n", csaAscii.alFree[11] / 1000.0);				//DelayTimeInTR usec -> sec
			json_Float(fp, "\t\"Tag2\": %g,\n", csaAscii.alFree[12] / 1000.0);				//DelayTimeInTR usec -> sec
			json_Float(fp, "\t\"Tag3\": %g,\n", csaAscii.alFree[13] / 1000.0);				//DelayTimeInTR usec -> sec
			int nPLD = 0;
			bool isValid = true; //detect gaps in PLD array: If user sets PLD1=250, PLD2=0 PLD3=375 only PLD1 was acquired
			for (int k = 30; k < 38; k++) {
				if ((isnan(csaAscii.alFree[k])) || (csaAscii.alFree[k] <= 0.0))
					isValid = false;
				if (isValid)
					nPLD++;
			} //for k
			if (nPLD > 0) { // record PostLabelDelays, these are listed as "PLD0","PLD1",etc in PDF
				fprintf(fp, "\t\"InitialPostLabelDelay\": [\n"); //https://docs.google.com/document/d/15tnn5F10KpgHypaQJNNGiNKsni9035GtDqJzWqkkP6c/edit#
				for (int i = 0; i < nPLD; i++) {
					if (i != 0)
						fprintf(fp, ",\n");
					fprintf(fp, "\t\t%g", csaAscii.alFree[i + 30] / 1000.0); //ms -> sec
				}
				fprintf(fp, "\t],\n");
			}
			/*
			json_Float(fp, "\t\"PLD0\": %g,\n", csaAscii.alFree[30]/1000.0);
			json_Float(fp, "\t\"PLD1\": %g,\n", csaAscii.alFree[31]/1000.0);
			json_Float(fp, "\t\"PLD2\": %g,\n", csaAscii.alFree[32]/1000.0);
			json_Float(fp, "\t\"PLD3\": %g,\n", csaAscii.alFree[33]/1000.0);
			json_Float(fp, "\t\"PLD4\": %g,\n", csaAscii.alFree[34]/1000.0);
			json_Float(fp, "\t\"PLD5\": %g,\n", csaAscii.alFree[35]/1000.0);
			*/
		}
		if (isOxfordASL) { //properties common to 2D and 3D ASL
			//labelling plane
			fprintf(fp, "\t\"TagPlaneDThickness\": %g,\n", csaAscii.dThickness);
			fprintf(fp, "\t\"TagPlaneUlShape\": %g,\n", csaAscii.ulShape);
			fprintf(fp, "\t\"TagPlaneSPositionDTra\": %g,\n", csaAscii.sPositionDTra);
			fprintf(fp, "\t\"TagPlaneSNormalDTra\": %g,\n", csaAscii.sNormalDTra);
		}
		if (isPCASL)
			fprintf(fp, "\t\"ArterialSpinLabelingType\": \"PCASL\",\n");
		if (isPASL)
			fprintf(fp, "\t\"ArterialSpinLabelingType\": \"PASL\",\n");
		//AcquisitionVoxelSize uses slice thickness (without gap)
		// https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#common-metadata-fields-applicable-to-both-pcasl-and-pasl
		if (((isPASL) || (isPCASL)) && (csaAscii.interp <= 0))
			fprintf(fp, "\t\"AcquisitionVoxelSize\": [\n\t\t%g,\n\t\t%g,\n\t\t%g\t],\n", d.xyzMM[1], d.xyzMM[2], d.zThick);
		// lund free waveform sequence, see https://github.com/filip-szczepankiewicz/fwf_sequence_tools
		if ( (strstr(pulseSequenceDetails, "ep2d_diff_fwf") != 0) || (strstr(pulseSequenceDetails, "ep2d_diff_sms_fwf_simple") != 0)) {
			for (int i = 0; i < kMaxWipFree; i++) {
				if (!isnan(csaAscii.adFree[i]))
					fprintf(fp, "\t\"FWF_adFree[%i]\": %g,\n", i, csaAscii.adFree[i]);
			}

			for (int i = 0; i < kMaxWipFree; i++) {
				if (!isnan(csaAscii.alFree[i]))
					fprintf(fp, "\t\"FWF_alFree[%i]\": %g,\n", i, csaAscii.alFree[i]);
			}

			for (int d = 0; d < 3; d++)
			{
				char str [4096];
				strcpy(str, "");
				for (int i = 0; i < csaAscii.freeDiffusionN;i++) {
					char tmp[10];
					snprintf(tmp, 10, "%1.4f", csaAscii.freeDiffusionVec[i].v[d]);
					strcat(str, tmp);
					if ( (i+1) < csaAscii.freeDiffusionN)
						strcat(str, ", ");
				}
				char dchar = 'x' + d;
				fprintf(fp, "\t\"FWF_DVS%c\": [ %s ],\n", dchar, str);
			}
		}
		//general properties
		if ((csaAscii.partialFourier > 0) && ((d.modality == kMODALITY_MR))) { //check MR, e.g. do not report for Siemens PET
			//https://github.com/ismrmrd/siemens_to_ismrmrd/blob/master/parameter_maps/IsmrmrdParameterMap_Siemens_EPI_FLASHREF.xsl
			if (csaAscii.partialFourier == 1)
				pf = 0.5; // 4/8
			if (csaAscii.partialFourier == 2)
				pf = 0.625; // 5/8
			if (csaAscii.partialFourier == 4)
				pf = 0.75;
			if (csaAscii.partialFourier == 8)
				pf = 0.875;
			fprintf(fp, "\t\"PartialFourier\": %g,\n", pf);
		}
		if (csaAscii.interp > 0) { //in-plane interpolation
			interp = true;
			fprintf(fp, "\t\"Interpolation2D\": %d,\n", interp);
		}
		if (csaAscii.baseResolution > 0)
			fprintf(fp, "\t\"BaseResolution\": %d,\n", csaAscii.baseResolution);
		if (shimSetting[0] != 0.0) {
			fprintf(fp, "\t\"ShimSetting\": [\n");
			for (int i = 0; i < 8; i++) {
				if (i != 0)
					fprintf(fp, ",\n");
				fprintf(fp, "\t\t%g", shimSetting[i]);
			}
			fprintf(fp, "\t],\n");
		}
		if (d.CSA.numDti > 0) { //
			if (csaAscii.difBipolar == 1)
				fprintf(fp, "\t\"DiffusionScheme\": \"Bipolar\",\n");
			if (csaAscii.difBipolar == 2)
				fprintf(fp, "\t\"DiffusionScheme\": \"Monopolar\",\n");
		}
		//DelayTimeInTR
		// https://groups.google.com/forum/#!topic/bids-discussion/nmg1BOVH1SU
		// https://groups.google.com/forum/#!topic/bids-discussion/seD7AtJfaFE
		json_Float(fp, "\t\"DelayTime\": %g,\n", delayTimeInTR / 1000000.0); //DelayTimeInTR usec -> sec
		if (d.modality == kMODALITY_MR)
			json_Float(fp, "\t\"TxRefAmp\": %g,\n", csaAscii.txRefAmp);
		if (d.modality == kMODALITY_MR)
			json_Float(fp, "\t\"PhaseResolution\": %g,\n", csaAscii.phaseResolution);
		json_Float(fp, "\t\"PhaseOversampling\": %g,\n", phaseOversampling);
		json_Float(fp, "\t\"VendorReportedEchoSpacing\": %g,\n", csaAscii.echoSpacing / 1000000.0); //usec -> sec
		//ETD and epiFactor not useful/reliable https://github.com/rordenlab/dcm2niix/issues/127
		//if (echoTrainDuration > 0) fprintf(fp, "\t\"EchoTrainDuration\": %g,\n", echoTrainDuration / 1000000.0); //usec -> sec
		//if (epiFactor > 0) fprintf(fp, "\t\"EPIFactor\": %d,\n", epiFactor);
		json_Str(fp, "\t\"ReceiveCoilName\": \"%s\",\n", coilID);
		if (d.modality == kMODALITY_MR)
			json_Str(fp, "\t\"ReceiveCoilActiveElements\": \"%s\",\n", coilElements);
		if (strcmp(coilElements, d.coilName) != 0)
			json_Str(fp, "\t\"CoilString\": \"%s\",\n", d.coilName);
		strcpy(d.coilName, "");
		json_Str(fp, "\t\"PulseSequenceDetails\": \"%s\",\n", pulseSequenceDetails);
		json_Str(fp, "\t\"FmriExternalInfo\": \"%s\",\n", fmriExternalInfo);
		json_Str(fp, "\t\"WipMemBlock\": \"%s\",\n", wipMemBlock);
		if (strlen(d.protocolName) < 1) //insert protocol name if it exists in CSA but not DICOM header: https://github.com/nipy/heudiconv/issues/80
			json_Str(fp, "\t\"ProtocolName\": \"%s\",\n", protocolName);
		if (csaAscii.refLinesPE > 0)
			fprintf(fp, "\t\"RefLinesPE\": %d,\n", csaAscii.refLinesPE);
		//https://github.com/bids-standard/bids-specification/pull/681#issuecomment-861767213
		if (csaAscii.combineMode == 1)
			fprintf(fp, "\t\"CoilCombinationMethod\": \"Sum of Squares\",\n");
		if (csaAscii.combineMode == 2)
			fprintf(fp, "\t\"CoilCombinationMethod\": \"Adaptive Combine\",\n");
		if ((csaAscii.ucMTC == 1) && (d.mtState < 0)) //precedence for 0018,9020 over CSA
			json_Bool(fp, "\t\"MTState\": %s,\n", 1);
		json_Str(fp, "\t\"ConsistencyInfo\": \"%s\",\n", consistencyInfo);
		if (csaAscii.accelFact3D > 0)
			d.accelFactOOP = csaAscii.accelFact3D;
		//see issue 672 if (csaAscii.accelFact3D > 1.01) json_Float(fp, "\t\"AccelFact3D\": %g,\n", csaAscii.accelFact3D); //see *spcR_44ns where "sPat.lAccelFactPE = 1", "sPat.lAccelFact3D = 2" (0051,1011) LO [p2], perhaps ParallelReductionFactorInPlane should be 1?
		if (csaAscii.parallelReductionFactorInPlane > 0) { //AccelFactorPE -> phase encoding
			//1=SENSE, 2=GRAPPA, 32=SMS??, 256=CompressedSense?
			if (csaAscii.patMode == 1)
				fprintf(fp, "\t\"MatrixCoilMode\": \"SENSE\",\n");
			if (csaAscii.patMode == 2)
				fprintf(fp, "\t\"MatrixCoilMode\": \"GRAPPA\",\n");
			d.accelFactPE = csaAscii.parallelReductionFactorInPlane; //issue672: csa precedence over value found in DICOM (0051,1011)
			if ((csaAscii.accelFact3D < 1.01) && (csaAscii.parallelReductionFactorInPlane != (int)(d.accelFactPE)))
				printWarning("ParallelReductionFactorInPlane reported in DICOM [0051,1011] (%d) does not match CSA series value %d\n", (int)(d.accelFactPE), csaAscii.parallelReductionFactorInPlane);
		}
		if ((csaAscii.patMode == 256) && (!isnan(csaAscii.accelFactTotal)) && (csaAscii.accelFactTotal > (d.accelFactPE * d.accelFactOOP) ))
			d.compressedSensingFactor = csaAscii.accelFactTotal; //see dcm_qa_cs_dl
	} else { //e.g. Siemens Vida does not have CSA header, but has many attributes
		json_Str(fp, "\t\"ReceiveCoilActiveElements\": \"%s\",\n", d.coilElements);
		if (strcmp(d.coilElements, d.coilName) != 0)
			json_Str(fp, "\t\"CoilString\": \"%s\",\n", d.coilName);
		int phaseEncodingLines = d.phaseEncodingLines;
		if (phaseEncodingLines < 1) //support enhanced DICOM terminology
			phaseEncodingLines = d.phaseEncodingSteps;
		if ((d.manufacturer == kMANUFACTURER_SIEMENS) && (!d.is3DAcq) && (phaseEncodingLines > d.echoTrainLength) && (d.echoTrainLength > 1)) {
			//ETL is > 1, as some GE files list 1, as an example see series mr_0005 in dcm_qa_nih
			float pf = (float)phaseEncodingLines;
			if (d.accelFactPE > 1)
				pf = (float)pf / (float)d.accelFactPE; //estimate: not sure if we round up or down
			pf = (float)d.echoTrainLength / (float)pf;
			if (pf < 1.0) //e.g. if difference between lines and echo length not all explained by iPAT (SENSE/GRAPPA)
				fprintf(fp, "\t\"PartialFourier\": %g,\n", pf);
		} //compute partial Fourier: not reported in XA10, so infer
		//printf("PhaseLines=%d EchoTrainLength=%d SENSE=%g\n", d.phaseEncodingLines, d.echoTrainLength, d.accelFactPE); //n.b. we can not distinguish pF from SENSE/GRAPPA for UIH
	}
#endif
		if (d.interp3D > 1) //through-plane interpolation e.g. GE ZIP2 through-plane http://mriquestions.com/zip.html
			fprintf(fp, "\t\"Interpolation3D\": %d,\n", d.interp3D);
	// https://neurostars.org/t/repetitiontime-parameters-what-are-they-and-where-to-find-them/20020/6
	json_Float(fp, "\t\"RepetitionTimePreparation\": %g,\n", repetitionTimePreparation);
	//Philips ASL specific tags, issue533
	//Philips ASL issue 533
	/*
	//see dcm_qa_philips_asl: this works for the mulit-PLD sequence, but not for other sequences. Also beware that value varies per slice, so incorrect values for descending
	if ( (d.aslFlags != kASL_FLAG_NONE) && (dti4D->triggerDelayTime[0] >= 0.0)) { //see BEP009 PET https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0
		bool isMultiPLD = false;
		for (int i = 0; i < h->dim[4]; i++)
			if (dti4D->triggerDelayTime[i] != dti4D->triggerDelayTime[0])
				isMultiPLD = true;
		if (isMultiPLD) {
			fprintf(fp, "\t\"InitialPostLabelDelay\": [\n");
			for (int i = 0; i < h->dim[4]; i++) {
				if (i != 0)
					fprintf(fp, ",\n");
				if (dti4D->triggerDelayTime[i] < 0)
					break;
				fprintf(fp, "\t\t%g", dti4D->triggerDelayTime[i] / 1000.0);
			}
			fprintf(fp, "\t],\n");
		} else //if all delays are the same, write scalar
			json_Float(fp, "\t\"InitialPostLabelDelay\": %g,\n", dti4D->triggerDelayTime[0] / 1000.0);
	}
	*/
	//generic public ASL tags
	if (d.postLabelDelay > 0)
		json_Float(fp, "\t\"PostLabelingDelay\": %g,\n", float(d.postLabelDelay) / 1000.0);
	//ASL BIDS tags
	if ((d.aslFlags & kASL_FLAG_GE_CONTINUOUS) || (d.aslFlags & kASL_FLAG_GE_3DCASL))
		fprintf(fp, "\t\"ArterialSpinLabelingType\": \"CASL\",\n");
	if ((d.aslFlags & kASL_FLAG_GE_PSEUDOCONTINUOUS) || (d.aslFlags &  kASL_FLAG_GE_3DPCASL))
		fprintf(fp, "\t\"ArterialSpinLabelingType\": \"PCASL\",\n");
	if (d.aslFlags & kASL_FLAG_GE_PULSED)
		fprintf(fp, "\t\"ArterialSpinLabelingType\": \"PASL\",\n");
	if (d.durationLabelPulseGE > 0) {
		json_Float(fp, "\t\"LabelingDuration\": %g,\n", d.durationLabelPulseGE / 1000.0);
		json_Float(fp, "\t\"PostLabelingDelay\": %g,\n", d.TI / 1000.0); //For GE ASL: InversionTime -> Post-label delay
		json_Float(fp, "\t\"NumberOfPointsPerArm\": %g,\n", d.numberOfPointsPerArm);
		json_Float(fp, "\t\"NumberOfArms\": %g,\n", d.numberOfArms);
	}
	if (d.numberOfExcitations > 1) json_Float(fp, "\t\"NumberOfExcitations\": %g,\n", d.numberOfExcitations);
	if ((d.CSA.multiBandFactor > 1) && (d.modality == kMODALITY_MR)) //AccelFactorSlice
		fprintf(fp, "\t\"MultibandAccelerationFactor\": %d,\n", d.CSA.multiBandFactor);
	json_Float(fp, "\t\"PercentPhaseFOV\": %g,\n", d.phaseFieldofView);
	json_Float(fp, "\t\"PercentSampling\": %g,\n", d.percentSampling);
	if (d.echoTrainLength > 1) //>1 as for Siemens EPI this is 1, Siemens uses EPI factor http://mriquestions.com/echo-planar-imaging.html
		fprintf(fp, "\t\"EchoTrainLength\": %d,\n", d.echoTrainLength); //0018,0091 Combination of partial fourier and in-plane parallel imaging
	if (d.partialFourierDirection == kPARTIAL_FOURIER_DIRECTION_PHASE)
		fprintf(fp, "\t\"PartialFourierDirection\": \"PHASE\",\n");
	if (d.partialFourierDirection == kPARTIAL_FOURIER_DIRECTION_FREQUENCY)
		fprintf(fp, "\t\"PartialFourierDirection\": \"FREQUENCY\",\n");
	if (d.partialFourierDirection == kPARTIAL_FOURIER_DIRECTION_SLICE_SELECT)
		fprintf(fp, "\t\"PartialFourierDirection\": \"SLICE_SELECT\",\n");
	if (d.partialFourierDirection == kPARTIAL_FOURIER_DIRECTION_COMBINATION)
		fprintf(fp, "\t\"PartialFourierDirection\": \"COMBINATION\",\n");
	if ((d.phaseEncodingSteps > 0) && (d.isPartialFourier) && (d.manufacturer == kMANUFACTURER_PHILIPS)) {
		//issue 377
		fprintf(fp, "\t\"PartialFourierEnabled\": \"YES\",\n");
		fprintf(fp, "\t\"PhaseEncodingStepsNoPartialFourier\": %d,\n", d.phaseEncodingSteps);
	} else if (d.phaseEncodingSteps > 0)
		fprintf(fp, "\t\"PhaseEncodingSteps\": %d,\n", d.phaseEncodingSteps);
	if (d.frequencyEncodingSteps > 0)
		fprintf(fp, "\t\"FrequencyEncodingSteps\": %d,\n", d.frequencyEncodingSteps);
	if (d.phaseEncodingStepsOutOfPlane > 0)
		fprintf(fp, "\t\"PhaseEncodingStepsOutOfPlane\": %d,\n", d.phaseEncodingStepsOutOfPlane);
	if ((d.phaseEncodingLines > 0) && (d.modality == kMODALITY_MR))
		fprintf(fp, "\t\"AcquisitionMatrixPE\": %d,\n", d.phaseEncodingLines);
	//Compute ReconMatrixPE
	// Actual size of the *reconstructed* data in the PE dimension, which does NOT match
	// phaseEncodingLines in the case of interpolation or phaseResolution < 100%
	// We'll need this for generating a value for effectiveEchoSpacing that is consistent
	// with the *reconstructed* data.
	int reconMatrixPE = d.phaseEncodingLines;
	if ((h->dim[2] > 0) && (h->dim[1] > 0)) {
		if (h->dim[1] == h->dim[2]) //phase encoding does not matter
			reconMatrixPE = h->dim[2];
		else if (d.phaseEncodingRC == 'C')
			reconMatrixPE = h->dim[2]; //see dcm_qa: NOPF_NOPAT_NOPOS_PERES100_ES0P59_BW2222_200PFOV_AP_0034
		else if (d.phaseEncodingRC == 'R')
			reconMatrixPE = h->dim[1];
	}
	if ((d.modality == kMODALITY_MR) && (reconMatrixPE > 0))
		fprintf(fp, "\t\"ReconMatrixPE\": %d,\n", reconMatrixPE);
	if ((d.accelFactPE > 1.0) && (d.manufacturer == kMANUFACTURER_PHILIPS) && strstr(d.parallelAcquisitionTechnique, "CSENSE") ) {
		//see dcm_qa_cs_dl: while GE allows you to set ASSET and compressed sense, Philips reports only CSENSE
		d.compressedSensingFactor = d.accelFactPE;
		d.accelFactPE = 1.0;
		d.parallelAcquisitionTechnique[0] = '\0';
	}
	double bandwidthPerPixelPhaseEncode = d.bandwidthPerPixelPhaseEncode;
	if (bandwidthPerPixelPhaseEncode == 0.0)
		bandwidthPerPixelPhaseEncode = d.CSA.bandwidthPerPixelPhaseEncode;
	json_Float(fp, "\t\"BandwidthPerPixelPhaseEncode\": %g,\n", bandwidthPerPixelPhaseEncode);
	//if ((!d.is3DAcq) && (d.accelFactPE > 1.0)) fprintf(fp, "\t\"ParallelReductionFactorInPlane\": %g,\n", d.accelFactPE);
	if (d.accelFactPE > 1.0)
		fprintf(fp, "\t\"ParallelReductionFactorInPlane\": %g,\n", d.accelFactPE);
	json_Str(fp, "\t\"ParallelAcquisitionTechnique\": \"%s\",\n", d.parallelAcquisitionTechnique);
	//https://github.com/rordenlab/dcm2niix/issues/314
	if (d.accelFactOOP > 1.0)
		json_Float(fp, "\t\"ParallelReductionFactorOutOfPlane\": %g,\n", d.accelFactOOP); //issue672
	if (d.compressedSensingFactor > 1.0)
		json_Float(fp, "\t\"CompressedSensingFactor\": %g,\n", d.compressedSensingFactor);
	//detect if Siemens data is DeepLearning: see dcm_qa_cs_dl
	if (d.manufacturer == kMANUFACTURER_SIEMENS) {
		//DRB,DRG,DRS DeepReveal Boost,Gain,Sharp
		d.isDeepLearning = (strstr(d.imageType, "_DRB_")|| strstr(d.imageType, "_DRG_") || strstr(d.imageType, "_DRS_") ||
			strstr(d.imageTypeText, "_DRB_")|| strstr(d.imageTypeText, "_DRG_") || strstr(d.imageTypeText, "_DRS_"));
	}
	if (d.isDeepLearning) {
		json_Bool(fp, "\t\"DeepLearning\": %s,\n", 1);
		json_Str(fp, "\t\"DeepLearningDetails\": \"%s\",\n", d.deepLearningText);
	}
	//EffectiveEchoSpacing
	// Siemens bandwidthPerPixelPhaseEncode already accounts for the effects of parallel imaging,
	// interpolation, phaseOversampling, and phaseResolution, in the context of the size of the
	// *reconstructed* data in the PE dimension
	double effectiveEchoSpacing = 0.0;
	//next: dicm2nii's method for determining effectiveEchoSpacing if bandwidthPerPixelPhaseEncode is unknown, see issue 315
	//if ((reconMatrixPE > 0) && (bandwidthPerPixelPhaseEncode <= 0.0) && (d.CSA.sliceMeasurementDuration >= 0))
	//	effectiveEchoSpacing = d.CSA.sliceMeasurementDuration / (reconMatrixPE * 1000.0);
	if ((reconMatrixPE > 0) && (bandwidthPerPixelPhaseEncode > 0.0))
		effectiveEchoSpacing = 1.0 / (bandwidthPerPixelPhaseEncode * reconMatrixPE);
	json_Float(fp, "\t\"WaterFatShift\": %g,\n", d.waterFatShift);
	if ((effectiveEchoSpacing == 0.0) && (d.imagingFrequency > 0.0) && (d.waterFatShift != 0.0) && (d.echoTrainLength > 0) && (reconMatrixPE > 1)) {
		//in theory we could use either fieldStrength or imagingFrequency, but the former is typically provided with low precision
		//https://github.com/rordenlab/dcm2niix/issues/377
		// EchoSpacing 1/BW/EPI_factor https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1308&L=FSL&D=0&P=113520
		// this formula from https://support.brainvoyager.com/brainvoyager/functional-analysis-preparation/29-pre-processing/78-epi-distortion-correction-echo-spacing-and-bandwidth
		// https://neurostars.org/t/consolidating-epi-echo-spacing-and-readout-time-for-philips-scanner/4406
		/*
		ActualEchoSpacing = WaterFatShift / (ImagingFrequency * 3.4 * (EPI_Factor + 1))
		TotalReadoutTIme = ActualEchoSpacing * EPI_Factor
		EffectiveEchoSpacing = TotalReadoutTime / (ReconMatrixPE - 1)
		WaterFatShift = 2001,1022
		ImagingFrequency = 0018,0084
		EPI_Factor = 0018,0091 or 2001,1013
		ReconMatrixPE = 0028,0010 or 0028,0011 depending on 0018,1312
		*/
		float actualEchoSpacing = d.waterFatShift / (d.imagingFrequency * 3.4 * (d.echoTrainLength + 1));
		float totalReadoutTime = actualEchoSpacing * d.echoTrainLength;
		float effectiveEchoSpacingPhil = totalReadoutTime / (reconMatrixPE - 1);
		json_Float(fp, "\t\"EstimatedEffectiveEchoSpacing\": %g,\n", effectiveEchoSpacingPhil);
		fprintf(fp, "\t\"EstimatedTotalReadoutTime\": %g,\n", totalReadoutTime);
	}
	if ((d.effectiveEchoSpacingGE > 0.0) && (reconMatrixPE > 1) && (d.accelFactPE > 0.0)) {
		//TotalReadoutTime = [ ceil (PE_AcquisitionMatrix / Asset_R_factor) - 1] * ESP
		float roundFactor = 2.0;
		if (d.isPartialFourier)
			roundFactor = 4.0;
		float NotPhysicalNumberOfAcquiredPELinesGE = (ceil(1 / roundFactor * d.phaseEncodingLines / d.accelFactPE) * roundFactor);
		float NotPhysicalTotalReadOutTimeGE = ( NotPhysicalNumberOfAcquiredPELinesGE - 1.0) * d.effectiveEchoSpacingGE * 0.000001;
		// printf("ASSET= %g PE_AcquisitionMatrix= %d ESP= %d TotalReadoutTimeGE= %g NumKyLineGE= %d\n", 
		//	d.accelFactPE, d.phaseEncodingLines, d.effectiveEchoSpacingGE, NotPhysicalTotalReadOutTimeGE, (int)NotPhysicalNumberOfAcquiredPELinesGE);
		//json_Float(fp, "\t\"TotalReadoutTime\": %g,\n", totalReadoutTime);
		effectiveEchoSpacing = NotPhysicalTotalReadOutTimeGE / (d.phaseEncodingLines - 1);
		// if this is considered acceptable, meaningful intermediate variables can be written, this might help the end-user. 
#ifdef MY_DEBUG
		fprintf(fp, "\t\"EchoSpacingMicroSecondsGE\": %d,\n", d.effectiveEchoSpacingGE);
		fprintf(fp, "\t\"NotPhysicalNumberOfAcquiredPELinesGE\": %d,\n", (int)(NotPhysicalNumberOfAcquiredPELinesGE));
		json_Float(fp, "\t\"NotPhysicalTotalReadOutTimeGE\": %g,\n", NotPhysicalTotalReadOutTimeGE);
#endif 
	}
	json_Float(fp, "\t\"EffectiveEchoSpacing\": %g,\n", effectiveEchoSpacing);
	// Calculate true echo spacing (should match what Siemens reports on the console)
	// i.e., should match "echoSpacing" extracted from the ASCII CSA header, when that exists
	double trueESfactor = 1.0;
	if (d.accelFactPE > 1.0)
		trueESfactor /= d.accelFactPE;
	if (phaseOversampling > 0.0)
		trueESfactor *= (1.0 + phaseOversampling);
	float derivedEchoSpacing = 0.0;
	derivedEchoSpacing = bandwidthPerPixelPhaseEncode * trueESfactor * reconMatrixPE;
	if (derivedEchoSpacing != 0)
		derivedEchoSpacing = 1 / derivedEchoSpacing;
	json_Float(fp, "\t\"DerivedVendorReportedEchoSpacing\": %g,\n", derivedEchoSpacing);
	//TotalReadOutTime: Really should be called "EffectiveReadOutTime", by analogy with "EffectiveEchoSpacing".
	// But BIDS spec calls it "TotalReadOutTime".
	// So, we DO NOT USE EchoTrainLength, because not trying to compute the actual (physical) readout time.
	// Rather, the point of computing "EffectiveEchoSpacing" properly is so that this
	// "Total(Effective)ReadOutTime" can be computed straightforwardly as the product of the
	// EffectiveEchoSpacing and the size of the *reconstructed* matrix in the PE direction.
	// see https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide#A--datain
	// FSL definition is start of first line until start of last line.
	// Other than the use of (n-1), the value is basically just 1.0/bandwidthPerPixelPhaseEncode.
	// https://github.com/rordenlab/dcm2niix/issues/130
	if (d.manufacturer != kMANUFACTURER_UIH) //issue606
		json_Float(fp, "\t\"AcquisitionDuration\": %g,\n", d.acquisitionDuration);
	if ((d.manufacturer == kMANUFACTURER_UIH) && (effectiveEchoSpacing <= 0.0)) //issue225, issue531
		json_Float(fp, "\t\"TotalReadoutTime\": %g,\n", d.acquisitionDuration / 1000.0);
	else if ((reconMatrixPE > 0) && (effectiveEchoSpacing > 0.0) )
	  fprintf(fp, "\t\"TotalReadoutTime\": %g,\n", effectiveEchoSpacing * (reconMatrixPE - 1.0));
	json_Float(fp, "\t\"PixelBandwidth\": %g,\n", d.pixelBandwidth);
	if ((d.manufacturer == kMANUFACTURER_SIEMENS) && (d.dwellTime > 0))
		fprintf(fp, "\t\"DwellTime\": %g,\n", d.dwellTime * 1E-9);
	// Phase encoding polarity
/*
following logic now occurs earlier to aid bids guess
	int phPos = d.CSA.phaseEncodingDirectionPositive;
	//next two conditionals updated: make GE match Siemens
	if (d.phaseEncodingGE == kGE_PHASE_ENCODING_POLARITY_UNFLIPPED)
		phPos = 1;
	if (d.phaseEncodingGE == kGE_PHASE_ENCODING_POLARITY_FLIPPED)
		phPos = 0;
*/
	//if ((phPos >= 0) && (d.phaseEncodingRC == 'R') && (d.manufacturer == kMANUFACTURER_UIH)) phPos = 1 - phPos; //issue410
	bool isSkipPhaseEncodingAxis = d.is3DAcq;
	if (d.echoTrainLength > 1)
		isSkipPhaseEncodingAxis = false; //issue 371: ignore phaseEncoding for 3D MP-RAGE/SPACE, but report for 3D EPI
	int phPos = d.CSA.phaseEncodingDirectionPositive;
	if (((d.phaseEncodingRC == 'R') || (d.phaseEncodingRC == 'C')) && (!isSkipPhaseEncodingAxis) && (phPos < 0)) {
		//when phase encoding axis is known but we do not know phase encoding polarity
		// https://github.com/rordenlab/dcm2niix/issues/163
		// This will typically correspond with InPlanePhaseEncodingDirectionDICOM
		if (d.phaseEncodingRC == 'C') //Values should be "R"ow, "C"olumn or "?"Unknown
			fprintf(fp, "\t\"PhaseEncodingAxis\": \"j\",\n");
		else if (d.phaseEncodingRC == 'R')
			fprintf(fp, "\t\"PhaseEncodingAxis\": \"i\",\n");
	}
	if (((d.phaseEncodingRC == 'R') || (d.phaseEncodingRC == 'C')) && (!isSkipPhaseEncodingAxis) && (phPos >= 0)) {
		//printf("%ld %d %d %c %d\n", d.seriesNum, d.echoTrainLength, isSkipPhaseEncodingAxis, d.phaseEncodingRC, phPos); //test issue 371
		if (d.phaseEncodingRC == 'C') //Values should be "R"ow, "C"olumn or "?"Unknown
			fprintf(fp, "\t\"PhaseEncodingDirection\": \"j");
		else if (d.phaseEncodingRC == 'R')
			fprintf(fp, "\t\"PhaseEncodingDirection\": \"i");
		else
			fprintf(fp, "\t\"PhaseEncodingDirection\": \"?");
		//phaseEncodingDirectionPositive has one of three values: UNKNOWN (-1), NEGATIVE (0), POSITIVE (1)
		//However, DICOM and NIfTI are reversed in the j (ROW) direction
		//Equivalent to dicm2nii's "if flp(iPhase), phPos = ~phPos; end"
		//for samples see https://github.com/rordenlab/dcm2niix/issues/125
		if (phPos < 0)
			fprintf(fp, "?"); //unknown
		else if ((phPos == 0) && (d.phaseEncodingRC != 'C'))
			fprintf(fp, "-");
		else if ((d.phaseEncodingRC == 'C') && (phPos == 1) && (opts.isFlipY))
			fprintf(fp, "-");
		else if ((d.phaseEncodingRC == 'C') && (phPos == 0) && (!opts.isFlipY))
			fprintf(fp, "-");
		fprintf(fp, "\",\n");
	} //only save PhaseEncodingDirection if BOTH direction and POLARITY are known
	//Slice Timing UIH or GE >>>>
	//in theory, we should also report XA10 slice times here, but see series 24 of https://github.com/rordenlab/dcm2niix/issues/236
	if ((d.modality != kMODALITY_CT) && (d.modality != kMODALITY_PT) && (!d.is3DAcq) && (h->dim[3] > 1) && (d.CSA.sliceTiming[1] >= 0.0) && (d.CSA.sliceTiming[0] >= 0.0)) {
		fprintf(fp, "\t\"SliceTiming\": [\n");
		for (int i = 0; i < h->dim[3]; i++) {
			if (i != 0)
				fprintf(fp, ",\n");
			fprintf(fp, "\t\t%g", d.CSA.sliceTiming[i] / 1000.0);
		}
		fprintf(fp, "\t],\n");
	}
	//DICOM orientation and phase encoding: useful for 3D undistortion. Original DICOM values: DICOM not NIfTI space, ignores if 3D image re-oriented
	float mxOrient = 0.0;
	for (int i = 1; i < 7; i++)
		mxOrient = max(mxOrient, fabs(d.orient[i]));
	if (! isSameFloatGE(mxOrient, 0.0)) { //if set
		fprintf(fp, "\t\"ImageOrientationPatientDICOM\": [\n");
		for (int i = 1; i < 7; i++) {
			if (i != 1)
				fprintf(fp, ",\n");
			fprintf(fp, "\t\t%g", d.orient[i]);
		}
		fprintf(fp, "\t],\n");
	}
	json_Str(fp, "\t\"ImageOrientationText\": \"%s\",\n", d.imageOrientationText);
	if (d.phaseEncodingRC == 'C')
		fprintf(fp, "\t\"InPlanePhaseEncodingDirectionDICOM\": \"COL\",\n");
	if (d.phaseEncodingRC == 'R')
		fprintf(fp, "\t\"InPlanePhaseEncodingDirectionDICOM\": \"ROW\",\n");
	if ((opts.isGuessBidsFilename) && (strlen(d.CSA.bidsDataType)) && (strlen(d.CSA.bidsDataType)))
		fprintf(fp, "\t\"BidsGuess\": [\"%s\",\"%s\"],\n",d.CSA.bidsDataType, d.CSA.bidsEntitySuffix);
	//json_Str(fp, "\t\"StationName\": \"%s\",\n", d.stationName);

	// Finish up with info on the conversion tool
	fprintf(fp, "\t\"ConversionSoftware\": \"dcm2niix\",\n");
	fprintf(fp, "\t\"ConversionSoftwareVersion\": \"%s\"\n", kDCMdate);
	//fprintf(fp, "\t\"ConversionSoftwareVersion\": \"%s\"\n", kDCMvers );kDCMdate
	fprintf(fp, "}\n");
	fclose(fp);
} // nii_SaveBIDSX()

void swapEndian(struct nifti_1_header *hdr, unsigned char *im, bool isNative) {
	//swap endian from big->little or little->big
	// must be told which is native to detect datatype and number of voxels
	// one could also auto-detect: hdr->sizeof_hdr==348
	if (!isNative)
#if defined(USING_MGH_NIFTI_IO) || defined(USING_R)
		swap_nifti_header(hdr, 1);
#else
		swap_nifti_header(hdr);
#endif
	int nVox = 1;
	for (int i = 1; i < 8; i++)
		if (hdr->dim[i] > 1)
			nVox = nVox * hdr->dim[i];
	int bitpix = hdr->bitpix;
	int datatype = hdr->datatype;
	if (isNative)
#if defined(USING_MGH_NIFTI_IO) || defined(USING_R)
		swap_nifti_header(hdr, 1);
#else
		swap_nifti_header(hdr);
#endif
	if (datatype == DT_RGBA32)
		return;
	//n.b. do not swap 8-bit, 24-bit RGB, and 32-bit RGBA
	if (bitpix == 16)
		nifti_swap_2bytes(nVox, im);
	if (bitpix == 32)
		nifti_swap_4bytes(nVox, im);
	if (bitpix == 64)
		nifti_swap_8bytes(nVox, im);
}

#ifndef USING_R

void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts, struct nifti_1_header *h, const char *filename) {
	struct TDTI4D *dti4D = (struct TDTI4D *)malloc(sizeof(struct TDTI4D));
	dti4D->sliceOrder[0] = -1;
	dti4D->volumeOnsetTime[0] = -1;
	dti4D->decayFactor[0] = -1;
	dti4D->triggerDelayTime[0] = -1.0;
	dti4D->intenScale[0] = 0.0;
	dti4D->repetitionTimeExcitation = 0.0;
	dti4D->repetitionTimeInversion = 0.0;
	nii_SaveBIDSX(pathoutname, d, opts, h, filename, dti4D);
	free(dti4D);
} // nii_SaveBIDSX()

#endif

unsigned char *removeADC(struct nifti_1_header *hdr, unsigned char *inImg, int numADC) {
	//for speed we just clip the number of volumes, the realloc routine would be nice
	// we do not want to copy input to a new smaller array since 4D DTI datasets can be huge
	// and that would require almost twice as much RAM
	if (numADC < 1)
		return inImg;
	hdr->dim[4] = hdr->dim[4] - numADC;
	if (hdr->dim[4] < 2)
		hdr->dim[0] = 3; //e.g. 4D 2-volume DWI+ADC becomes 3D DWI if ADC is removed
	return inImg;
} //removeADC()

//#define naive_reorder_vols //for simple, fast re-ordering that consumes a lot of RAM
#ifdef naive_reorder_vols
unsigned char *reorderVolumes(struct nifti_1_header *hdr, unsigned char *inImg, int *volOrderIndex) {
	//reorder volumes to place ADC at end and (optionally) B=0 at start
	// volOrderIndex[0] reports location of desired first volume
	// naive solution creates an output buffer that doubles RAM usage (2 *numVol)
	int numVol = hdr->dim[4];
	int numVolBytes = hdr->dim[1] * hdr->dim[2] * hdr->dim[3] * (hdr->bitpix / 8);
	if ((!volOrderIndex) || (numVol < 1) || (numVolBytes < 1))
		return inImg;
	unsigned char *outImg = (unsigned char *)malloc(numVolBytes * numVol);
	int outPos = 0;
	for (int i = 0; i < numVol; i++) {
		memcpy(&outImg[outPos], &inImg[volOrderIndex[i] * numVolBytes], numVolBytes); // dest, src, bytes
		outPos += numVolBytes;
	} //for each volume
	free(volOrderIndex);
	free(inImg);
	return outImg;
} //reorderVolumes()
#else // naive_reorder_vols
unsigned char *reorderVolumes(struct nifti_1_header *hdr, unsigned char *inImg, int *volOrderIndex) {
	//reorder volumes to place ADC at end and (optionally) B=0 at start
	// volOrderIndex[0] reports location of desired first volume
	// complicated by fact that 4D DTI data is often huge
	// simple solutions would create an output buffer that would double RAM usage (2 *numVol)
	// here we bubble-sort volumes in place to use numVols+1 memory
	int numVol = hdr->dim[4];
	int numVolBytes = hdr->dim[1] * hdr->dim[2] * hdr->dim[3] * (hdr->bitpix / 8);
	int *inPos = (int *)malloc(numVol * sizeof(int));
	for (int i = 0; i < numVol; i++)
		inPos[i] = i;
	unsigned char *tempVol = (unsigned char *)malloc(numVolBytes);
	for (int o = 0; o < numVol; o++) {
		int i = inPos[volOrderIndex[o]]; //input volume
		if (i == o)
			continue; //volume in correct order
		memcpy(&tempVol[0], &inImg[o * numVolBytes], numVolBytes); //make temp
		memcpy(&inImg[o * numVolBytes], &inImg[i * numVolBytes], numVolBytes); //copy volume to desire location dest, src, bytes
		memcpy(&inImg[i * numVolBytes], &tempVol[0], numVolBytes); //copy unsorted volume
		inPos[o] = i;
	} //for each volume
	free(inPos);
	free(volOrderIndex);
	free(tempVol);
	return inImg;
} //reorderVolumes()
#endif // naive_reorder_vols

float *bvals; //global variable for cmp_bvals
int cmp_bvals(const void *a, const void *b) {
	int ia = *(int *)a;
	int ib = *(int *)b;
	//return bvals[ia] > bvals[ib] ? -1 : bvals[ia] < bvals[ib];
	return bvals[ia] < bvals[ib] ? -1 : bvals[ia] > bvals[ib];
} // cmp_bvals()

bool isAllZeroFloat(float v1, float v2, float v3) {
	if (!isSameFloatGE(v1, 0.0))
		return false;
	if (!isSameFloatGE(v2, 0.0))
		return false;
	if (!isSameFloatGE(v3, 0.0))
		return false;
	return true;
}

int *nii_saveDTI(char pathoutname[], int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata dcmList[], struct TDCMopts opts, int sliceDir, struct TDTI4D *dti4D, int *numADC, int numVol) {
	//reports non-zero if any volumes should be excluded (e.g. philip stores an ADC maps)
	*numADC = 0;
	if (opts.isOnlyBIDS)
		return NULL;
	uint64_t indx0 = dcmSort[0].indx; //first volume
	if (isnan(dcmList[indx0].patientPosition[1]))
		return NULL; //issue606 do not save bvec for non-spatial data (e.g. physio)
	int numDti = dcmList[indx0].CSA.numDti;
#ifdef USING_R
	ImageList *images = (ImageList *)opts.imageList;
#endif
	//https://github.com/rordenlab/dcm2niix/issues/352
	bool allB0 = dcmList[indx0].isDiffusion;
	bool isDerived = dcmList[indx0].isDerived;
	if (dcmList[indx0].isDerived)
		allB0 = false; //e.g. FA map
	if ((numDti == numVol) && (numDti > 1))
		allB0 = false;
	if (numDti > 1)
		allB0 = false;
	if (nConvert > 1) {
		for (int i = 0; i < nConvert; i++) { //for each image
			float b0 = dcmList[dcmSort[i].indx].CSA.dtiV[0];
			if (!isSameFloat(b0, 0.0))
				allB0 = false;
		}
	}
	if ((numDti == 1) && (dti4D->S[0].V[0] > 50.0))
		allB0 = false;
	if (allB0) {
		if (opts.isVerbose)
			printMessage("Diffusion image without gradients: assuming %d volume B=0 series\n", numVol);
#ifdef USING_R
		// The image hasn't been created yet, so the attributes must be deferred
		images->addDeferredAttribute("bValues", std::vector<double>(numVol, 0.0));
		images->addDeferredAttribute("bVectors", std::vector<double>(numVol * 3, 0.0), numVol, 3);
#else
		char sep = '\t';
		if (opts.isCreateBIDS)
			sep = ' ';
		//save bval
		char txtname[2048] = {""};
		strcpy(txtname, pathoutname);
		strcat(txtname, ".bval");
		FILE *fp = fopen(txtname, "w");
		for (int i = 0; i < (numVol); i++)
			fprintf(fp, "%d%c", 0, sep);
		fprintf(fp, "\n");
		fclose(fp);
		//save bvec
		strcpy(txtname, pathoutname);
		strcat(txtname, ".bvec");
		fp = fopen(txtname, "w");
		for (int v = 0; v < (3); v++) {
			for (int i = 0; i < (numVol); i++)
				fprintf(fp, "%d%c", 0, sep);
			fprintf(fp, "\n");
		}
		fclose(fp);
#endif
	}
	if (numDti < 1)
		return NULL;
	if ((numDti < 2) && (nConvert < 2))
		return NULL;
	TDTI *vx = NULL;
	if (numDti > 1) {
		vx = (TDTI *)malloc(numDti * sizeof(TDTI));
		for (int i = 0; i < numDti; i++) //for each direction
			for (int v = 0; v < 4; v++) //for each vector+B-value
				vx[i].V[v] = dti4D->S[i].V[v];
	} else { //if (numDti == 1) {//extract DTI from different slices
		vx = (TDTI *)malloc(nConvert * sizeof(TDTI));
		numDti = 0;
		for (int i = 0; i < nConvert; i++) { //for each image
			if ((dcmList[indx0].CSA.mosaicSlices > 1) || (isSamePosition(dcmList[indx0], dcmList[dcmSort[i].indx]))) {
				//if (numDti < kMaxDTIv)
				for (int v = 0; v < 4; v++)									//for each vector+B-value
					vx[numDti].V[v] = dcmList[dcmSort[i].indx].CSA.dtiV[v]; //dcmList[indx0].CSA.dtiV[numDti][v] = dcmList[dcmSort[i].indx].CSA.dtiV[0][v];
				numDti++;
			}								//for slices with repeats
		}									//for each file
		dcmList[indx0].CSA.numDti = numDti; //warning structure not changed outside scope!
	}
	bool bValueVaries = false;
	for (int i = 1; i < numDti; i++) //check if all bvalues match first volume
		if (vx[i].V[0] != vx[0].V[0])
			bValueVaries = true;
	//optional: record b-values even without variability
	float minBval = vx[0].V[0];
	for (int i = 1; i < numDti; i++) //check if all bvalues match first volume
		if (vx[i].V[0] < minBval)
			minBval = vx[i].V[0];
	if (minBval > 50.0)
		bValueVaries = true;
	//start issue394: experimental, single volume per series, Siemens XA
	if (!isAllZeroFloat(vx[0].V[1], vx[0].V[2], vx[0].V[3]))
		bValueVaries = true;
	//end issue394
	if (!bValueVaries) {
		bool bVecVaries = false;
		for (int i = 1; i < numDti; i++) { //check if all bvalues match first volume
			if (vx[i].V[1] != vx[0].V[1])
				bVecVaries = true;
			if (vx[i].V[2] != vx[0].V[2])
				bVecVaries = true;
			if (vx[i].V[3] != vx[0].V[3])
				bVecVaries = true;
		}
		if (!bVecVaries) {
			free(vx);
			return NULL;
		}
		if (opts.isVerbose) {
			for (int i = 0; i < numDti; i++)
				printMessage("bxyz %g %g %g %g\n", vx[i].V[0], vx[i].V[1], vx[i].V[2], vx[i].V[3]);
		}
		//Stutters XINAPSE7 seem to save B=0 as B=2000, but these are not derived? https://github.com/rordenlab/dcm2niix/issues/182
		bool bZeroBvec = false;
		for (int i = 0; i < numDti; i++) { //check if all bvalues match first volume
			if (isAllZeroFloat(vx[i].V[1], vx[i].V[2], vx[i].V[3])) {
				vx[i].V[0] = 0;
				//printWarning("volume %d might be B=0\n", i);
				bZeroBvec = true;
			}
		}
		if (bZeroBvec)
			printWarning("Assuming volumes without gradients are actually B=0\n");
		else {
			printWarning("No bvec/bval files created. Only one B-value reported for all volumes: %g\n", vx[0].V[0]);
			free(vx);
			return NULL;
		}
	}
	//report values:
	//for (int i = 1; i < numDti; i++) //check if all bvalues match first volume
	// printMessage("%d bval= %g bvec= %g %g %g\n",i, vx[i].V[0], vx[i].V[1], vx[i].V[2], vx[i].V[3]);
	int minB0idx = 0;
	float minB0 = vx[0].V[0];
	for (int i = 0; i < numDti; i++)
		if (vx[i].V[0] < minB0) {
			minB0 = vx[i].V[0];
			minB0idx = i;
		}
	float maxB0 = vx[0].V[0];
	for (int i = 0; i < numDti; i++)
		if (vx[i].V[0] > maxB0)
			maxB0 = vx[i].V[0];
	if (!isDerived) { //no warnings for derived data
		//for CMRR sequences unweighted volumes are not actually B=0 but they have B near zero
		if (minB0 > 50)
			printWarning("This diffusion series does not have a B0 (reference) volume\n");
		if ((!opts.isSortDTIbyBVal) && (minB0idx > 0))
			printMessage("Note: B0 not the first volume in the series (FSL eddy reference volume is %d)\n", minB0idx);
	}
	float kADCval = maxB0 + 1; //mark as unusual
	*numADC = 0;
	bvals = (float *)malloc(numDti * sizeof(float));
	int numGEwarn = 0;
	bool isGEADC = (dcmList[indx0].numberOfDiffusionDirectionGE == 0); // GE non-DTI
	for (int i = 0; i < numDti; i++) {
		bvals[i] = vx[i].V[0];
		//printMessage("---bxyz %g %g %g %g\n",vx[i].V[0],vx[i].V[1],vx[i].V[2],vx[i].V[3]);
		//Philips includes derived isotropic images
		//if (((dcmList[indx0].manufacturer == kMANUFACTURER_GE) || (dcmList[indx0].manufacturer == kMANUFACTURER_PHILIPS)) && (isADCnotDTI(vx[i]))) {
		if (((dcmList[indx0].manufacturer == kMANUFACTURER_GE)) && (isADCnotDTI(vx[i]))) {
			numGEwarn += 1;
			if (isGEADC) { //e.g. GE Trace where bval=900, bvec=0,0,0
				*numADC = *numADC + 1;
				//printWarning("GE ADC volume %d\n", i+1);
				bvals[i] = kADCval;
			} else
				vx[i].V[0] = 0; //e.g. GE raw B=0 where bval=900, bvec=0,0,0
		} //see issue 245, however this does impact some anonymized files where bvec but not bval removed https://neurostars.org/t/dcm2bids-after-conversion-to-bids-bvals-are-zeros/20198/11
		if (((dcmList[indx0].manufacturer == kMANUFACTURER_PHILIPS)) && (isADCnotDTI(vx[i]))) {
			*numADC = *numADC + 1;
			bvals[i] = kADCval;
			//printMessage("+++bxyz %d\n",i);
		}
		bvals[i] = bvals[i] + (0.5 * i / numDti); //add a small bias so ties are kept in sequential order
	}
	// See issue 777: removed the warning because GE DTI b=0 with bval>0 but bvec=0 (prior to version 29.1) will be handled by geCorrectBvecs()
	// if (numGEwarn > 0)
	//	printWarning("Some images had bval>0 but bvec=0 (either Trace or b=0, see issue 245)\n");
	/*if ((*numADC == numDti) || (numGEwarn == numDti)) { //issue 405: we now save bvals file for isotropic series
		//all isotropic/ADC images - no valid bvecs
		*numADC = 0;
		free(bvals);
		free(vx);
		return NULL;
	}*/
	bool isIsotropic = false;
	if ((*numADC == numDti) || (numGEwarn == numDti)) //issue 405: we now save bvals file for isotropic series
		isIsotropic = true;
	if (*numADC > 0) {
		// DWIs (i.e. short diffusion scans with too few directions to
		// calculate tensors...they typically acquire b=0 + 3 b > 0 so
		// the isotropic trace or MD can be calculated) often come as
		// b=0 and trace pairs, with the b=0 and trace in either order,
		// and often as "ORIGINAL", even though the trace is not.
		// The bval file is needed for downstream processing to know
		// * which is the b=0 and which is the trace, and
		// * what b is for the trace,
		// so dcm2niix should *always* write the bval and bvec files,
		// AND include the b for the trace for DWIs.
		// One hackish way to accomplish that is to set *numADC = 0
		// when *numADC == 1 && numDti == 2.
		// - Rob Reid, 2017-11-29.
		if ((*numADC == 1) && ((numDti - *numADC) < 2)) {
			*numADC = 0;
			printMessage("Note: this appears to be a b=0+trace DWI; ADC/trace removal has been disabled.\n");
		} else {
			if ((numDti - *numADC) < 2) {
			/*if (!dcmList[indx0].isDerived) //no need to warn if images are derived Trace/ND pair
			printWarning("No bvec/bval files created: only single value after ADC excluded\n");
			*numADC = 0;
			free(bvals);
			free(vx);
			return NULL;*/
				printMessage("Warning: Isotropic DWI series, all bvecs are zero (issue 405)\n");
				*numADC = 0;
			} else
				printMessage("Note: %d volumes appear to be ADC or trace images that will be removed to allow processing\n", *numADC);
		}
	}
	//sort ALL including ADC
	int *volOrderIndex = (int *)malloc(numDti * sizeof(int));
	for (int i = 0; i < numDti; i++)
		volOrderIndex[i] = i;
	if (opts.isSortDTIbyBVal)
		qsort(volOrderIndex, numDti, sizeof(*volOrderIndex), cmp_bvals);
	else if (*numADC > 0) {
		int o = 0;
		for (int i = 0; i < numDti; i++) {
			if (bvals[i] < kADCval) {
				volOrderIndex[o] = i;
				o++;
			} //if not ADC
		} //for each volume
	} //if sort else if has ADC
	free(bvals);
	//save VX as sorted
	TDTI *vxOrig = (TDTI *)malloc(numDti * sizeof(TDTI));
	for (int i = 0; i < numDti; i++)
		vxOrig[i] = vx[i];
	//remove ADC
	numDti = numDti - *numADC;
	free(vx);
	vx = (TDTI *)malloc(numDti * sizeof(TDTI));
	for (int i = 0; i < numDti; i++)
		vx[i] = vxOrig[volOrderIndex[i]];
	free(vxOrig);
	//if no ADC or sequential, the is no need to re-order volumes
	bool isSequential = true;
	for (int i = 1; i < (numDti + *numADC); i++)
		if (volOrderIndex[i] <= volOrderIndex[i - 1])
			isSequential = false;
	if (isSequential) {
		free(volOrderIndex);
		volOrderIndex = NULL;
	}
	if (!isSequential)
		printMessage("DTI volumes re-ordered by ascending b-value\n");
#ifdef RAW_BVEC //save raw bvecs as reported by DICOM, not rotated to image space
	char txtname[2048] = {""};
	strcpy(txtname, pathoutname);
	strcat(txtname, ".rvec");
	FILE *fp = fopen(txtname, "w");
	for (int i = 0; i < numDti; i++)
		fprintf(fp, "%g\t", vx[i].V[1]);
	fprintf(fp, "\n");
	for (int i = 0; i < numDti; i++)
		fprintf(fp, "%g\t", vx[i].V[2]);
	fprintf(fp, "\n");
	for (int i = 0; i < numDti; i++)
		fprintf(fp, "%g\t", vx[i].V[3]);
	fprintf(fp, "\n");
	fclose(fp);
#endif
	dcmList[indx0].CSA.numDti = numDti; //warning structure not changed outside scope!
	geCorrectBvecs(&dcmList[indx0], sliceDir, vx, opts.isVerbose);
	siemensPhilipsCorrectBvecs(&dcmList[indx0], sliceDir, vx, opts.isVerbose);
	if (dcmList[indx0].CSA.numDti < 1) { //issue449
		free(vx);
		return NULL;
	}
	if (!opts.isFlipY) { //!FLIP_Y&& (dcmList[indx0].CSA.mosaicSlices < 2) mosaics are always flipped in the Y direction
		//the order of rows is flipped: flip the y-polarity
		for (int i = 0; i < (numDti); i++) {
			if (fabs(vx[i].V[2]) > FLT_EPSILON)
				vx[i].V[2] = -vx[i].V[2];
		} //for each direction
		//less intuitively: we have now flipped the determinant, so we must swap the x-polarity
		for (int i = 0; i < (numDti); i++) {
			if (fabs(vx[i].V[1]) > FLT_EPSILON)
				vx[i].V[1] = -vx[i].V[1];
		} //for each direction
	} //if not a mosaic

#ifdef USING_DCM2NIIXFSWRAPPER
        // make adjustments for MGH bvecs output
        for (int i = 0; i < (numDti); i++) {
	  if (sliceDir < 0)
	  {
            // at this point, bvecs output is calculated as not isFlipY, assuming isFlipZ, determinant is positive.
            // So, bvecs first column is reversed for FSL.
            // MGH conversion: not isFlipY, slice direction not flipped, determinant is negative, 
            // 1. we need to reverse bvecs column 1 back, 
            // 2. also need to reverse bvecs column 3
            
            float tmp = vx[i].V[1];
            vx[i].V[1] = -vx[i].V[1];
            if (getenv("DCM2NIIXFSWRAPPER_DEBUG") != NULL && strcmp(getenv("DCM2NIIXFSWRAPPER_DEBUG"), "yes") == 0)
	    {
              if (i < 6)
	        printf("nii_saveDTI() (BVECS_DEBUG) (mgh adj. sliceDir < 0) flip bvecs sign column 1: %f => %f\n", tmp, vx[i].V[1]);
            }

            if (fabs(vx[i].V[3]) > FLT_EPSILON)
	    {
              tmp = vx[i].V[3];
	      vx[i].V[3] = -vx[i].V[3];
              if (getenv("DCM2NIIXFSWRAPPER_DEBUG") != NULL && strcmp(getenv("DCM2NIIXFSWRAPPER_DEBUG"), "yes") == 0)
	      {
                if (i < 6)
		  printf("nii_saveDTI() (BVECS_DEBUG) (mgh adj. sliceDir < 0) flip bvecs sign column 3: %f => %f\n", tmp, vx[i].V[3]);
              }
	    }
          }
	  else if (abs(sliceDir) == kSliceOrientMosaicNegativeDeterminant)
	  {
            // swap signs for every column
            for (int j = 1; j < 4; j++)
	    {
              if (fabs(vx[i].V[j]) > FLT_EPSILON)
	      {
                float tmp = vx[i].V[j];
	        vx[i].V[j] = -vx[i].V[j];
                if (getenv("DCM2NIIXFSWRAPPER_DEBUG") != NULL && strcmp(getenv("DCM2NIIXFSWRAPPER_DEBUG"), "yes") == 0)
	        {
                  if (i < 6)
                    printf("nii_saveDTI() (BVECS_DEBUG) (mgh adj. abs(sliceDir) == kSliceOrientMosaicNegativeDeterminant) flip bvecs sign column j: %f => %f\n", tmp, vx[i].V[j]);
                }
	      }
            }
	  }
          else  // sliceDir >= 0 && abs(sliceDir) != kSliceOrientMosaicNegativeDeterminant
	  {	
            // MGH conversion: not flip Y, image determinant is positive, bvecs first column is reversed for FSL.
            // So, we need to flip bvecs first column.
            if (fabs(vx[i].V[1]) > FLT_EPSILON)
	    {
              float tmp = vx[i].V[1];
	      vx[i].V[1] = -vx[i].V[1];
              if (getenv("DCM2NIIXFSWRAPPER_DEBUG") != NULL && strcmp(getenv("DCM2NIIXFSWRAPPER_DEBUG"), "yes") == 0)
	      {
                if (i < 6)
		  printf("nii_saveDTI() (BVECS_DEBUG) (mgh adj. abs(sliceDir) != kSliceOrientMosaicNegativeDeterminant) flip bvecs sign column 1: %f => %f\n", tmp, vx[i].V[1]);
              }
	    }
          }
        } //for each direction

        mrifsStruct.numDti = numDti;
        mrifsStruct.tdti = (TDTI *)malloc(numDti * sizeof(TDTI));
        for (int i = 0; i < numDti; i++)
	{
            mrifsStruct.tdti[i].V[0] = vx[i].V[0];
            mrifsStruct.tdti[i].V[1] = vx[i].V[1];
            mrifsStruct.tdti[i].V[2] = vx[i].V[2];
            mrifsStruct.tdti[i].V[3] = vx[i].V[3];
        }
#endif

	if (opts.isVerbose) {
		for (int i = 0; i < (numDti); i++) {
			printMessage("%d\tB=\t%g\tVec=\t%g\t%g\t%g\n", i, vx[i].V[0], vx[i].V[1], vx[i].V[2], vx[i].V[3]);
		} //for each direction
	}
	//printMessage("%f\t%f\t%f",dcmList[indx0].CSA.dtiV[1][1],dcmList[indx0].CSA.dtiV[1][2],dcmList[indx0].CSA.dtiV[1][3]);
#ifdef USING_R
	std::vector<double> bValues(numDti);
	std::vector<double> bVectors(numDti * 3);
	for (int i = 0; i < numDti; i++) {
		bValues[i] = vx[i].V[0];
		for (int j = 0; j < 3; j++)
			bVectors[i + j * numDti] = vx[i].V[j + 1];
	}
	// The image hasn't been created yet, so the attributes must be deferred
	images->addDeferredAttribute("bValues", bValues);
	images->addDeferredAttribute("bVectors", bVectors, numDti, 3);
#else
	if (opts.saveFormat != kSaveFormatNIfTI) {
		if (numDti < kMaxDTI4D) {
			dcmList[indx0].CSA.numDti = numDti;
			for (int i = 0; i < numDti; i++) //for each direction
				for (int v = 0; v < 4; v++) //for each vector+B-value
					dti4D->S[i].V[v] = vx[i].V[v];
		}
		free(vx);
		return volOrderIndex;
	}

#ifndef USING_DCM2NIIXFSWRAPPER
	char txtname[2048] = {""};
	strcpy(txtname, pathoutname);
	strcat(txtname, ".bval");
	//printMessage("Saving DTI %s\n",txtname);
	FILE *fp = fopen(txtname, "w");
	if (fp == NULL) {
		free(vx);
		return volOrderIndex;
	}
	for (int i = 0; i < (numDti - 1); i++) {
		if (opts.isCreateBIDS) {
			fprintf(fp, "%g ", vx[i].V[0]);
		} else {
			fprintf(fp, "%g\t", vx[i].V[0]);
		}
	}
	fprintf(fp, "%g\n", vx[numDti - 1].V[0]);
	fclose(fp);
#endif
	if (isIsotropic) { //issue 405: ISOTROPIC images have bval but not bvec
		free(vx);
		return volOrderIndex;
	}

#ifndef USING_DCM2NIIXFSWRAPPER
	strcpy(txtname, pathoutname);
	if (dcmList[indx0].isVectorFromBMatrix)
		strcat(txtname, ".mvec");
	else
		strcat(txtname, ".bvec");
	//printMessage("Saving DTI %s\n",txtname);
	fp = fopen(txtname, "w");
	if (fp == NULL) {
		free(vx);
		return volOrderIndex;
	}
	for (int v = 1; v < 4; v++) {
		for (int i = 0; i < (numDti - 1); i++) {
			if (opts.isCreateBIDS) {
				fprintf(fp, "%g ", vx[i].V[v]);
			} else {
				fprintf(fp, "%g\t", vx[i].V[v]);
			}
		}
		fprintf(fp, "%g\n", vx[numDti - 1].V[v]);
	}
	fclose(fp);
#endif
#endif

	free(vx);
	return volOrderIndex;
} // nii_saveDTI()

float sqr(float v) {
	return v * v;
} // sqr()

#ifdef newTilt //see issue 254
float vec3Length(vec3 v) { //normalize vector length
	return sqrt((v.v[0] * v.v[0]) + (v.v[1] * v.v[1]) + (v.v[2] * v.v[2]));
}

float vec3maxMag(vec3 v) { //return signed vector with maximum magnitude
	float mx = v.v[0];
	if (fabs(v.v[1]) > fabs(mx))
		mx = v.v[1];
	if (fabs(v.v[2]) > fabs(mx))
		mx = v.v[2];
	return mx;
}

vec3 makePositive(vec3 v) {
	//we do not no order of cross product or order of instance number (e.g. head->foot, foot->head)
	// this function matches the polarity of slice direction inferred from patient position and image orient
	vec3 ret = v;
	if (vec3maxMag(v) >= 0.0)
		return ret;
	ret.v[0] = -ret.v[0];
	ret.v[1] = -ret.v[1];
	ret.v[2] = -ret.v[2];
	return ret;
}

void vecRep(vec3 v) { //normalize vector length
	printMessage("[%g %g %g]\n", v.v[0], v.v[1], v.v[2]);
}

//Precise method for determining gantry tilt
// rationale:
// gantry tilt (0018,1120) is optional
// some tools may correct gantry tilt but not reset 0018,1120
// 0018,1120 might be saved at low precision (though patientPosition, orient might be as well)
//https://github.com/rordenlab/dcm2niix/issues/253
float computeGantryTiltPrecise(struct TDICOMdata d1, struct TDICOMdata d2, int isVerbose) {
	float ret = 0.0;
	if (isNanPosition(d1))
		return ret;
	vec3 slice_vector = setVec3(d2.patientPosition[1] - d1.patientPosition[1],
		d2.patientPosition[2] - d1.patientPosition[2],
		d2.patientPosition[3] - d1.patientPosition[3]);
	float len = vec3Length(slice_vector);
	if (isSameFloat(len, 0.0)) {
		slice_vector = setVec3(d1.patientPositionLast[1] - d1.patientPosition[1],
			d1.patientPositionLast[2] - d1.patientPosition[2],
			d1.patientPositionLast[3] - d1.patientPosition[3]);
		len = vec3Length(slice_vector);
		if (isSameFloat(len, 0.0))
			return ret;
	}
	if (isnan(slice_vector.v[0]))
		return ret;
	slice_vector = makePositive(slice_vector);
	vec3 read_vector = setVec3(d1.orient[1], d1.orient[2], d1.orient[3]);
	vec3 phase_vector = setVec3(d1.orient[4], d1.orient[5], d1.orient[6]);
	vec3 slice_vector90 = crossProduct(read_vector, phase_vector); //perpendicular
	slice_vector90 = makePositive(slice_vector90);
	float len90 = vec3Length(slice_vector90);
	if (isSameFloat(len90, 0.0))
		return ret;
	float dotX = dotProduct(slice_vector90, slice_vector);
	float cosX = dotX / (len * len90);
	float degX = acos(cosX) * (180.0 / M_PI); //arccos, radian -> degrees
	if (!isSameFloatGE(cosX, 1.0))
		ret = degX;
	if ((isSameFloat(ret, 0.0)) && (isSameFloat(ret, d1.gantryTilt)))
		return 0.0;
	//determine if gantry tilt is positive or negative
	vec3 signv = crossProduct(slice_vector, slice_vector90);
	float sign = vec3maxMag(signv);
	if (isSameFloatGE(ret, 0.0))
		return 0.0; //parallel vectors
	if (sign > 0.0)
		ret = -ret; //the length of len90 was negative, negative gantry tilt
					//while (ret >= 89.99) ret -= 90;
					//while (ret <= -89.99) ret += 90;
	if (isSameFloatGE(ret, 0.0))
		return 0.0;
	if ((isVerbose) || (isnan(ret))) {
		printMessage("Gantry Tilt Parameters (see issue 253)\n");
		printMessage(" Read =");
		vecRep(read_vector);
		printMessage(" Phase =");
		vecRep(phase_vector);
		printMessage(" CrossReadPhase =");
		vecRep(slice_vector90);
		printMessage(" Slice =");
		vecRep(slice_vector);
	}
	printMessage("Gantry Tilt based on 0018,1120 %g, estimated from slice vector %g\n", d1.gantryTilt, ret);
	return ret;
}
#endif //newTilt //see issue 254

float intersliceDistance(struct TDICOMdata d1, struct TDICOMdata d2) {
	//some MRI scans have gaps between slices, some CT have overlapping slices. Comparing adjacent slices provides measure for dx between slices
	if (isNanPosition(d1) || isNanPosition(d2))
		return d1.xyzMM[3];
	float tilt = 1.0;
	//printMessage("0020,0032 %g %g %g -> %g %g %g\n",d1.patientPosition[1],d1.patientPosition[2],d1.patientPosition[3],d2.patientPosition[1],d2.patientPosition[2],d2.patientPosition[3]);
	if (d1.gantryTilt != 0)
		tilt = (float)cos(d1.gantryTilt * M_PI / 180); //for CT scans with gantry tilt, we need to compute distance between slices, not distance along bed
	return tilt * sqrt(sqr(d1.patientPosition[1] - d2.patientPosition[1]) +
		sqr(d1.patientPosition[2] - d2.patientPosition[2]) +
		sqr(d1.patientPosition[3] - d2.patientPosition[3]));
} //intersliceDistance()

//#define myInstanceNumberOrderIsNotSpatial
//instance number is virtually always ordered based on spatial position.
// interleaved/multi-band conversion will be disrupted if instance number refers to temporal order
// these functions reorder images based on spatial position
// this situation is exceptionally rare, and there is a performance penalty
// further, there may be unintended consequences.
// Therefore, use of myInstanceNumberOrderIsNotSpatial is NOT recommended
// a better solution is to fix the sequences that generated those files
// as such images will probably disrupt most tools.
// This option is only to salvage borked data.
// This code has also not been tested on data stored in TXYZ rather than XYZT order
//#ifdef myInstanceNumberOrderIsNotSpatial

float intersliceDistanceSigned(struct TDICOMdata d1, struct TDICOMdata d2) {
// Compute the signed slice position on the through-slice axis
//  https://nipy.org/nibabel/dicom/dicom_orientation.html#working-out-the-z-coordinates-for-a-set-of-slices
//  https://itk.org/pipermail/insight-users/2003-September/004762.html
//reports distance between two slices, signed as 2nd slice can be in front or behind 1st
	vec3 slice_vector = setVec3(d2.patientPosition[1] - d1.patientPosition[1],
								d2.patientPosition[2] - d1.patientPosition[2],
								d2.patientPosition[3] - d1.patientPosition[3]);
	float len = vec3Length(slice_vector);
	if (isSameFloat(len, 0.0))
		return len;
	if (d1.gantryTilt != 0)
		len = len * cos(d1.gantryTilt * M_PI / 180);
	vec3 read_vector = setVec3(d1.orient[1], d1.orient[2], d1.orient[3]);
	vec3 phase_vector = setVec3(d1.orient[4], d1.orient[5], d1.orient[6]);
	vec3 slice_vector90 = crossProduct(read_vector, phase_vector); //perpendicular
	float dot = dotProduct(slice_vector90, slice_vector);
	if (dot < 0.0)
		return -len;
	return len;
}

//https://stackoverflow.com/questions/36714030/c-sort-float-array-while-keeping-track-of-indices/36714204
struct TFloatSort {
	float position;
	int volume, index;
};

int compareTFloatSort(const void *a, const void *b) {
	struct TFloatSort *a1 = (struct TFloatSort *)a;
	struct TFloatSort *a2 = (struct TFloatSort *)b;
	if ((*a1).volume > (*a2).volume)
		return 1;
	if ((*a1).volume < (*a2).volume)
		return -1;
	if ((*a1).position > (*a2).position)
		return 1;
	if ((*a1).position < (*a2).position)
		return -1;
	//if value is tied, retain index order (useful for TXYZ images?)
	if ((*a1).index > (*a2).index)
		return 1;
	if ((*a1).index < (*a2).index)
		return -1;
	return 0;
} // compareTFloatSort()


int isSameFloatT(float a, float b, float tolerance) {
	return (fabs(a - b) <= tolerance);
}

bool ensureSequentialSlicePositions(int d3, int d4, struct TDCMsort dcmSort[], struct TDICOMdata dcmList[], int verbose) {
	//ensure slice position is sequential: either ascending [1 2 3] or descending [3 2 1], not [1 3 2], [3 1 2] etc.
	//n.b. as currently designed, this will force swapDim3Dim4() for 4D data
	int nConvert = d3 * d4;
	if (d3 < 3)
		return true; //always consistent
	//first pass: check order: issue 622
	int i = 0;
	bool isSequential = true;
	for (int t = 0; t < d4; t++) { //for each volume
		float dx = intersliceDistanceSigned(dcmList[dcmSort[i].indx], dcmList[dcmSort[i + 1].indx]);
		for (int z = 0; z < d3; z++) { //for slice
			if (z > 0) {
				float dx2 = intersliceDistanceSigned(dcmList[dcmSort[i - 1].indx], dcmList[dcmSort[i].indx]);
				if (!isSameFloatT(dx, dx2, kSliceTolerance))
					isSequential = false;
			} //if not 1st slice (which does not have prior slice)
			i++;
		} //for each slice
	} //for each volume
	if (isSequential)
		return true;
	//second pass: fix if required
	printWarning("Instance Number (0020,0013) order is not spatial.\n");
	TFloatSort *floatSort = (TFloatSort *)malloc(nConvert * sizeof(TFloatSort));
	int minVol = dcmList[dcmSort[0].indx].rawDataRunNumber;
	int maxVol = minVol;
	int maxVolNotADC = -1;
	int minInstance = dcmList[dcmSort[0].indx].imageNum;
	int maxInstance = minInstance;
	int maxPhase = 1; //Philips Multi-Phase
	for (int i = 0; i < nConvert; i++) {
		int vol = dcmList[dcmSort[i].indx].rawDataRunNumber;
		minVol = min(minVol, vol);
		maxVol = max(maxVol, vol);
		if (vol < kMaxDTI4D)
			maxVolNotADC = max(maxVolNotADC, vol);
		int instance = dcmList[dcmSort[i].indx].imageNum;
		minInstance = min(minInstance, instance);
		maxInstance = max(maxInstance, instance);
		maxPhase = max(maxPhase, dcmList[dcmSort[i].indx].phaseNumber);
	}
	bool isUseFrameReferenceTimeForVolume = false;
	if (dcmList[dcmSort[0].indx].frameReferenceTime >= 0.0)
		isUseFrameReferenceTimeForVolume = true;
	bool isUseInstanceNumberForVolume = false;
	if ((!isUseFrameReferenceTimeForVolume) && (d4 > 1) && (maxPhase == 1) && (minVol == maxVolNotADC) && (minInstance < maxInstance)) {
		printWarning("Volume number does not vary (0019,10A2; 0020,0100; 2005,1063; 2005,1413), assuming meaningful instance number (0020,0013).\n");
		isUseInstanceNumberForVolume = true;
	}
	bool isVerbose = (verbose > 1); //issue533
	if (isVerbose)
		printMessage("Ranges volume %d..%d instance %d..%d\n", minVol, maxVolNotADC, minInstance, maxInstance); //TODO
	bool isASL = (dcmList[dcmSort[0].indx].aslFlags != kASL_FLAG_NONE);
	//we will renumber volumes for Philips ASL (Contrast/Label, phase) and DWI (derived trace)
	int minVolOut = kMaxDTI4D + 1;
	int maxVolOut = -1;
	bool isUsePhaseForVol = false;
	if ((!isASL) && (minVol == maxVol) && (maxPhase > 1)) isUsePhaseForVol = true;//e.g. TurboQUASAR
	bool isPhaseIsBValNumber =false;
	if ((!isASL) && (minVol < maxVol) && (maxPhase > 1)) isPhaseIsBValNumber = true;//DWI track both gradient number and vector number issue 546
	if (isVerbose)
		printMessage("InstanceNumber\tPosition\tVolume\tRepeat\tASLlabel\tPhase\tTriggerTime\n");
	for (int i = 0; i < nConvert; i++) {
		int vol = dcmList[dcmSort[i].indx].rawDataRunNumber;
		int rawvol = vol;
		int instance = dcmList[dcmSort[i].indx].imageNum;
		int phase = max(1, dcmList[dcmSort[i].indx].phaseNumber);
		int refTime = (int)dcmList[dcmSort[i].indx].frameReferenceTime; //issue577: refTime in ms, so int conversion sufficient
		if (isUsePhaseForVol) vol = phase;
		if (isPhaseIsBValNumber) vol += phase * maxVol;
		int isAslLabel = dcmList[dcmSort[i].indx].aslFlags == kASL_FLAG_PHILIPS_LABEL;
		float dx = intersliceDistanceSigned(dcmList[dcmSort[0].indx], dcmList[dcmSort[i].indx]);
		if (isASL) {
			#ifdef myMatchEnhanced00209157 //issue533: make classic DICOMs match enhanced DICOM volume order
				//disk order: slice < repeat < phase < label/control
				vol += (phase - 1) * maxVol;
				if (isAslLabel)
					vol += maxPhase * maxVol;
			#else
				//"temporal" disk order: slice < phase < label/control < repeat : should match instance number
				vol = phase;
				if (isAslLabel)
					vol += maxPhase;
				vol += (rawvol - 1) * (2 * maxPhase);
			#endif
		}
		if (isUseInstanceNumberForVolume)
			vol = instance;
		if (isVerbose) //only report slice data for logorrheic verbosity
			printMessage("%d\t%g\t%d\t%d\t%d\t%d\t%g\n", instance, dx, vol, rawvol, isAslLabel, phase, dcmList[dcmSort[i].indx].triggerDelayTime);
		if (vol > kMaxDTI4D) //issue529 Philips derived Trace/ADC embedded into DWI
			vol = maxVol + 1;
		if (isUseFrameReferenceTimeForVolume)
			vol = refTime;
		minVolOut = min(minVolOut, vol);
		maxVolOut = max(maxVolOut, vol);
		floatSort[i].volume = vol;
		floatSort[i].position = dx;
		floatSort[i].index = i;
	}
	//n.b. should we change dim[3] and dim[4] if number of volumes = dim[3]?
	if (isUseFrameReferenceTimeForVolume)
		printWarning("Reordering volumes based on FrameReferenceTime (0054,1300; issue 577)\n");
	else if ((!isPhaseIsBValNumber) && ((maxVolOut-minVolOut+1) != d4))
		printError("Check sorted order: 4D dataset has %d volumes, but volume index ranges from %d..%d\n", d4, minVolOut, maxVolOut);
	TDCMsort *dcmSortIn = (TDCMsort *)malloc(nConvert * sizeof(TDCMsort));
	for (int i = 0; i < nConvert; i++)
		dcmSortIn[i] = dcmSort[i];
	qsort(floatSort, nConvert, sizeof(struct TFloatSort), compareTFloatSort); //sort based on series and image numbers....
	for (int i = 0; i < nConvert; i++)
		dcmSort[i] = dcmSortIn[floatSort[i].index];
	free(floatSort);
	free(dcmSortIn);
	return false;
} // ensureSequentialSlicePositions()

void swapDim3Dim4(int d3, int d4, struct TDCMsort dcmSort[]) {
	//swap space and time: input A0,A1...An,B0,B1...Bn output A0,B0,A1,B1,...
	int nConvert = d3 * d4;
	TDCMsort *dcmSortIn = (TDCMsort *)malloc(nConvert * sizeof(TDCMsort));
	for (int i = 0; i < nConvert; i++)
		dcmSortIn[i] = dcmSort[i];
	int i = 0;
	for (int b = 0; b < d3; b++)
		for (int a = 0; a < d4; a++) {
			int k = (a * d3) + b;
			//printMessage("%d -> %d %d ->%d\n",i,a, b, k);
			dcmSort[k] = dcmSortIn[i];
			i++;
		}
	free(dcmSortIn);
} //swapDim3Dim4()

bool intensityScaleVaries(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata dcmList[]) {
	//detect whether some DICOM images report different intensity scaling
	//some Siemens PET scanners generate 16-bit images where slice has its own scaling factor.
	// since NIfTI provides a single scaling factor for each file, these images require special consideration
	if (nConvert < 2)
		return false;
	int dt = dcmList[dcmSort[0].indx].bitsAllocated;
	float iScale = dcmList[dcmSort[0].indx].intenScale;
	float iInter = dcmList[dcmSort[0].indx].intenIntercept;
	for (int i = 1; i < nConvert; i++) { //stack additional images
		uint64_t indx = dcmSort[i].indx;
		if (dcmList[indx].bitsAllocated != dt)
			return true;
		if (fabs(dcmList[indx].intenScale - iScale) > FLT_EPSILON)
			return true;
		if (fabs(dcmList[indx].intenIntercept - iInter) > FLT_EPSILON)
			return true;
	}
	return false;
} //intensityScaleVaries()

/*unsigned char * nii_bgr2rgb(unsigned char* bImg, struct nifti_1_header *hdr) {
 //DICOM planarappears to be BBB..B,GGG..G,RRR..R, NIfTI RGB saved in planes RRR..RGGG..GBBBB..B
 // see http://www.barre.nom.fr/medical/samples/index.html US-RGB-8-epicard
 if (hdr->datatype != DT_RGB24) return bImg;
 int dim3to7 = 1;
 for (int i = 3; i < 8; i++)
 if (hdr->dim[i] > 1) dim3to7 = dim3to7 * hdr->dim[i];
 int sliceBytes24 = hdr->dim[1]*hdr->dim[2] * hdr->bitpix/8;
 int sliceBytes8 = hdr->dim[1]*hdr->dim[2];
 //Byte bImg[ bSz ];
 //[img getBytes:&bImg length:bSz];
 unsigned char slice24[sliceBytes24];
 int sliceOffsetR = 0;
 for (int sl = 0; sl < dim3to7; sl++) { //for each 2D slice
 memcpy(&slice24, &bImg[sliceOffsetR], sliceBytes24);
 memcpy( &bImg[sliceOffsetR], &slice24[sliceBytes8*2], sliceBytes8);
 sliceOffsetR += sliceBytes8;
 memcpy( &bImg[sliceOffsetR], &slice24[sliceBytes8], sliceBytes8);
 sliceOffsetR += sliceBytes8;
 memcpy( &bImg[sliceOffsetR], &slice24[0], sliceBytes8);
 sliceOffsetR += sliceBytes8;
 } //for each slice
 return bImg;
 } */

void niiDeleteFnm(const char *outname, const char *ext) {
	char niiname[2048] = {""};
	strcat(niiname, outname);
	strcat(niiname, ext);
	if (is_fileexists(niiname))
		remove(niiname);
}

void niiDelete(const char *niiname) {
	//for niiname "~/d/img" delete img.nii, img.bvec, img.bval, img.json
	niiDeleteFnm(niiname, ".nii");
	niiDeleteFnm(niiname, ".nii.gz");
	niiDeleteFnm(niiname, ".nrrd");
	niiDeleteFnm(niiname, ".nhdr");
	niiDeleteFnm(niiname, ".raw.gz");
	niiDeleteFnm(niiname, ".json");
	niiDeleteFnm(niiname, ".bval");
	niiDeleteFnm(niiname, ".bvec");
}

bool niiExists(const char *pathoutname) {
	char niiname[2048] = {""};
	strcat(niiname, pathoutname);
	strcat(niiname, ".nii");
	if (is_fileexists(niiname))
		return true;
	char gzname[2048] = {""};
	strcat(gzname, pathoutname);
	strcat(gzname, ".nii.gz");
	if (is_fileexists(gzname))
		return true;
	strcpy(niiname, pathoutname);
	strcat(niiname, ".nrrd");
	if (is_fileexists(niiname))
		return true;
	strcpy(niiname, pathoutname);
	strcat(niiname, ".nhdr");
	if (is_fileexists(niiname))
		return true;
	return false;
} //niiExists()

#ifndef W_OK
#define W_OK 2 /* write mode check */
#endif

int strcicmp(char const *a, char const *b) //case insensitive compare
{
	for (;; a++, b++) {
		int d = tolower(*a) - tolower(*b);
		if (d != 0 || !*a)
			return d;
	}
} // strcicmp()

bool isExt(char *file_name, const char *ext) {
	char *p_extension;
	if ((p_extension = strrchr(file_name, '.')) != NULL)
		if (strcicmp(p_extension, ext) == 0)
			return true;
	//if(strcmp(p_extension,ext) == 0) return true;
	return false;
} // isExt()

void cleanISO8859(char *cString) {
	int len = strlen(cString);
	if (len < 1)
		return;
	for (int i = 0; i < len; i++)
		//assume specificCharacterSet (0008,0005) is ISO_IR 100 http://en.wikipedia.org/wiki/ISO/IEC_8859-1
		if (cString[i] < 1) {
			unsigned char c = (unsigned char)cString[i];
			if ((c >= 192) && (c <= 198))
				cString[i] = 'A';
			if (c == 199)
				cString[i] = 'C';
			if ((c >= 200) && (c <= 203))
				cString[i] = 'E';
			if ((c >= 204) && (c <= 207))
				cString[i] = 'I';
			if (c == 208)
				cString[i] = 'D';
			if (c == 209)
				cString[i] = 'N';
			if ((c >= 210) && (c <= 214))
				cString[i] = 'O';
			if (c == 215)
				cString[i] = 'x';
			if (c == 216)
				cString[i] = 'O';
			if ((c >= 217) && (c <= 220))
				cString[i] = 'O';
			if (c == 221)
				cString[i] = 'Y';
			if ((c >= 224) && (c <= 230))
				cString[i] = 'a';
			if (c == 231)
				cString[i] = 'c';
			if ((c >= 232) && (c <= 235))
				cString[i] = 'e';
			if ((c >= 236) && (c <= 239))
				cString[i] = 'i';
			if (c == 240)
				cString[i] = 'o';
			if (c == 241)
				cString[i] = 'n';
			if ((c >= 242) && (c <= 246))
				cString[i] = 'o';
			if (c == 248)
				cString[i] = 'o';
			if ((c >= 249) && (c <= 252))
				cString[i] = 'u';
			if (c == 253)
				cString[i] = 'y';
			if (c == 255)
				cString[i] = 'y';
		}
}

void createDummyBidsBoilerplate(char *pth, bool isFunc) {
	//https://remi-gau.github.io/bids_cookbook/#starters
	char pathSep[2] = {"a"};
	pathSep[0] = kPathSeparator;
	char descfnm[PATH_MAX] = {""};
	char taskfnm[PATH_MAX] = {""};
	char fnm[PATH_MAX] = {""};
	strcat(fnm, pth);
	strcat(fnm, pathSep);
	strcat(taskfnm, fnm);
	strcat(descfnm, fnm);
	snprintf(fnm + strlen(fnm), PATH_MAX - strlen(fnm), "%s", "README.md");
	if (!is_fileexists(fnm)) {
		FILE *fp = fopen(fnm, "w");
		static const char readmePre[] = "Generated using dcm2niix (";
		static const char readmePost[] = ")\n\nDescribe your dataset here. This file was generated by dcm2niix in a single pass. Details like IntendedFor, Subject ID, Session and tasks are not defined.";

		if (fp != NULL)
			fprintf(fp, readmePre);
			fprintf(fp, kDCMdate);
			fprintf(fp, readmePost);
		fclose(fp);
	}
	snprintf(descfnm + strlen(descfnm), PATH_MAX - strlen(descfnm), "%s", "dataset_description.json");
	if (!is_fileexists(descfnm)) {
		FILE *fp = fopen(descfnm, "w");
		static const char readme[] = "{\n    \"Name\": \"dcm2niix dummy dataset\",\n    \"Authors\": [\"Chris Rorden\", \"Alex Teghipco\"],\n    \"BIDSVersion\": \"1.6.0\"\n}\n";
		if (fp != NULL)
			fprintf(fp, readme);
		fclose(fp);
	}
	if (!isFunc)
		return; //only functional data gets a task file
	snprintf(taskfnm + strlen(taskfnm), PATH_MAX - strlen(taskfnm), "%s", "task-rest_bold.json");
	if (!is_fileexists(taskfnm)) {
		FILE *fp = fopen(taskfnm, "w");
		static const char taskRest[] = "{\n\"TaskName\": \"rest\",\n\"CogAtlasID\": \"https://www.cognitiveatlas.org/task/id/trm_4c8a834779883/\"\n}\n";
		if (fp != NULL)
			fprintf(fp, taskRest);
		fclose(fp);
	}

}

int nii_createFilename(struct TDICOMdata dcm, char *niiFilename, struct TDCMopts opts) {
	char pth[PATH_MAX] = {""};
	if (strlen(opts.outdir) > 0) {
		strcpy(pth, opts.outdir);
		int w = access(pth, W_OK);
		if (w != 0) {
			//should never happen except with "-b i": see kEXIT_OUTPUT_FOLDER_READ_ONLY for early termination
			// with "-b i" the code below generates a warning but no files are created
			if (getcwd(pth, sizeof(pth)) != NULL) {
#ifdef USE_CWD_IF_OUTDIR_NO_WRITE //optional: fall back to current working directory
				w = access(pth, W_OK);
				if (w != 0) {
					printError("You do not have write permissions for the directory %s\n", opts.outdir);
					return EXIT_FAILURE;
				}
				printWarning("%s write permission denied. Saving to working directory %s \n", opts.outdir, pth);
#else
				printError("You do not have write permissions for the directory %s\n", opts.outdir);
				return EXIT_FAILURE;
#endif
			}
		}
	}
	char inname[PATH_MAX] = {""}; //{"test%t_%av"}; //% a = acquisition, %n patient name, %t time
	strcpy(inname, opts.filename);
	bool isDcmExt = isExt(inname, ".dcm"); // "%r.dcm" with multi-echo should generate "1.dcm", "1e2.dcm"
	if (isDcmExt) {
		inname[strlen(inname) - 4] = '\0';
	}
	char outname[PATH_MAX] = {""};
	char newstr[PATH_MAX];
	if (strlen(inname) < 1) {
		strcpy(inname, "T%t_N%n_S%s");
	}
	const char kTempPathSeparator = '\a';
	char pathSep[2] = {"a"};
	pathSep[0] = kTempPathSeparator;
	for (size_t pos = 0; pos < strlen(inname); pos++)
		if ((inname[pos] == '\\') || (inname[pos] == '/'))
			inname[pos] = kTempPathSeparator;

	size_t start = 0;
	size_t pos = 0;
	bool isAddNamePostFixes = opts.isAddNamePostFixes;
	bool isCoilReported = false;
	bool isEchoReported = false;
	bool isSeriesReported = false;
	//bool isAcquisitionReported = false;
	bool isImageNumReported = false;
	while (pos < strlen(inname)) {
		if (inname[pos] == '%') {
			if (pos > start) {
				strncpy(&newstr[0], &inname[0] + start, pos - start);
				newstr[pos - start] = '\0';
				strcat(outname, newstr);
			}
			pos++; //extra increment: skip both % and following character
			char f = 'P';
			if (pos < strlen(inname))
				f = toupper(inname[pos]);
			if (f == 'A') {
				isCoilReported = true;
				strcat(outname, dcm.coilName);
			}
			if (f == 'B')
				strcat(outname, dcm.imageBaseName);
			if (f == 'C')
				strcat(outname, dcm.imageComments);
			if (f == 'D')
				strcat(outname, dcm.seriesDescription);
			if (f == 'E') {
				isEchoReported = true;
				snprintf(newstr, PATH_MAX, "%d", dcm.echoNum);
				strcat(outname, newstr);
			}
			if (f == 'F')
				strcat(outname, opts.indirParent);
			if (f == 'G')
				strcat(outname, dcm.accessionNumber);
			if (f == 'H') {
				printWarning("hazardous (%%h) bids naming experimental\n");
				char bidsSubject[kOptsStr] = "sub-";
				if (strlen(opts.bidsSubject) <= 0)
					strcat(bidsSubject, "1");
				else
					strcat(bidsSubject, opts.bidsSubject);
				char bidsSession[kOptsStr] = "ses-";
				if (strlen(opts.bidsSession) <= 0)
					strcat(bidsSession, "1");
				else
					strcat(bidsSession, opts.bidsSession);
				createDummyBidsBoilerplate(pth, (strstr(dcm.CSA.bidsDataType, "func") != NULL));
				if (strlen(dcm.CSA.bidsDataType) < 1) {
					strcat(outname, "Unknown");
					snprintf(newstr, PATH_MAX, "%c", kTempPathSeparator);
					strcat(outname, newstr);
					snprintf(newstr, PATH_MAX, "%ld", dcm.seriesNum);
					strcat(outname, newstr);
					strcat(outname, "_");
					strcat(outname, dcm.protocolName);
					
				} else {
					isAddNamePostFixes = false;
					strcat(outname, bidsSubject);
					strcat(outname, pathSep);
					strcat(outname, bidsSession);
					strcat(outname, pathSep);
					strcat(outname, dcm.CSA.bidsDataType);
					strcat(outname, pathSep);
					strcat(outname, bidsSubject);
					strcat(outname, "_");
					strcat(outname, bidsSession);
					if (strstr(dcm.CSA.bidsDataType, "func") != NULL) {
						strcat(outname, "_task-");
						if (strlen(dcm.CSA.bidsTask) > 0)
							strcat(outname, dcm.CSA.bidsTask);
						else
							strcat(outname, "rest");
					}
					strcat(outname, dcm.CSA.bidsEntitySuffix);
				}
			}
			if (f == 'I')
				strcat(outname, dcm.patientID);
			if (f == 'J')
				strcat(outname, dcm.seriesInstanceUID);
			if (f == 'K')
				strcat(outname, dcm.studyInstanceUID);
			if (f == 'L') //"L"ocal Institution-generated description or classification of the Procedure Step that was performed.
				strcat(outname, dcm.procedureStepDescription);
			if (f == 'M') {
				if (dcm.manufacturer == kMANUFACTURER_BRUKER)
					strcat(outname, "Br");
				else if (dcm.manufacturer == kMANUFACTURER_GE)
					strcat(outname, "GE");
				else if (dcm.manufacturer == kMANUFACTURER_TOSHIBA)
					strcat(outname, "To");
				else if (dcm.manufacturer == kMANUFACTURER_CANON)
					strcat(outname, "Ca");
				else if (dcm.manufacturer == kMANUFACTURER_UIH)
					strcat(outname, "UI");
				else if (dcm.manufacturer == kMANUFACTURER_PHILIPS)
					strcat(outname, "Ph");
				else if (dcm.manufacturer == kMANUFACTURER_SIEMENS)
					strcat(outname, "Si");
				else if (dcm.manufacturer == kMANUFACTURER_MEDISO)
					strcat(outname, "Me");
				else if (dcm.manufacturer == kMANUFACTURER_MRSOLUTIONS)
					strcat(outname, "MR");
				else if (dcm.manufacturer == kMANUFACTURER_HYPERFINE)
					strcat(outname, "Hy");
				else
					strcat(outname, "NA"); //manufacturer name not available
			}
			if (f == 'N')
				strcat(outname, dcm.patientName);
			if (f == 'O') {
				strcat(outname, dcm.instanceUID);
				if (strlen(dcm.instanceUID) > 0)
					isAddNamePostFixes = false; //should be unique, so no need to post-fix
			}
			if (f == 'P') {
				strcat(outname, dcm.protocolName);
				if (strlen(dcm.protocolName) < 1)
					printWarning("Unable to append protocol name (0018,1030) to filename (it is empty).\n");
			}
			if (f == 'R') {
				snprintf(newstr, PATH_MAX, "%d", dcm.imageNum);
				strcat(outname, newstr);
				isImageNumReported = true;
			}
			if (f == 'Q')
				strcat(outname, dcm.scanningSequence);
			if (f == 'S') {
				snprintf(newstr, PATH_MAX, "%ld", dcm.seriesNum);
				strcat(outname, newstr);
				isSeriesReported = true;
			}
			if (f == 'T') {
				snprintf(newstr, PATH_MAX, "%0.0f", dcm.dateTime);
				strcat(outname, newstr);
			}
			if (f == 'U') {
				if (opts.isRenameNotConvert) {
					snprintf(newstr, PATH_MAX, "%d", dcm.acquNum);
					strcat(outname, newstr);
					//isAcquisitionReported = true;
				} else {
					snprintf(newstr, PATH_MAX, "%d", dcm.acquNum);
					strcat(outname, newstr);
#ifdef mySegmentByAcq
	//isAcquisitionReported = true;
#else
					printWarning("'%%u' in output filename can be misleading (issue 526)\n");
#endif
				}
			}
			if (f == 'V') {
				if (dcm.manufacturer == kMANUFACTURER_BRUKER)
					strcat(outname, "Bruker");
				else if (dcm.manufacturer == kMANUFACTURER_CANON)
					strcat(outname, "Canon");
				else if (dcm.manufacturer == kMANUFACTURER_GE)
					strcat(outname, "GE");
				else if (dcm.manufacturer == kMANUFACTURER_HYPERFINE)
					strcat(outname, "Hyperfine");
				else if (dcm.manufacturer == kMANUFACTURER_MEDISO)
					strcat(outname, "Mediso");
				else if (dcm.manufacturer == kMANUFACTURER_MRSOLUTIONS)
					strcat(outname, "MRsolutions");
				else if (dcm.manufacturer == kMANUFACTURER_PHILIPS)
					strcat(outname, "Philips");
				else if (dcm.manufacturer == kMANUFACTURER_SIEMENS)
					strcat(outname, "Siemens");
				else if (dcm.manufacturer == kMANUFACTURER_TOSHIBA)
					strcat(outname, "Toshiba");
				else if (dcm.manufacturer == kMANUFACTURER_UIH)
					strcat(outname, "UIH");
				else
					strcat(outname, "NA");
			}
			if (f == 'W') {//Weird includes personal data in filename patientWeight
				snprintf(newstr, PATH_MAX, "dob%sg%cwt%d", dcm.patientBirthDate, dcm.patientSex, (int)round(dcm.patientWeight));
				if (strstr(dcm.institutionName, "Richland"))
					strcat(newstr, "R");
				strcat(outname, newstr);
			}
			if ((f == 'Y') && (dcm.rawDataRunNumber >= 0)) {
				snprintf(newstr, PATH_MAX, "%d", dcm.rawDataRunNumber); //GE (0019,10A2) else (0020,0100)
				strcat(outname, newstr);
			}
			if (f == 'X')
				strcat(outname, dcm.studyID);
			if ((f == 'Y') && (dcm.rawDataRunNumber >= 0)) {
				snprintf(newstr, PATH_MAX, "%d", dcm.rawDataRunNumber); //GE (0019,10A2) else (0020,0100)
				strcat(outname, newstr);
			}
			if (f == 'Z')
				strcat(outname, dcm.sequenceName);
			if ((f >= '0') && (f <= '9')) {
				if ((pos < strlen(inname)) && (toupper(inname[pos + 1]) == 'S')) {
					char zeroPad[128] = {""};
					snprintf(zeroPad, 128, "%%0%dd", f - '0');
					snprintf(newstr, PATH_MAX, zeroPad, dcm.seriesNum);
					strcat(outname, newstr);
					pos++; // e.g. %3f requires extra increment: skip both number and following character
				}
				if ((pos < strlen(inname)) && (toupper(inname[pos + 1]) == 'R')) {
					char zeroPad[128] = {""};
					snprintf(zeroPad, 128, "%%0%dd", f - '0');
					snprintf(newstr, PATH_MAX, zeroPad, dcm.imageNum);
					isImageNumReported = true;
					strcat(outname, newstr);
					pos++; // e.g. %3f requires extra increment: skip both number and following character
				}
				if ((pos < strlen(inname)) && (toupper(inname[pos + 1]) == 'Y') && (dcm.rawDataRunNumber >= 0)) {
					char zeroPad[128] = {""};
					snprintf(zeroPad, 128, "%%0%dd", f - '0');
					snprintf(newstr, PATH_MAX, zeroPad, dcm.rawDataRunNumber); //GE (0019,10A2) else (0020,0100)
					strcat(outname, newstr);
					pos++; // e.g. %3f requires extra increment: skip both number and following character
				}
			}
			start = pos + 1;
		} //found a % character
		pos++;
	} //for each character in input
	if (pos > start) { //append any trailing characters
		strncpy(&newstr[0], &inname[0] + start, pos - start);
		newstr[pos - start] = '\0';
		strcat(outname, newstr);
	}
	if ((isAddNamePostFixes) && (!isCoilReported) && (dcm.isCoilVaries)) {
		//snprintf(newstr, PATH_MAX, "_c%d", dcm.coilNum);
		//strcat (outname,newstr);
		strcat(outname, "_c");
		strcat(outname, dcm.coilName);
#ifdef USING_DCM2NIIXFSWRAPPER
		sprintf(mrifsStruct.namePostFixes, "%s_c%s", mrifsStruct.namePostFixes, dcm.coilName);
#endif
	}
	if ((isAddNamePostFixes) && (dcm.numberOfTR > 1) && (dcm.TR > 0)) {
		snprintf(newstr, PATH_MAX, "_r%g", dcm.TR);
		strcat(outname, newstr);
	}
// myMultiEchoFilenameSkipEcho1 https://github.com/rordenlab/dcm2niix/issues/237
#ifdef myMultiEchoFilenameSkipEcho1
	if ((isAddNamePostFixes) && (!isEchoReported) && (dcm.isMultiEcho)) { //multiple echoes saved as same series
#else
	if ((isAddNamePostFixes) && (!isEchoReported) && ((dcm.isMultiEcho) || (dcm.echoNum > 1))) { //multiple echoes saved as same series
#endif
		if ((dcm.echoNum < 1) && (dcm.TE > 0))
			snprintf(newstr, PATH_MAX, "_e%g", dcm.TE); //issue568: Siemens XA20 might omit echo number
		else
			snprintf(newstr, PATH_MAX, "_e%d", dcm.echoNum);
		strcat(outname, newstr);
		isEchoReported = true;
#ifdef USING_DCM2NIIXFSWRAPPER
		sprintf(mrifsStruct.namePostFixes, "%s%s", mrifsStruct.namePostFixes, newstr);
#endif
	}
	if ((isAddNamePostFixes) && (!isSeriesReported) && (!isEchoReported) && (dcm.echoNum > 1)) { //last resort: user provided no method to disambiguate echo number in filename
		snprintf(newstr, PATH_MAX, "_e%d", dcm.echoNum);
		strcat(outname, newstr);
		isEchoReported = true;
#ifdef USING_DCM2NIIXFSWRAPPER
		sprintf(mrifsStruct.namePostFixes, "%s%s", mrifsStruct.namePostFixes, newstr);
#endif
	}
	if ((dcm.isNonParallelSlices) && (!isImageNumReported)) {
		snprintf(newstr, PATH_MAX, "_i%05d", dcm.imageNum);
		strcat(outname, newstr);
#ifdef USING_DCM2NIIXFSWRAPPER
		sprintf(mrifsStruct.namePostFixes, "%s%s", mrifsStruct.namePostFixes, newstr);
#endif
	}
	/*if (dcm.maxGradDynVol > 0) { //Philips segmented
	snprintf(newstr, PATH_MAX, "_v%04d", dcm.gradDynVol+1); //+1 as indexed from zero
	strcat (outname,newstr);
	}*/
	if ((isAddNamePostFixes) && (dcm.isHasImaginary)) {
		strcat(outname, "_imaginary"); //has phase map
#ifdef USING_DCM2NIIXFSWRAPPER
		sprintf(mrifsStruct.namePostFixes, "%s_imaginary", mrifsStruct.namePostFixes);
#endif
	}
	if ((isAddNamePostFixes) && (dcm.isHasReal) && (dcm.isRealIsPhaseMapHz)) {
		strcat(outname, "_fieldmaphz"); //has field map
#ifdef USING_DCM2NIIXFSWRAPPER
		sprintf(mrifsStruct.namePostFixes, "%s_fieldmaphz", mrifsStruct.namePostFixes);
#endif
	}
	if ((isAddNamePostFixes) && (dcm.isHasReal) && (!dcm.isRealIsPhaseMapHz)) {
		strcat(outname, "_real"); //has phase map
#ifdef USING_DCM2NIIXFSWRAPPER
		sprintf(mrifsStruct.namePostFixes, "%s_real", mrifsStruct.namePostFixes);
#endif
	}
	if ((isAddNamePostFixes) && (dcm.isHasPhase)) {
		strcat(outname, "_ph"); //has phase map
		if (dcm.isHasMagnitude)
			strcat(outname, "Mag"); //Philips enhanced with BOTH phase and Magnitude in single file
#ifdef USING_DCM2NIIXFSWRAPPER
		sprintf(mrifsStruct.namePostFixes, "%s_ph", mrifsStruct.namePostFixes);
#endif
	}
	if ((isAddNamePostFixes) && (dcm.aslFlags == kASL_FLAG_NONE) && (dcm.triggerDelayTime >= 1) && (dcm.manufacturer != kMANUFACTURER_GE)) { //issue 336 GE uses this for slice timing
		snprintf(newstr, PATH_MAX, "_t%d", (int)roundf(dcm.triggerDelayTime));
		strcat(outname, newstr);
#ifdef USING_DCM2NIIXFSWRAPPER
		sprintf(mrifsStruct.namePostFixes, "%s%s", mrifsStruct.namePostFixes, newstr);
#endif
	}
	//could add (isAddNamePostFixes) to these next two, but consequences could be catastrophic
	if (dcm.isRawDataStorage) //avoid name clash for Philips XX_ files
		strcat(outname, "_Raw");
	if (dcm.isGrayscaleSoftcopyPresentationState) //avoid name clash for Philips PS_ files
		strcat(outname, "_PS");
	if (isDcmExt)
		strcat(outname, ".dcm");
	if (strlen(outname) < 1)
		strcpy(outname, "dcm2nii_invalidName");
	if (outname[0] == '.')
		outname[0] = '_'; //make sure not a hidden file
//eliminate illegal characters http://msdn.microsoft.com/en-us/library/windows/desktop/aa365247(v=vs.85).aspx
// https://github.com/rordenlab/dcm2niix/issues/237
#ifdef myOsSpecificFilenameMask
#define kMASK_WINDOWS_SPECIAL_CHARACTERS 0
#else
#define kMASK_WINDOWS_SPECIAL_CHARACTERS 1
#endif
#if defined(_WIN64) || defined(_WIN32) || defined(kMASK_WINDOWS_SPECIAL_CHARACTERS) //https://stackoverflow.com/questions/1976007/what-characters-are-forbidden-in-windows-and-linux-directory-names
	for (size_t pos = 0; pos < strlen(outname); pos++)
		if ((outname[pos] == '\\') || (outname[pos] == '/') || (outname[pos] == ' ') || (outname[pos] == '<') || (outname[pos] == '>') || (outname[pos] == ':') || (outname[pos] == ';') || (outname[pos] == '"') // || (outname[pos] == '/') || (outname[pos] == '\\')
			//|| (outname[pos] == '^') issue398
			|| (outname[pos] == '$') //issue749
			|| (outname[pos] == '*') || (outname[pos] == '|') || (outname[pos] == '?'))
			outname[pos] = '_';
#else
	for (size_t pos = 0; pos < strlen(outname); pos++)
		if (outname[pos] == ':') //not allowed by MacOS
			outname[pos] = '_';
#endif
#if !defined(_WIN64) || !defined(_WIN32)
	for (size_t pos = 0; pos < strlen(outname); pos++)
		if (outname[pos] == '`' || outname[pos] == '$') // unix shell expansion characters
			outname[pos] = '_';
#endif
	cleanISO8859(outname);
	//re-insert explicit path separators: -f %t/%s_%p will have folder for time, but will not segment a protocol named "fMRI\bold"
	for (int pos = 0; pos < (int)strlen(outname); pos++) {
		if (outname[pos] == kTempPathSeparator)
			outname[pos] = kPathSeparator; //e.g. for Windows, convert "/" to "\"
		if (outname[pos] < 32) //https://en.wikipedia.org/wiki/ASCII#Control_characters
			outname[pos] = '_';
	}
	char baseoutname[2048] = {""};
	strcat(baseoutname, pth);
	char appendChar[2] = {"a"};
	appendChar[0] = kPathSeparator;
	if ((strlen(pth) > 0) && (pth[strlen(pth) - 1] != kPathSeparator) && (outname[0] != kPathSeparator))
		strcat(baseoutname, appendChar);
	//remove redundant underscores
	int len = strlen(outname);
	int outpos = 0;
	for (int inpos = 0; inpos < len; inpos++) {
		if ((outpos > 0) && (outname[inpos] == '_') && (outname[outpos - 1] == '_'))
			continue;
		outname[outpos] = outname[inpos];
		outpos++;
	}
	outname[outpos] = 0;
	//Allow user to specify new folders, e.g. "-f dir/%p" or "-f %s/%p/%m"
	// These folders are created if they do not exist
	char *sep = strchr(outname, kPathSeparator);
#if defined(USING_R) && (defined(_WIN64) || defined(_WIN32))
	// R also uses forward slash on Windows, so allow it here
	if (!sep)
		sep = strchr(outname, '/');
#endif
	if (sep) {
		char newdir[2048] = {""};
		strcat(newdir, baseoutname);
		//struct stat st = {0};
		for (size_t pos = 0; pos < strlen(outname); pos++) {
			if (outname[pos] == kPathSeparator) {
				//if (stat(newdir, &st) == -1)
				if (!is_dir(newdir, true))
#if defined(_WIN64) || defined(_WIN32)
					mkdir(newdir);
#else
					mkdir(newdir, 0700);
#endif
			}
			char ch[128] = {""};
			snprintf(ch, 128, "%c", outname[pos]);
			strcat(newdir, ch);
		}
	}
	//printMessage("path='%s' name='%s'\n", pathoutname, outname);
	//make sure outname is unique
	strcat(baseoutname, outname);
	char pathoutname[2048] = {""};
	strcat(pathoutname, baseoutname);
	if ((niiExists(pathoutname)) && (opts.nameConflictBehavior == kNAME_CONFLICT_SKIP)) {
		printWarning("Skipping existing file named %s\n", pathoutname);
		return EXIT_FAILURE;
	}
	if ((niiExists(pathoutname)) && (opts.nameConflictBehavior == kNAME_CONFLICT_OVERWRITE)) {
		printWarning("Overwriting existing file with the name %s\n", pathoutname);
		niiDelete(pathoutname);
		strcpy(niiFilename, pathoutname);
		return EXIT_SUCCESS;
	}
	int i = 0;
	while (niiExists(pathoutname) && (i < 26)) {
		strcpy(pathoutname, baseoutname);
		appendChar[0] = 'a' + i;
		strcat(pathoutname, appendChar);
		i++;
	}
	if (i >= 26) {
		printError("Too many NIFTI images with the name %s\n", baseoutname);
		return EXIT_FAILURE;
	}
	//printMessage("-->%s\n",pathoutname); return EXIT_SUCCESS;
	//printMessage("outname=%s\n", pathoutname);
	strcpy(niiFilename, pathoutname);
	return EXIT_SUCCESS;
} //nii_createFilename()

void nii_createDummyFilename(char *niiFilename, struct TDCMopts opts) {
	//generate string that illustrating sample of filename
	struct TDICOMdata d = clear_dicom_data();
	strcpy(d.patientName, "John_Doe");
	strcpy(d.patientID, "ID123");
	strcpy(d.accessionNumber, "ID123");
	strcpy(d.imageType, "ORIGINAL");
	strcpy(d.imageComments, "imgComments");
	strcpy(d.studyDate, "1/1/1977");
	strcpy(d.studyTime, "11:11:11");
	strcpy(d.protocolName, "MPRAGE");
	strcpy(d.seriesDescription, "T1_mprage");
	strcpy(d.sequenceName, "T1");
	strcpy(d.scanningSequence, "tfl3d1_ns");
	strcpy(d.sequenceVariant, "tfl3d1_ns");
	strcpy(d.manufacturersModelName, "N/A");
	strcpy(d.procedureStepDescription, "");
	strcpy(d.seriesInstanceUID, "");
	strcpy(d.studyInstanceUID, "");
	strcpy(d.bodyPartExamined, "");
	strcpy(opts.indirParent, "myFolder");
	char niiFilenameBase[PATH_MAX] = {"/usr/myFolder/dicom.dcm"};
	nii_createFilename(d, niiFilenameBase, opts);
	strcpy(niiFilename, "Example output filename: '");
	strcat(niiFilename, niiFilenameBase);
	if (opts.saveFormat == kSaveFormatMGH) {
		if (opts.isGz)
			strcat(niiFilename, ".mgz'");
		else
			strcat(niiFilename, ".mgh'");
	} else if (opts.saveFormat == kSaveFormatNRRD) {
		if (opts.isGz)
			strcat(niiFilename, ".nhdr'");
		else
			strcat(niiFilename, ".nrrd'");
	#ifdef myEnableJNIFTI
	} else if (opts.saveFormat == kSaveFormatJNII) {
		strcat(niiFilename, ".jnii'");
	} else if (opts.saveFormat == kSaveFormatBNII) {
		strcat(niiFilename, ".bnii'");
	#endif
	} else {
		if (opts.isGz)
			strcat(niiFilename, ".nii.gz'");
		else
			strcat(niiFilename, ".nii'");
	}
} // nii_createDummyFilename()

#ifndef myDisableZLib

#ifndef MiniZ
unsigned long mz_compressBound(unsigned long source_len) {
	return compressBound(source_len);
}

unsigned long mz_crc32(unsigned long crc, const unsigned char *ptr, size_t buf_len) {
	return crc32(crc, ptr, (uInt)buf_len);
}
#endif

#ifndef MZ_UBER_COMPRESSION //defined in miniz, not defined in zlib
#define MZ_UBER_COMPRESSION 9
#endif

#ifndef MZ_DEFAULT_LEVEL
#define MZ_DEFAULT_LEVEL 6
#endif

void writeNiiGz(char *baseName, struct nifti_1_header hdr, unsigned char *src_buffer, unsigned long src_len, int gzLevel, bool isSkipHeader) {
	//create gz file in RAM, save to disk http://www.zlib.net/zlib_how.html
	// in general this single-threaded approach is slower than PIGZ but is useful for slow (network attached) disk drives
	char fname[2048] = {""};
	strcpy(fname, baseName);
	if (!isSkipHeader)
		strcat(fname, ".nii.gz");
	unsigned long hdrPadBytes = sizeof(hdr) + 4; //348 byte header + 4 byte pad
	if (isSkipHeader)
		hdrPadBytes = 0;
	unsigned long cmp_len = mz_compressBound(src_len + hdrPadBytes);
	unsigned char *pCmp = (unsigned char *)malloc(cmp_len);
	z_stream strm;
	strm.total_in = 0;
	strm.total_out = 0;
	strm.zalloc = Z_NULL;
	strm.zfree = Z_NULL;
	strm.opaque = Z_NULL;
	strm.next_out = pCmp;					// output char array
	strm.avail_out = (unsigned int)cmp_len; // size of output
	int zLevel = MZ_DEFAULT_LEVEL;			//Z_DEFAULT_COMPRESSION;
	if ((gzLevel > 0) && (gzLevel < 11))
		zLevel = gzLevel;
	if (zLevel > MZ_UBER_COMPRESSION)
		zLevel = MZ_UBER_COMPRESSION;
	if (deflateInit(&strm, zLevel) != Z_OK) {
		free(pCmp);
		return;
	}
	unsigned char *pHdr;
	if (!isSkipHeader) {
		//add header
		pHdr = (unsigned char *)malloc(hdrPadBytes);
		pHdr[hdrPadBytes - 1] = 0;
		pHdr[hdrPadBytes - 2] = 0;
		pHdr[hdrPadBytes - 3] = 0;
		pHdr[hdrPadBytes - 4] = 0;
		memcpy(pHdr, &hdr, sizeof(hdr));
		strm.avail_in = (unsigned int)hdrPadBytes; // size of input
		strm.next_in = (uint8_t *)pHdr; // input header -- TPX strm.next_in = (Bytef *)pHdr; uint32_t
		deflate(&strm, Z_NO_FLUSH);
	}
	//add image
	strm.avail_in = (unsigned int)src_len; // size of input
	strm.next_in = (uint8_t *)src_buffer; // input image -- TPX strm.next_in = (Bytef *)src_buffer;
	deflate(&strm, Z_FINISH); //Z_NO_FLUSH;
	//finish up
	deflateEnd(&strm);
	unsigned long file_crc32 = mz_crc32(0L, Z_NULL, 0);
	if (!isSkipHeader)
		file_crc32 = mz_crc32(file_crc32, pHdr, (unsigned int)hdrPadBytes);
	file_crc32 = mz_crc32(file_crc32, src_buffer, (unsigned int)src_len);
	cmp_len = strm.total_out;
	if (cmp_len <= 0) {
		free(pCmp);
		free(src_buffer);
		return;
	}
	FILE *fileGz = fopen(fname, "wb");
	if (!fileGz) {
		free(pCmp);
		free(src_buffer);
		return;
	}
	//write header http://www.gzip.org/zlib/rfc-gzip.html
	fputc((char)0x1f, fileGz); //ID1
	fputc((char)0x8b, fileGz); //ID2
	fputc((char)0x08, fileGz); //CM - use deflate compression method
	fputc((char)0x00, fileGz); //FLG - no addition fields
	fputc((char)0x00, fileGz); //MTIME0
	fputc((char)0x00, fileGz); //MTIME1
	fputc((char)0x00, fileGz); //MTIME2
	fputc((char)0x00, fileGz); //MTIME2
	fputc((char)0x00, fileGz); //XFL
	fputc((char)0xff, fileGz); //OS
	//write Z-compressed data
	fwrite(&pCmp[2], sizeof(char), cmp_len - 6, fileGz); //-6 as LZ78 format has 2 bytes header (typically 0x789C) and 4 bytes tail (ADLER 32)
	//write tail: write redundancy check and uncompressed size as bytes to ensure LITTLE-ENDIAN order
	fputc((unsigned char)(file_crc32), fileGz);
	fputc((unsigned char)(file_crc32 >> 8), fileGz);
	fputc((unsigned char)(file_crc32 >> 16), fileGz);
	fputc((unsigned char)(file_crc32 >> 24), fileGz);
	fputc((unsigned char)(strm.total_in), fileGz);
	fputc((unsigned char)(strm.total_in >> 8), fileGz);
	fputc((unsigned char)(strm.total_in >> 16), fileGz);
	fputc((unsigned char)(strm.total_in >> 24), fileGz);
	fclose(fileGz);
	free(pCmp);
	if (!isSkipHeader)
		free(pHdr);
} //writeNiiGz()
#endif

#ifndef USING_R

int pigz_File(char *fname, struct TDCMopts opts, size_t imgsz) {
	//given "/dir/file.nii" creates "/dir/file.nii.gz"
	char blockSize[768];
	strcpy(blockSize, "");
	//-b 960 increases block size from 128 to 960: each block has 32kb lead in... so less redundancy
	if (imgsz > 1000000)
		strcpy(blockSize, " -b 960");
	char command[768];
	strcpy(command, "\"");
	strcat(command, opts.pigzname);
	if ((opts.gzLevel > 0) && (opts.gzLevel < 12)) {
		char newstr[256];
		snprintf(newstr, 256, "\"%s -n -f -%d \"", blockSize, opts.gzLevel);
		//749 snprintf(newstr, 256, "\"%s -n -f -%d '", blockSize, opts.gzLevel);
		strcat(command, newstr);
	} else {
		char newstr[256];
		snprintf(newstr, 256, "\"%s -n \"", blockSize);
		//749 snprintf(newstr, 256, "\"%s -n '", blockSize);
		strcat(command, newstr);
	}
	strcat(command, fname);
	//issue749 use single quote to prevent expansion of $
	//749 strcat(command, "'"); //add quotes in case spaces in filename 'pigz "c:\my dir\img.nii"'
	strcat(command, "\""); //add quotes in case spaces in filename 'pigz "c:\my dir\img.nii"'
#if defined(_WIN64) || defined(_WIN32) //using CreateProcess instead of system to run in background (avoids screen flicker)
	DWORD exitCode;
	PROCESS_INFORMATION ProcessInfo = {0};
	STARTUPINFO startupInfo = {0};
	startupInfo.cb = sizeof(startupInfo);
	//StartupInfo.cb = sizeof StartupInfo ; //Only compulsory field
	if (CreateProcess(NULL, command, NULL, NULL, FALSE, NORMAL_PRIORITY_CLASS | CREATE_NO_WINDOW, NULL, NULL, &startupInfo, &ProcessInfo)) {
		//printMessage("compression --- %s\n",command);
		WaitForSingleObject(ProcessInfo.hProcess, INFINITE);
		CloseHandle(ProcessInfo.hThread);
		CloseHandle(ProcessInfo.hProcess);
	} else
		printMessage("Compression failed %s\n", command);
#else //if win else linux
	int ret = system(command);
	if (ret == -1)
		printWarning("Failed to execute: %s\n", command);
#endif //else linux
	printMessage("Compress: %s\n", command);
	return EXIT_SUCCESS;
} // pigz_File()

#define kMGHpad 97

#ifdef __GNUC__
#define PACKD(...) __VA_ARGS__ __attribute__((__packed__))
#else
#define PACKD(...) __pragma(pack(push, 1)) __VA_ARGS__ __pragma(pack(pop))
#endif

PACKD(typedef struct {
	int32_t version, width,height,depth,nframes,type,dof;
	int16_t goodRASFlag;
	float spacingX,spacingY,spacingZ,xr,xa,xs,yr,ya,ys,zr,za,zs,cr,ca,cs;
	int16_t pad[kMGHpad];
}) Tmgh;

PACKD(typedef struct {
	float TR, FlipAngle, TE, TI;
}) TmghFooter;

void writeMghGz(char *baseName, Tmgh hdr, TmghFooter footer, unsigned char *src_buffer, unsigned long src_len, int gzLevel) {
	//create gz file in RAM, save to disk http://www.zlib.net/zlib_how.html
	// in general this single-threaded approach is slower than PIGZ but is useful for slow (network attached) disk drives
	char fname[2048] = {""};
	strcpy(fname, baseName);
	unsigned long hdrPadBytes = sizeof(hdr); //348 byte header + 4 byte pad
	unsigned long cmp_len = mz_compressBound(src_len + hdrPadBytes);
	unsigned char *pCmp = (unsigned char *)malloc(cmp_len);
	z_stream strm;
	strm.total_in = 0;
	strm.total_out = 0;
	strm.zalloc = Z_NULL;
	strm.zfree = Z_NULL;
	strm.opaque = Z_NULL;
	strm.next_out = pCmp;					// output char array
	strm.avail_out = (unsigned int)cmp_len; // size of output
	int zLevel = MZ_DEFAULT_LEVEL;			//Z_DEFAULT_COMPRESSION;
	if ((gzLevel > 0) && (gzLevel < 11))
		zLevel = gzLevel;
	if (zLevel > MZ_UBER_COMPRESSION)
		zLevel = MZ_UBER_COMPRESSION;
	if (deflateInit(&strm, zLevel) != Z_OK) {
		free(pCmp);
		return;
	}
	//add header
	strm.avail_in = (unsigned int)sizeof(hdr); // size of input
	strm.next_in = (uint8_t *) &hdr.version;
	deflate(&strm, Z_NO_FLUSH);
	//add image
	strm.avail_in = (unsigned int)src_len; // size of input
	strm.next_in = (uint8_t *)src_buffer; // input image -- TPX strm.next_in = (Bytef *)src_buffer;
	deflate(&strm, Z_FINISH);
	//add footer
	strm.avail_in = (unsigned int)sizeof(footer); // size of input
	strm.next_in = (uint8_t *) &footer.TR;
	deflate(&strm, Z_NO_FLUSH);
	//finish up
	deflateEnd(&strm);
	unsigned long file_crc32 = mz_crc32(0L, Z_NULL, 0);
	file_crc32 = mz_crc32(file_crc32, (uint8_t *) &hdr.version, (unsigned int)sizeof(hdr));
	file_crc32 = mz_crc32(file_crc32, src_buffer, (unsigned int)src_len);
	file_crc32 = mz_crc32(file_crc32, (uint8_t *) &footer.TR, (unsigned int)sizeof(footer));
	cmp_len = strm.total_out;
	if (cmp_len <= 0) {
		free(pCmp);
		free(src_buffer);
		return;
	}
	FILE *fileGz = fopen(fname, "wb");
	if (!fileGz) {
		free(pCmp);
		free(src_buffer);
		return;
	}
	//write header http://www.gzip.org/zlib/rfc-gzip.html
	fputc((char)0x1f, fileGz); //ID1
	fputc((char)0x8b, fileGz); //ID2
	fputc((char)0x08, fileGz); //CM - use deflate compression method
	fputc((char)0x00, fileGz); //FLG - no addition fields
	fputc((char)0x00, fileGz); //MTIME0
	fputc((char)0x00, fileGz); //MTIME1
	fputc((char)0x00, fileGz); //MTIME2
	fputc((char)0x00, fileGz); //MTIME2
	fputc((char)0x00, fileGz); //XFL
	fputc((char)0xff, fileGz); //OS
	//write Z-compressed data
	fwrite(&pCmp[2], sizeof(char), cmp_len - 6, fileGz); //-6 as LZ78 format has 2 bytes header (typically 0x789C) and 4 bytes tail (ADLER 32)
	//write tail: write redundancy check and uncompressed size as bytes to ensure LITTLE-ENDIAN order
	fputc((unsigned char)(file_crc32), fileGz);
	fputc((unsigned char)(file_crc32 >> 8), fileGz);
	fputc((unsigned char)(file_crc32 >> 16), fileGz);
	fputc((unsigned char)(file_crc32 >> 24), fileGz);
	fputc((unsigned char)(strm.total_in), fileGz);
	fputc((unsigned char)(strm.total_in >> 8), fileGz);
	fputc((unsigned char)(strm.total_in >> 16), fileGz);
	fputc((unsigned char)(strm.total_in >> 24), fileGz);
	fclose(fileGz);
	free(pCmp);
} //writeMghGz()

int nii_saveMGH(char *niiFilename, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts, struct TDICOMdata d, struct TDTI4D *dti4D, int numDTI) {
// FreeeSurfer does not use a permissive license, so we must reverse engineer code
// https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
	int nDim = hdr.dim[0];
	//printMessage("NRRD writer is experimental\n");
	if (nDim < 1)
		return EXIT_FAILURE;
	bool isGz = opts.isGz;
	size_t imgsz = nii_ImgBytes(hdr);
	if ((isGz) && (imgsz >= 2147483647)) {
		printWarning("Saving huge image uncompressed (many GZip tools have 2 Gb limit).\n");
		isGz = false;
	}
	//fill the footer
	TmghFooter footer;
	footer.TR = d.TR;
	footer.FlipAngle = d.flipAngle;
	footer.TE = d.TE;
	footer.TI = d.TI;
	#ifdef __LITTLE_ENDIAN__ //mgh data ALWAYS big endian!
		nifti_swap_4bytes(4, &footer.TR);
	#endif
	//fill the header
	Tmgh mgh;
	mgh.version = 1;
	mgh.width = hdr.dim[1];
	mgh.height = hdr.dim[2];
	mgh.depth = hdr.dim[3];
	mgh.nframes = max(hdr.dim[4],1);
	if (hdr.datatype == DT_UINT8)
		mgh.type = 0;
	else if (hdr.datatype == DT_INT16)
		mgh.type = 4;
	else if (hdr.datatype == DT_INT32)
		mgh.type = 1;
	else if (hdr.datatype == DT_FLOAT32)
		mgh.type = 3;
	else {
		printError("MGH format does not support NIfTI datatype %d\n", hdr.datatype);
		return EXIT_FAILURE;
	}
	mgh.dof = 0;
	mgh.goodRASFlag = 1;
	float xmm = hdr.pixdim[1];
	float ymm = hdr.pixdim[2];
	float zmm = hdr.pixdim[3];
	//avoid divide by zero errors:
	if (xmm <= 0.0) xmm = 1.0;
	if (ymm <= 0.0) ymm = 1.0;
	if (zmm <= 0.0) zmm = 1.0;
	mgh.spacingX = xmm;
	mgh.spacingY = ymm;
	mgh.spacingZ = zmm;
	mgh.xr = hdr.srow_x[0] / xmm;
	mgh.xa = hdr.srow_y[0] / xmm;
	mgh.xs = hdr.srow_z[0] / xmm;
	mgh.yr = hdr.srow_x[1] / ymm;
	mgh.ya = hdr.srow_y[1] / ymm;
	mgh.ys = hdr.srow_z[1] / ymm;
	mgh.zr = hdr.srow_x[2] / zmm;
	mgh.za = hdr.srow_y[2] / zmm;
	mgh.zs = hdr.srow_z[2] / zmm;
	float vec[3];
	vec[0] = hdr.dim[1] * 0.5;
	vec[1] = hdr.dim[2] * 0.5;
	vec[2] = hdr.dim[3] * 0.5;
	mgh.cr = hdr.srow_x[0]*vec[0] + hdr.srow_x[1]*vec[1] + hdr.srow_x[2]*vec[2]  + hdr.srow_x[3];
	mgh.ca = hdr.srow_y[0]*vec[0] + hdr.srow_y[1]*vec[1] + hdr.srow_y[2]*vec[2]  + hdr.srow_y[3];
	mgh.cs = hdr.srow_z[0]*vec[0] + hdr.srow_z[1]*vec[1] + hdr.srow_z[2]*vec[2]  + hdr.srow_z[3];
	#ifdef __LITTLE_ENDIAN__ //mgh data ALWAYS big endian!
		nifti_swap_4bytes(7, &mgh.version);
		nifti_swap_2bytes(1, &mgh.goodRASFlag);
		nifti_swap_4bytes(15, &mgh.spacingX);
	#endif
	for (int i = 0; i < kMGHpad; i++)
		mgh.pad[i] = 0;
	//write the data
	char fname[2048] = {""};
	strcpy(fname, niiFilename);
	#ifdef __LITTLE_ENDIAN__ //mgh data ALWAYS big endian!
		swapEndian(&hdr, im, true); //byte-swap endian (e.g. little->big)
	#endif
	if (isGz) {
		strcat(fname, ".mgz");
		writeMghGz(fname, mgh, footer, im, imgsz, opts.gzLevel);
	} else {
		strcat(fname, ".mgh");
		FILE *fp = fopen(fname, "wb");
		if (!fp)
			return EXIT_FAILURE;
		fwrite(&mgh, sizeof(Tmgh), 1, fp);
		fwrite(&im[0], imgsz, 1, fp);
		fwrite(&footer, sizeof(TmghFooter), 1, fp);
		fclose(fp);
	}
	#ifdef __LITTLE_ENDIAN__ //mgh data ALWAYS big endian!
		swapEndian(&hdr, im, false); //byte-swap endian (e.g. little->big)
	#endif
	return EXIT_SUCCESS;
} // nii_saveMGH()

int nii_saveNRRD(char *niiFilename, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts, struct TDICOMdata d, struct TDTI4D *dti4D, int numDTI) {
	int n, nDim = hdr.dim[0];
	//printMessage("NRRD writer is experimental\n");
	if (nDim < 1)
		return EXIT_FAILURE;
	bool isGz = opts.isGz;
	size_t imgsz = nii_ImgBytes(hdr);
	if ((isGz) && (imgsz >= 2147483647)) {
		printWarning("Saving huge image uncompressed (many GZip tools have 2 Gb limit).\n");
		isGz = false;
	}
	char fname[2048] = {""};
	strcpy(fname, niiFilename);
	if (isGz)
		strcat(fname, ".nhdr"); //nrrd or nhdr
	else
		strcat(fname, ".nrrd"); //nrrd or nhdr
	FILE *fp = fopen(fname, "w");
	fprintf(fp, "NRRD0005\n");
	fprintf(fp, "# Complete NRRD file format specification at:\n");
	fprintf(fp, "# http://teem.sourceforge.net/nrrd/format.html\n");
	fprintf(fp, "# dcm2niix %s NRRD export transforms by Tashrif Billah\n", kDCMdate);
	char rgbNoneStr[10] = {""};
	//type tag
	switch (hdr.datatype) {
	case DT_RGB24:
		fprintf(fp, "type: uint8\n");
		strcpy(rgbNoneStr, " none");
		break;
	case DT_UINT8:
		fprintf(fp, "type: uint8\n");
		break;
	case DT_INT16:
		fprintf(fp, "type: int16\n");
		break;
	case DT_UINT16:
		fprintf(fp, "type: uint16\n");
		break;
	case DT_FLOAT32:
		fprintf(fp, "type: float\n");
		break;
	case DT_INT32:
		fprintf(fp, "type: int32\n");
		break;
	case DT_FLOAT64:
		fprintf(fp, "type: double\n");
		break;
	default:
		printError("Unknown NRRD datatype %d\n", hdr.datatype);
		fclose(fp);
		return EXIT_FAILURE;
	}
	//dimension tag
	if (hdr.datatype == DT_RGB24)
		fprintf(fp, "dimension: %d\n", nDim + 1); //RGB is first dimension
	else
		fprintf(fp, "dimension: %d\n", nDim);
	//space tag
	fprintf(fp, "space: right-anterior-superior\n");
	//sizes tag
	fprintf(fp, "sizes:");
	if (hdr.datatype == DT_RGB24)
		fprintf(fp, " 3");
	for (int i = 1; i <= hdr.dim[0]; i++)
		fprintf(fp, " %d", hdr.dim[i]);
	fprintf(fp, "\n");
	//thicknesses
	if ((d.zThick > 0.0) && (nDim >= 3)) {
		fprintf(fp, "thicknesses: NaN NaN %g", d.zThick);
		int n = 3;
		while (n < nDim) {
			fprintf(fp, " NaN");
			n++;
		}
		fprintf(fp, "\n");
	}
	//byteskip only for .nhdr, not .nrrd
	if (littleEndianPlatform()) //raw data in native format
		fprintf(fp, "endian: little\n");
	else
		fprintf(fp, "endian: big\n");
	if (isGz) {
		fprintf(fp, "encoding: gzip\n");
		strcpy(fname, niiFilename);
		strcat(fname, ".raw.gz");
		char basefname[2048] = {""};
		getFileNameX(basefname, fname, 2048);
		fprintf(fp, "data file: %s\n", basefname);
	} else
		fprintf(fp, "encoding: raw\n");
	fprintf(fp, "space units: \"mm\" \"mm\" \"mm\"\n");
	//origin
	fprintf(fp, "space origin: (%g,%g,%g)\n", hdr.srow_x[3], hdr.srow_y[3], hdr.srow_z[3]);
	//space directions:
	fprintf(fp, "space directions:%s (%g,%g,%g) (%g,%g,%g) (%g,%g,%g)", rgbNoneStr, hdr.srow_x[0], hdr.srow_y[0], hdr.srow_z[0],
			hdr.srow_x[1], hdr.srow_y[1], hdr.srow_z[1], hdr.srow_x[2], hdr.srow_y[2], hdr.srow_z[2]);
	n = 3;
	while (n < nDim) {
		fprintf(fp, " none");
		n++;
	}
	fprintf(fp, "\n");
	//centerings tag
	if (hdr.dim[0] < 4) //*check RGB, more dims
		fprintf(fp, "centerings:%s cell cell cell\n", rgbNoneStr);
	else
		fprintf(fp, "centerings:%s cell cell cell ???\n", rgbNoneStr);
	//kinds tag
	fprintf(fp, "kinds:");
	if (hdr.datatype == DT_RGB24)
		fprintf(fp, " RGB-color");
	n = 0;
	while ((n < nDim) && (n < 3)) {
		fprintf(fp, " space"); //dims 1..3
		n++;
	}
	while (n < nDim) {
		fprintf(fp, " list"); //dims 4..7
		n++;
	}
	fprintf(fp, "\n");
	//http://teem.sourceforge.net/nrrd/format.html
	bool isFloat = (hdr.datatype == DT_FLOAT64) || (hdr.datatype == DT_FLOAT32);
	if (((!isSameFloat(hdr.scl_inter, 0.0)) || (!isSameFloat(hdr.scl_slope, 1.0))) && (!isFloat)) {
		//http://teem.sourceforge.net/nrrd/format.html
		double dtMin = 0.0; //DT_UINT8, DT_RGB24, DT_UINT16
		if (hdr.datatype == DT_INT16)
			dtMin = -32768.0;
		if (hdr.datatype == DT_INT32)
			dtMin = -2147483648.0;
		fprintf(fp, "oldmin: %8.8f\n", (dtMin * hdr.scl_slope) + hdr.scl_inter);
		double dtMax = 255.00; //DT_UINT8, DT_RGB24
		if (hdr.datatype == DT_INT16)
			dtMax = 32767.0;
		if (hdr.datatype == DT_UINT16)
			dtMax = 65535.0;
		if (hdr.datatype == DT_INT32)
			dtMax = 2147483647.0;
		fprintf(fp, "oldmax: %8.8f\n", (dtMax * hdr.scl_slope) + hdr.scl_inter);
	}
	//Slicer DWIconvert values
	if (d.modality == kMODALITY_MR)
		fprintf(fp, "DICOM_0008_0060_Modality:=MR\n");
	if (d.modality == kMODALITY_CT)
		fprintf(fp, "DICOM_0008_0060_Modality:=CT\n");
	if (d.manufacturer == kMANUFACTURER_SIEMENS)
		fprintf(fp, "DICOM_0008_0070_Manufacturer:=SIEMENS\n");
	if (d.manufacturer == kMANUFACTURER_PHILIPS)
		fprintf(fp, "DICOM_0008_0070_Manufacturer:=Philips Medical Systems\n");
	if (d.manufacturer == kMANUFACTURER_GE)
		fprintf(fp, "DICOM_0008_0070_Manufacturer:=GE MEDICAL SYSTEMS\n");
	if (strlen(d.manufacturersModelName) > 0)
		fprintf(fp, "DICOM_0008_1090_ManufacturerModelName:=%s\n", d.manufacturersModelName);
	if (strlen(d.scanOptions) > 0)
		fprintf(fp, "DICOM_0018_0022_ScanOptions:=%s\n", d.scanOptions);
	if (d.is2DAcq)
		fprintf(fp, "DICOM_0018_0023_MRAcquisitionType:=2D\n");
	if (d.is3DAcq)
		fprintf(fp, "DICOM_0018_0023_MRAcquisitionType:=3D\n");
	//if (strlen(d.mrAcquisitionType) > 0) fprintf(fp,"DICOM_0018_0023_MRAcquisitionType:=%s\n",d.mrAcquisitionType);
	if (d.TR > 0.0)
		fprintf(fp, "DICOM_0018_0080_RepetitionTime:=%g\n", d.TR);
	if ((d.TE > 0.0) && (!d.isXRay))
		fprintf(fp, "DICOM_0018_0081_EchoTime:=%g\n", d.TE);
	if ((d.TE > 0.0) && (d.isXRay))
		fprintf(fp, "DICOM_0018_1152_XRayExposure:=%g\n", d.TE);
	if (d.numberOfAverages > 0.0)
		fprintf(fp, "DICOM_0018_0083_NumberOfAverages:=%g\n", d.numberOfAverages);
	if (d.fieldStrength > 0.0)
		fprintf(fp, "DICOM_0018_0087_MagneticFieldStrength:=%g\n", d.fieldStrength);
	if (strlen(d.softwareVersions) > 0)
		fprintf(fp, "DICOM_0018_1020_SoftwareVersions:=%s\n", d.softwareVersions);
	if (d.flipAngle > 0.0)
		fprintf(fp, "DICOM_0018_1314_FlipAngle:=%g\n", d.flipAngle);
	//multivolume but NOT DTI, e.g. fMRI/DCE see https://www.slicer.org/wiki/Documentation/4.4/Modules/MultiVolumeExplorer
	// https://github.com/QIICR/PkModeling/blob/master/PkSolver/IO/MultiVolumeMetaDictReader.cxx#L34-L58
	// for "MultiVolume.FrameLabels:="
	// https://www.slicer.org/wiki/Documentation/4.4/Modules/MultiVolumeExplorer
	// for "axis 0 index values:="
	// https://github.com/mhe/pynrrd/issues/71
	// "I don't know if it is a good idea for dcm2niix to mimic Slicer converter tags" Andrey Fedorov
	/*
	if ((nDim > 3) && (hdr.dim[4] > 1) && (numDTI < 1)) {
		if ((d.TE > 0.0) && (!d.isXRay)) fprintf(fp,"MultiVolume.DICOM.EchoTime:=%g\n",d.TE);
		if (d.flipAngle > 0.0) fprintf(fp,"MultiVolume.DICOM.FlipAngle:=%g\n",d.flipAngle);
		if (d.TR > 0.0) fprintf(fp,"MultiVolume.DICOM.RepetitionTime:=%g\n",d.TR);
		fprintf(fp,"MultiVolume.FrameIdentifyingDICOMTagName:=TriggerTime\n");
		fprintf(fp,"MultiVolume.FrameIdentifyingDICOMTagUnits:=ms\n");
		fprintf(fp,"MultiVolume.FrameLabels:=");
		double frameTime = d.TR;
		if (d.triggerDelayTime > 0.0)
			frameTime = d.triggerDelayTime / (hdr.dim[4] - 1); //GE dce data
		for (int i = 0; i < (hdr.dim[4]-1); i++)
			fprintf(fp,"%g,", i * frameTime);
		fprintf(fp,"%g\n", (hdr.dim[4]-1) * frameTime);
		fprintf(fp,"MultiVolume.NumberOfFrames:=%d\n",hdr.dim[4]);
	} */
	//DWI values
	if ((nDim > 3) && (numDTI > 0) && (numDTI < kMaxDTI4D)) {
		mat33 inv;
		LOAD_MAT33(inv, hdr.pixdim[1], 0.0, 0.0, 0.0, hdr.pixdim[2], 0.0, 0.0, 0.0, hdr.pixdim[3]);
		inv = nifti_mat33_inverse(inv);
		mat33 s;
		LOAD_MAT33(s, hdr.srow_x[0], hdr.srow_x[1], hdr.srow_x[2],
			hdr.srow_y[0], hdr.srow_y[1], hdr.srow_y[2],
			hdr.srow_z[0], hdr.srow_z[1], hdr.srow_z[2]);
		mat33 mf = nifti_mat33_mul(inv, s);
		fprintf(fp, "measurement frame: (%g,%g,%g) (%g,%g,%g) (%g,%g,%g)\n",
				mf.m[0][0], mf.m[1][0], mf.m[2][0],
				mf.m[0][1], mf.m[1][1], mf.m[2][1],
				mf.m[0][2], mf.m[1][2], mf.m[2][2]);
		//modality tag
		fprintf(fp, "modality:=DWMRI\n");
		float b_max = 0.0;
		for (int i = 0; i < numDTI; i++)
			if (dti4D->S[i].V[0] > b_max)
				b_max = dti4D->S[i].V[0];
		fprintf(fp, "DWMRI_b-value:=%g\n", b_max);
		//gradient tag, e.g. DWMRI_gradient_0000:=0.0 0.0 0.0
		for (int i = 0; i < numDTI; i++) {
			float factor = 0.0;
			if (b_max > 0)
				factor = sqrt(dti4D->S[i].V[0] / b_max);
			if ((dti4D->S[i].V[0] > 50.0) && (isSameFloatGE(0.0, dti4D->S[i].V[1])) && (isSameFloatGE(0.0, dti4D->S[i].V[2])) && (isSameFloatGE(0.0, dti4D->S[i].V[3]))) {
				//On May 2, 2019, at 10:47 AM, Gordon L. Kindlmann <> wrote:
				//(assuming b_max 2000, we write "isotropic" for the b=2000 isotropic image, and specify the b-value if it is an isotropic image but not b-bax
				// DWMRI_gradient_0003:=isotropic b=1000
				// DWMRI_gradient_0004:=isotropic
				if (isSameFloatGE(b_max, dti4D->S[i].V[0]))
					fprintf(fp, "DWMRI_gradient_%04d:=isotropic\n", i);
				else
					fprintf(fp, "DWMRI_gradient_%04d:=isotropic b=%g\n", i, dti4D->S[i].V[0]);
			} else
				fprintf(fp, "DWMRI_gradient_%04d:=%.17g %.17g %.17g\n", i, factor * dti4D->S[i].V[1], factor * dti4D->S[i].V[2], factor * dti4D->S[i].V[3]);
			//printf("%g = %g %g %g>>>>\n",dti4D->S[i].V[0], dti4D->S[i].V[1],dti4D->S[i].V[2],dti4D->S[i].V[3]);
		}
	}
	fprintf(fp, "\n"); //blank line: end of NRRD header
	if (!isGz)
		fwrite(&im[0], imgsz, 1, fp);
	fclose(fp);
	if (!isGz)
		return EXIT_SUCCESS;
//below: gzip file
#ifdef myDisableZLib
	if (strlen(opts.pigzname) < 1) { //internal compression
		printError("Compiled without gz support, unable to compress %s\n", fname);
		return EXIT_FAILURE;
	}
#else
	if (strlen(opts.pigzname) < 1) { //internal compression
		writeNiiGz(fname, hdr, im, imgsz, opts.gzLevel, true);
		return EXIT_SUCCESS;
	}
#endif
	//below pigz
	strcpy(fname, niiFilename); //without gz
	strcat(fname, ".raw");
	fp = fopen(fname, "wb");
	fwrite(&im[0], imgsz, 1, fp);
	fclose(fp);
	return pigz_File(fname, opts, imgsz);
} // nii_saveNRRD()

enum TZipMethod {zmZlib, zmGzip, zmBase64};

#ifdef myEnableJNIFTI
#ifdef Z_DEFLATED

int zmat_run(const size_t inputsize, unsigned char *inputstr, size_t *outputsize, unsigned char **outputbuf, const int zipid, int *ret, const int iscompress){
	z_stream zs;
	size_t buflen[2]={0};
	*outputbuf=NULL;

	zs.zalloc = Z_NULL;
	zs.zfree  = Z_NULL;
	zs.opaque = Z_NULL;

	if(inputsize==0)
		return -1;

	if(iscompress){
		/** perform compression or encoding */
		if(zipid==zmBase64){
			/** base64 encoding  */
			*outputbuf=base64_encode((const unsigned char*)inputstr, inputsize, outputsize);
		}else if(zipid==zmZlib || zipid==zmGzip){
			/** zlib (.zip) or gzip (.gz) compression  */
			if(zipid==zmZlib){
				if(deflateInit(&zs,  (iscompress>0) ? Z_DEFAULT_COMPRESSION : (-iscompress)) != Z_OK)
					return -2;
			}else{
				if(deflateInit2(&zs, (iscompress>0) ? Z_DEFAULT_COMPRESSION : (-iscompress), Z_DEFLATED, 15|16, MAX_MEM_LEVEL, Z_DEFAULT_STRATEGY) != Z_OK)
					return -2;
			}
			buflen[0] =deflateBound(&zs,inputsize);
			*outputbuf=(unsigned char *)malloc(buflen[0]);
			zs.avail_in = inputsize; /* size of input, string + terminator*/
			zs.next_in = (Bytef *)inputstr; /* input char array*/
			zs.avail_out = buflen[0]; /* size of output*/

			zs.next_out =  (Bytef *)(*outputbuf); /*(Bytef *)(); // output char array*/

			*ret=deflate(&zs, Z_FINISH);
			*outputsize=zs.total_out;
			if(*ret!=Z_STREAM_END && *ret!=Z_OK)
				return -3;
			deflateEnd(&zs);
		}else{
			return -7;
		}
	}else{
		/** perform decompression or decoding */
		if(zipid==zmBase64){
			/** base64 decoding  */
			*outputbuf=base64_decode((const unsigned char*)inputstr, inputsize, outputsize);
		}else if(zipid==zmZlib || zipid==zmGzip){
			/** zlib (.zip) or gzip (.gz) decompression */
			int count=1;
			if(zipid==zmZlib){
				if(inflateInit(&zs) != Z_OK)
					return -2;
			}else{
				if(inflateInit2(&zs, 15|32) != Z_OK)
					return -2;
			}

			buflen[0] =inputsize*20;
			*outputbuf=(unsigned char *)malloc(buflen[0]);

			zs.avail_in = inputsize; /* size of input, string + terminator*/
			zs.next_in =inputstr; /* input char array*/
			zs.avail_out = buflen[0]; /* size of output*/

			zs.next_out =  (Bytef *)(*outputbuf); /*(Bytef *)(); // output char array*/

			while((*ret=inflate(&zs, Z_SYNC_FLUSH))!=Z_STREAM_END && count<=10){
				*outputbuf=(unsigned char *)realloc(*outputbuf, (buflen[0]<<count));
				zs.next_out =  (Bytef *)(*outputbuf+(buflen[0]<<(count-1)));
				zs.avail_out = (buflen[0]<<(count-1)); /* size of output*/
				count++;
			}
			*outputsize=zs.total_out;
			if(*ret!=Z_STREAM_END && *ret!=Z_OK)
				return -3;
			inflateEnd(&zs);
		}else{
			return -7;
		}
	}
	return 0;
}

#endif //Z_DEFLATED 

int jnifti_lookup(int *keyid, int keylen, int val){
	for(int i=0;i<keylen;i++){
		if(val==keyid[i]){
			return i;
		}
	}
	return keylen; /*last element is unknown type ""*/
}

void write_ubjsonint(void *dat, int bytelen, int count, FILE *fp){
	void *tmp=malloc(count*bytelen);
	memcpy(tmp,dat,count*bytelen);
	if (!&littleEndianPlatform){
		if(bytelen==2)
			nifti_swap_2bytes(count, tmp);
		else if(bytelen==4)
			nifti_swap_4bytes(count, tmp);
		else if(bytelen==8)
			nifti_swap_8bytes(count, tmp);
	}
	fwrite(tmp,count,bytelen,fp);
	free(tmp);
}

int nii_savebnii(char *bniifile, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts, unsigned char ndim,
	 size_t totalbytes, const char *dtype, const char *slicetype, const char *intent, const char *lunit, const char *tunit,
	 const char *jdtype, int jdataelemlen, char jdatamarker) {
	int markerlen=0, dim[8]={0};
	const char *output[]={
	"{",
		"N","","_DataInfo_","{",
			"N","","JNIFTIVersion","S","","0.5",
			"N","","Comment","S","","Created by dcm2niix and NeuroJSON (http://neurojson.org)",
			"N","","AnnotationFormat","S","","https://github.com/NeuroJSON/jnifti/blob/master/JNIfTI_specification.md",
				"N","","SerialFormat","S","","https://github.com/NeuroJSON/bjdata/blob/master/Binary_JData_Specification.md",
				"N","","Parser","{",
					"N","","Python","S","","https://pypi.org/project/jdata\thttps://pypi.org/project/bjdata",
					"N","","MATLAB","S","","https://github.com/NeuroJSON/jnifty",
					"N","","JavaScript","S","","https://github.com/NeuroJSON/jsdata",
				"}",
		"}",
		"N","","NIFTIHeader","{",
			"N","","NIIHeaderSize","l","?1",
			"N","","Dim","[$I#U","?2","?3",
			"N","","Param1","d","?4",
			"N","","Param2","d","?5",
			"N","","Param3","d","?6",
			"N","","Intent","S","","?7",
			"N","","DataType","S","","?8",
				"N","","BitDepth","U","?9",
				"N","","FirstSliceID","I","?10",
				"N","","VoxelSize","[$d#U","?11","?12",
				"N","","Orientation","{",
					"N","","x","S","U\x01","?13",
					"N","","y","S","","a",
					"N","","z","S","","s",
				"}",
				"N","","ScaleSlope","d","?14",
				"N","","ScaleOffset","d","?15",
				"N","","LastSliceID","I","?16",
				"N","","SliceType","S","","?17",
				"N","","Unit","{",
					"N","","L","S","","?18",
					"N","","T","S","","?19",
				"}",
				"N","","MaxIntensity","d","?20",
				"N","","MinIntensity","d","?21",
				"N","","SliceTime","d","?22",
				"N","","TimeOffset","d","?23",
				"N","","Description","S","","?24",
				"N","","AuxFile","S","","?25",
				"N","","QForm","I","?26",
				"N","","SForm","I","?27",
				"N","","Quatern","{",
					"N","","b","d","?28",
					"N","","c","d","?29",
					"N","","d","d","?30",
				"}",
				"N","","QuaternOffset","{",
					"N","","x","d","?31",
					"N","","y","d","?32",
					"N","","z","d","?33",
				"}",
				"N","","Affine","[$d#[$U#U\x02\x03\x04","?34", // Affine is a 2D (\x02) 3x4 (\x03\x04) float [d] matrix
				"N","","Name","S","","?35",
				"N","","NIIFormat","S","","?36",
				"N","","NIIByteOffset","l","?37",
		"}",
		"N","","NIFTIData","{",
			"N","","_ArrayType_","S","","?38",
			"N","","_ArraySize_","[$l#U","?39","?40",
			"N","","_ArrayOrder_","S","","c", // NIfTI array is column-major
#ifdef Z_DEFLATED
			"N","","_ArrayZipType_","S","","?41",
			"N","","_ArrayZipSize_","l","?42",
			"N","","_ArrayZipData_","[$U#","","?43",
#else
			"N","","_ArrayData_","[$U#","","?41",
#endif
		"}",
	"}"
	};
	FILE *fp = fopen(bniifile,"wb");
	if (fp == NULL)
		return EXIT_FAILURE;

	markerlen=sizeof(output)/sizeof(char*);
	for(int i=1;i<8;i++)
		dim[i-1]=hdr.dim[i];
	if(jdataelemlen>1)
		dim[ndim++]=jdataelemlen;

	for(int i=0;i<markerlen;i++){
		int slen=strlen(output[i]);
		if(slen>0 && output[i][0]!='?'){ // take care all name-tags and constant string values
			if(!(slen==1 && output[i][0]=='N'))
				fwrite(output[i],1,slen,fp);
			if(slen==1 && (output[i][0]=='N' || output[i][0]=='S') && i+2<markerlen && output[i+1][0]=='\0' && output[i+2][0]!='?'){
				unsigned int keylen=strlen(output[i+2]);
				if(keylen<256){
					unsigned char keylenbyte=keylen;
					fputc('U',fp);
					fwrite(&keylenbyte,1,sizeof(keylenbyte),fp);
				}else{
					fputc('l',fp);
					write_ubjsonint(&keylen,sizeof(keylen),1,fp);
				}
			}
		}else if(slen>0){
			int slotid=0;
			if(sscanf(output[i],"\?%d",&slotid)==1 && slotid>0){
				unsigned char *compressed=NULL;
				size_t compressedbytes;
				int ret=0, status=0;
				switch(slotid){ // mapping data to the pre-defined slots in the form of "?number" in the template
					case  1: {write_ubjsonint(&hdr.sizeof_hdr,sizeof(hdr.sizeof_hdr),1,fp);break;}
					case  2: {fputc(ndim,fp);break;}
					case  3: {write_ubjsonint(hdr.dim+1, sizeof(hdr.dim[0]), ndim,fp);break;}
					case  4: {write_ubjsonint(&hdr.intent_p1,1,sizeof(hdr.intent_p1),fp);break;}
					case  5: {write_ubjsonint(&hdr.intent_p2,1,sizeof(hdr.intent_p2),fp);break;}
					case  6: {write_ubjsonint(&hdr.intent_p3,1,sizeof(hdr.intent_p3),fp);break;}
					case  7: {unsigned char val=strlen(intent);fputc('U',fp);fputc(val,fp); fwrite(intent,1,val,fp);break;}
					case  8: {unsigned char val=strlen(dtype); fputc('U',fp);fputc(val,fp); fwrite(dtype,1,val,fp);break;}
					case  9: {fputc(hdr.bitpix,fp);break;}
					case 10: {write_ubjsonint(&hdr.slice_start, sizeof(hdr.slice_start),1,fp);break;}
					case 11: {fputc(ndim,fp);break;}
					case 12: {write_ubjsonint(&hdr.pixdim[1],ndim,sizeof(hdr.pixdim[1]),fp);break;}
					case 13: {fputc((int)hdr.pixdim[0] ? 'l' : 'r',fp);break;}
					case 14: {write_ubjsonint(&hdr.scl_slope,1,sizeof(hdr.scl_slope),fp);break;}
					case 15: {write_ubjsonint(&hdr.scl_inter,1,sizeof(hdr.scl_inter),fp);break;}
					case 16: {write_ubjsonint(&hdr.slice_end,sizeof(hdr.slice_end),1,fp);break;}
					case 17: {unsigned char val=strlen(slicetype);fputc('U',fp);fputc(val,fp); fwrite(slicetype,1,val,fp);break;}
					case 18: {unsigned char val=strlen(lunit);fputc('U',fp);fputc(val,fp); fwrite(lunit,1,val,fp);break;}
					case 19: {unsigned char val=strlen(tunit);fputc('U',fp);fputc(val,fp); fwrite(tunit,1,val,fp);break;}
					case 20: {write_ubjsonint(&hdr.cal_max,1,sizeof(hdr.cal_max),fp);break;}
					case 21: {write_ubjsonint(&hdr.cal_min,1,sizeof(hdr.cal_min),fp);break;}
					case 22: {write_ubjsonint(&hdr.slice_duration,1,sizeof(hdr.slice_duration),fp);break;}
					case 23: {write_ubjsonint(&hdr.toffset,1,sizeof(hdr.toffset),fp);break;}
					case 24: {unsigned char val=strlen(hdr.descrip);fputc('U',fp);fputc(val,fp); fwrite(hdr.descrip,1,val,fp);break;}
					case 25: {unsigned char val=strlen(hdr.aux_file);fputc('U',fp);fputc(val,fp); fwrite(hdr.aux_file,1,val,fp);break;}
					case 26: {write_ubjsonint(&hdr.qform_code,sizeof(hdr.qform_code),1,fp);break;}
					case 27: {write_ubjsonint(&hdr.sform_code,sizeof(hdr.sform_code),1,fp);break;}
					case 28: {write_ubjsonint(&hdr.quatern_b,1,sizeof(hdr.quatern_b),fp);break;}
					case 29: {write_ubjsonint(&hdr.quatern_c,1,sizeof(hdr.quatern_c),fp);break;}
					case 30: {write_ubjsonint(&hdr.quatern_d,1,sizeof(hdr.quatern_d),fp);break;}
					case 31: {write_ubjsonint(&hdr.qoffset_x,1,sizeof(hdr.qoffset_x),fp);break;}
					case 32: {write_ubjsonint(&hdr.qoffset_y,1,sizeof(hdr.qoffset_y),fp);break;}
					case 33: {write_ubjsonint(&hdr.qoffset_z,1,sizeof(hdr.qoffset_z),fp);break;}
					case 34: {
						write_ubjsonint(&hdr.srow_x[0],4,sizeof(hdr.srow_x[0]),fp);
						write_ubjsonint(&hdr.srow_y[0],4,sizeof(hdr.srow_y[0]),fp);
						write_ubjsonint(&hdr.srow_z[0],4,sizeof(hdr.srow_z[0]),fp);
						break;
					}
					case 35: {unsigned char val=strlen(hdr.intent_name);fputc('U',fp);fputc(val,fp); fwrite(hdr.intent_name,1,val,fp);break;}
					case 36: {unsigned char val=strlen(hdr.magic);fputc('U',fp);fputc(val,fp); fwrite(hdr.magic,1,val,fp);break;}
					case 37: {int val=hdr.vox_offset;write_ubjsonint(&val, sizeof(val), 1,fp);break;}
					case 38: {unsigned char val=strlen(jdtype);fputc('U',fp);fputc(val,fp); fwrite(jdtype,1,val,fp);break;}
					case 39: {fputc(ndim,fp);break;}
					case 40: {
						write_ubjsonint(dim, sizeof(dim[0]), ndim, fp);
						if(!opts.isGz){
							const char *datastub="U\x0b_ArrayData_[$";
							fwrite(datastub,1,strlen(datastub),fp);
							fputc(jdatamarker,fp);
							fputc('#',fp);

							size_t totalelem=(totalbytes/(hdr.bitpix>>3));
							unsigned int clen=totalelem;
							if((size_t)clen==totalelem){
								fputc('l',fp);
								write_ubjsonint(&clen, sizeof(clen), 1,fp);
							}else{
								fputc('L',fp);
								write_ubjsonint(&totalelem, sizeof(totalelem), 1,fp);
							}
							fwrite(im,1,totalbytes,fp);
							fputc('}',fp); // end of NIFTIData
							fputc('}',fp); // end of the root object
						}
						break;
					}
#ifdef Z_DEFLATED
					case 41: {fputc('U',fp);fputc(4,fp);fwrite("zlib",1,4,fp);break;}
					case 42: {unsigned int val=(totalbytes/(hdr.bitpix>>3));write_ubjsonint(&val,sizeof(val), 1,fp);break;}
					case 43:
						ret=zmat_run(totalbytes, im, &compressedbytes, (unsigned char **)&compressed, zmZlib, &status, -opts.gzLevel);
						if(!ret){
							unsigned int clen=compressedbytes;
							if((size_t)clen==compressedbytes){
								fputc('l',fp);
								write_ubjsonint(&clen, sizeof(clen), 1,fp);
							}else{
								fputc('L',fp);
								write_ubjsonint(&compressedbytes, sizeof(compressedbytes), 1,fp);
							}
							fwrite(compressed,1,compressedbytes,fp);
						}else{
							printError("Failed to compress data stream, error code=%d, status code=%d\n", ret, status);
							return EXIT_FAILURE;
						}
						if(compressed)
							free(compressed);
						break;
#endif
				}
				if(!opts.isGz && slotid==40)
					break;
			}
		}
	}
	fclose(fp);
	return EXIT_SUCCESS;
}

int nii_savejnii(char *niiFilename, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts, struct TDICOMdata d, struct TDTI4D *dti4D, int numDTI) {
// JNIfTI is a JSON wrapper to the NIfTI-1/2 format, supports both plain-text (.jnii) and binary (.bnii) formats
// Specification:  https://github.com/NeuroJSON/jnifti/blob/master/JNIfTI_specification.md
// jnii is a plain JSON file and can be parsed in nearly all JSON parsers; to decode the
// embedded binary data as strings, the NIFTIData section can be be parsed in MATLAB using
// jnifty (https://github.com/NeuroJSON/jnifty) and Python using jdata (https://github.com/NeuroJSON/pyjdata)

	FILE *fp;
	int dim[8]={0}, ndim=0;  /* extra dimension in dim to hold the split data from complex voxel types, such as complex64 */

	cJSON *root=NULL, *info=NULL, *jhdr=NULL, *dat=NULL, *sub=NULL;
	char *jsonstr=NULL;
	size_t compressedbytes, totalbytes;
	unsigned char *compressed=NULL, *buf=NULL;

	/*jnifti converts code-based header fields to human-readable/standardized strings*/
	int datatypeidx;
	const char *datatypestr[]={"uint8","int16","int32","single","complex64","double",
				"rgb24" ,"int8","uint16","uint32","int64","uint64",
				"double128","complex128","complex256","rgba32",""};
	const char *jdatatypestr[]={"uint8","int16","int32","single","double","double",
				"uint8" ,"int8","uint16","uint32","int64","uint64",
				"uint8","double","uint8","uint8","uint8"};
	const char jdatamarker[]={'U','I','l','d','D','D','U','i','u','m','L','M',
				'U','D','U','U','U'};
	unsigned char jdataelemlen[]={1,1,1,1,2,1,3,1,1,1,1,1,16,2,32,4,1};
	int datatypeid[]={NIFTI_TYPE_UINT8,NIFTI_TYPE_INT16,NIFTI_TYPE_INT32,
				NIFTI_TYPE_FLOAT32,NIFTI_TYPE_COMPLEX64,NIFTI_TYPE_FLOAT64,
				NIFTI_TYPE_RGB24,NIFTI_TYPE_INT8,NIFTI_TYPE_UINT16,
				NIFTI_TYPE_UINT32,NIFTI_TYPE_INT64,NIFTI_TYPE_UINT64,
				NIFTI_TYPE_FLOAT128,NIFTI_TYPE_COMPLEX128,
				NIFTI_TYPE_COMPLEX256,NIFTI_TYPE_RGBA32};

	int lunitidx, tunitidx;
	const char *unitstr[]={"m","mm","um","s","ms","us","hz","ppm","rad",""};
	int unitid[]={NIFTI_UNITS_METER,NIFTI_UNITS_MM,NIFTI_UNITS_MICRON,
				NIFTI_UNITS_SEC,NIFTI_UNITS_MSEC,NIFTI_UNITS_USEC,
				NIFTI_UNITS_HZ,NIFTI_UNITS_PPM,NIFTI_UNITS_RADS};

	int slicetypeidx;
	const char *slicetypestr[]={"","seq+","seq-","alt+","alt-","alt2+","alt2-",""};
	int slicetypeid[]={NIFTI_SLICE_UNKNOWN,NIFTI_SLICE_SEQ_INC,
				NIFTI_SLICE_SEQ_DEC,NIFTI_SLICE_ALT_INC,NIFTI_SLICE_ALT_DEC,
				NIFTI_SLICE_ALT_INC2,NIFTI_SLICE_ALT_DEC2};

	int intentidx;
	const char *intentstr[]={"","corr","ttest","ftest","zscore","chi2","beta","binomial",
				"gamma","poisson","normal","ncftest","ncchi2","logistic","laplace",
				"uniform","ncttest","weibull","chi","invgauss","extval","pvalue",
				"logpvalue","log10pvalue","estimate","label","neuronames","matrix",
				"symmatrix","dispvec","vector","point","triangle","quaternion",
				"unitless","tseries","elem","rgb","rgba","shape",""};
	int intentid[]={NIFTI_INTENT_NONE,NIFTI_INTENT_CORREL,NIFTI_INTENT_TTEST,
				NIFTI_INTENT_FTEST,NIFTI_INTENT_ZSCORE,NIFTI_INTENT_CHISQ,
				NIFTI_INTENT_BETA,NIFTI_INTENT_BINOM,NIFTI_INTENT_GAMMA,
				NIFTI_INTENT_POISSON,NIFTI_INTENT_NORMAL,NIFTI_INTENT_FTEST_NONC,
				NIFTI_INTENT_CHISQ_NONC,NIFTI_INTENT_LOGISTIC,NIFTI_INTENT_LAPLACE,
				NIFTI_INTENT_UNIFORM,NIFTI_INTENT_TTEST_NONC,NIFTI_INTENT_WEIBULL,
				NIFTI_INTENT_CHI,NIFTI_INTENT_INVGAUSS,NIFTI_INTENT_EXTVAL,
				NIFTI_INTENT_PVAL,NIFTI_INTENT_LOGPVAL,NIFTI_INTENT_LOG10PVAL,
				NIFTI_INTENT_ESTIMATE,NIFTI_INTENT_LABEL,NIFTI_INTENT_NEURONAME,
				NIFTI_INTENT_GENMATRIX,NIFTI_INTENT_SYMMATRIX,NIFTI_INTENT_DISPVECT,
				NIFTI_INTENT_VECTOR,NIFTI_INTENT_POINTSET,NIFTI_INTENT_TRIANGLE,
				NIFTI_INTENT_QUATERNION,NIFTI_INTENT_DIMLESS,NIFTI_INTENT_TIME_SERIES,
				NIFTI_INTENT_NODE_INDEX,NIFTI_INTENT_RGB_VECTOR,NIFTI_INTENT_RGBA_VECTOR,
				NIFTI_INTENT_SHAPE};
	char fname[2048] = {""};
	strcpy(fname, niiFilename);
	if (opts.saveFormat == kSaveFormatBNII)
		strcat(fname, ".bnii");
	else
		strcat(fname, ".jnii");

	/* preprocess nifti header to convert to human-readable jnifti fields */
	totalbytes=nii_ImgBytes(hdr);
	ndim=hdr.dim[0];
	for(int i=1;i<8;i++)
		dim[i-1]=hdr.dim[i];

	datatypeidx=jnifti_lookup(datatypeid, sizeof(datatypeid)/sizeof(int), hdr.datatype);
	slicetypeidx=jnifti_lookup(slicetypeid, sizeof(slicetypeid)/sizeof(int), hdr.slice_code);
	intentidx=jnifti_lookup(intentid, sizeof(intentid)/sizeof(int), hdr.intent_code);
	lunitidx=sizeof(unitid)/sizeof(unitid[0]);
	tunitidx=sizeof(unitid)/sizeof(unitid[0]);
	for(int i=0;i<sizeof(unitid)/sizeof(unitid[0]);i++){
		if(XYZT_TO_SPACE(hdr.xyzt_units)==unitid[i])
			lunitidx=i;
		else if(XYZT_TO_TIME(hdr.xyzt_units)==unitid[i])
			tunitidx=i;
	}

	if (opts.saveFormat == kSaveFormatBNII)
		return nii_savebnii(fname, hdr, im, opts, (unsigned char)ndim, totalbytes,
					datatypestr[datatypeidx], slicetypestr[slicetypeidx],
					intentstr[intentidx], unitstr[lunitidx], unitstr[tunitidx],
					jdatatypestr[datatypeidx], jdataelemlen[datatypeidx], jdatamarker[datatypeidx]);

	root=cJSON_CreateObject();

	/* write the "NIFTIHeader" section */
	cJSON_AddItemToObject(root, "_DataInfo_", info = cJSON_CreateObject());
	cJSON_AddStringToObject(info, "JNIFTIVersion", "0.5");
	cJSON_AddStringToObject(info, "Comment", "Created by dcm2niix and NeuroJSON (http://neurojson.org)");
	cJSON_AddStringToObject(info, "AnnotationFormat", "https://github.com/NeuroJSON/jnifti/blob/master/JNIfTI_specification.md");
	cJSON_AddStringToObject(info, "SerialFormat", "http://json.org");
	cJSON_AddItemToObject(info, "Parser", sub = cJSON_CreateObject());
	cJSON_AddStringToObject(sub, "Python", "https://pypi.org/project/jdata\thttps://pypi.org/project/bjdata");
	cJSON_AddStringToObject(sub, "MATLAB", "https://github.com/NeuroJSON/jnifty");
	cJSON_AddStringToObject(sub, "JavaScript", "https://github.com/NeuroJSON/jsdata");

	cJSON_AddItemToObject(root, "NIFTIHeader", jhdr = cJSON_CreateObject());
	cJSON_AddNumberToObject(jhdr, "NIIHeaderSize", hdr.sizeof_hdr);
	cJSON_AddItemToObject(jhdr, "Dim", cJSON_CreateIntArray(dim,ndim));
	cJSON_AddNumberToObject(jhdr, "Param1", hdr.intent_p1);
	cJSON_AddNumberToObject(jhdr, "Param2", hdr.intent_p2);
	cJSON_AddNumberToObject(jhdr, "Param3", hdr.intent_p3);
	cJSON_AddStringToObject(jhdr, "Intent", intentstr[intentidx]);
	cJSON_AddStringToObject(jhdr, "DataType", datatypestr[datatypeidx]);
	cJSON_AddNumberToObject(jhdr, "BitDepth", hdr.bitpix);
	cJSON_AddNumberToObject(jhdr, "FirstSliceID", hdr.slice_start);
	cJSON_AddItemToObject(jhdr, "VoxelSize", cJSON_CreateFloatArray(hdr.pixdim+1,ndim));
	cJSON_AddItemToObject(jhdr, "Orientation", sub=cJSON_CreateObject());
	if((int)hdr.pixdim[0])
		cJSON_AddStringToObject(sub, "x", "l");
	else
		cJSON_AddStringToObject(sub, "x", "r");
	cJSON_AddStringToObject(sub, "y", "a");
	cJSON_AddStringToObject(sub, "z", "s");
	cJSON_AddNumberToObject(jhdr, "ScaleSlope", hdr.scl_slope);
	cJSON_AddNumberToObject(jhdr, "ScaleOffset", hdr.scl_inter);
	cJSON_AddNumberToObject(jhdr, "LastSliceID", hdr.slice_end);

	cJSON_AddStringToObject(jhdr, "SliceType", slicetypestr[slicetypeidx]);
	cJSON_AddItemToObject(jhdr, "Unit", sub=cJSON_CreateObject());
	cJSON_AddStringToObject(sub, "L", unitstr[lunitidx]);
	cJSON_AddStringToObject(sub, "T", unitstr[tunitidx]);
	for(int i=0;i<sizeof(unitid)/sizeof(unitid[0]);i++){
		if(hdr.xyzt_units>=NIFTI_UNITS_HZ && hdr.xyzt_units==unitid[i])
			cJSON_AddStringToObject(sub, "Special", unitstr[i]);
	}
	cJSON_AddNumberToObject(jhdr, "MaxIntensity", hdr.cal_max);
	cJSON_AddNumberToObject(jhdr, "MinIntensity", hdr.cal_min);
	cJSON_AddNumberToObject(jhdr, "SliceTime", hdr.slice_duration);
	cJSON_AddNumberToObject(jhdr, "TimeOffset", hdr.toffset);
	cJSON_AddStringToObject(jhdr, "Description", hdr.descrip);
	cJSON_AddStringToObject(jhdr, "AuxFile", hdr.aux_file);
	cJSON_AddNumberToObject(jhdr, "QForm", hdr.qform_code);
	cJSON_AddNumberToObject(jhdr, "SForm", hdr.sform_code);
	cJSON_AddItemToObject(jhdr, "Quatern", sub=cJSON_CreateObject());
	cJSON_AddNumberToObject(sub, "b", hdr.quatern_b);
	cJSON_AddNumberToObject(sub, "c", hdr.quatern_c);
	cJSON_AddNumberToObject(sub, "d", hdr.quatern_d);
	cJSON_AddItemToObject(jhdr, "QuaternOffset", sub=cJSON_CreateObject());
	cJSON_AddNumberToObject(sub, "x", hdr.qoffset_x);
	cJSON_AddNumberToObject(sub, "y", hdr.qoffset_y);
	cJSON_AddNumberToObject(sub, "z", hdr.qoffset_z);
	cJSON_AddItemToObject(jhdr, "Affine", sub=cJSON_CreateArray());
	cJSON_AddItemToArray(sub, cJSON_CreateFloatArray(hdr.srow_x,4));
	cJSON_AddItemToArray(sub, cJSON_CreateFloatArray(hdr.srow_y,4));
	cJSON_AddItemToArray(sub, cJSON_CreateFloatArray(hdr.srow_z,4));
	cJSON_AddStringToObject(jhdr, "Name", hdr.intent_name);
	cJSON_AddStringToObject(jhdr, "NIIFormat", hdr.magic);

	/* save depreciated header flags if non-trival values are provided */
	if(hdr.vox_offset)
		cJSON_AddNumberToObject(jhdr, "NIIByteOffset", hdr.vox_offset);
	if(strlen(hdr.data_type))
		cJSON_AddStringToObject(jhdr, "A75DataTypeName", hdr.data_type);
	if(strlen(hdr.db_name))
		cJSON_AddStringToObject(jhdr, "A75DBName", hdr.db_name);
	if(hdr.extents)
		cJSON_AddNumberToObject(jhdr, "A75Extends", hdr.extents);
	if(hdr.session_error)
		cJSON_AddNumberToObject(jhdr, "A75SessionError", hdr.session_error);
	if(hdr.regular)
		cJSON_AddNumberToObject(jhdr, "A75DataTypeName", hdr.regular);
	if(hdr.glmax)
		cJSON_AddNumberToObject(jhdr, "A75GlobalMax", hdr.glmax);
	if(hdr.glmin)
		cJSON_AddNumberToObject(jhdr, "A75GlobalMin", hdr.glmin);

	/* the "NIFTIData" section stores volumetric data */
	cJSON_AddItemToObject(root, "NIFTIData",dat = cJSON_CreateObject());
	cJSON_AddStringToObject(dat,"_ArrayType_",jdatatypestr[datatypeidx]);
	if(jdataelemlen[datatypeidx]>1)
		dim[ndim++]=jdataelemlen[datatypeidx];
	cJSON_AddItemToObject(dat,  "_ArraySize_",cJSON_CreateIntArray(dim,ndim));
	cJSON_AddStringToObject(dat,"_ArrayOrder_","c"); // NIfTI array is column-major

#ifdef Z_DEFLATED
	if(opts.isGz){
		int ret=0, status=0;
		cJSON_AddStringToObject(dat, "_ArrayZipType_", "zlib");
		cJSON_AddNumberToObject(dat, "_ArrayZipSize_",totalbytes/(hdr.bitpix>>3));

		ret=zmat_run(totalbytes, im, &compressedbytes, (unsigned char **)&compressed, zmZlib, &status, -opts.gzLevel);

		if(!ret){
			ret=zmat_run(compressedbytes, compressed, &totalbytes, (unsigned char **)&buf, zmBase64, &status,1);
			cJSON_AddStringToObject(dat,  "_ArrayZipData_",(const char *)buf);
		}else{
			printError("Failed to compress data stream, error code=%d, status code=%d\n", ret, status);
			return EXIT_FAILURE;
		}
		if(compressed)
			free(compressed);
	}else{
		cJSON_AddStringToObject(dat, "_ArrayZipType_", "base64");
		cJSON_AddNumberToObject(dat, "_ArrayZipSize_",totalbytes/(hdr.bitpix>>3));
		buf=base64_encode(im, totalbytes, &compressedbytes);
		cJSON_AddStringToObject(dat,"_ArrayZipData_", (const char*)buf);
	}
#else
	cJSON_AddStringToObject(dat, "_ArrayZipType_", "base64");
	cJSON_AddNumberToObject(dat, "_ArrayZipSize_",totalbytes/(hdr.bitpix>>3));
	buf=base64_encode(im, totalbytes, &compressedbytes);
	cJSON_AddStringToObject(dat,"_ArrayZipData_", (const char*)buf);
#endif
	if(buf)
		free(buf);

	/* now save JSON to file */
	jsonstr=cJSON_Print(root);
	if(jsonstr==NULL){
		printMessage("Error: error when converting to JNIfTI\n");
		return EXIT_FAILURE;
	}

	fp=fopen(fname,"wt");
	if(fp==NULL){
		printMessage("Error: error when writing to JNIfTI file\n");
		return EXIT_FAILURE;
	}
	fprintf(fp,"%s\n",jsonstr);
	fclose(fp);

	if(jsonstr)
		free(jsonstr);
	if(root)
		cJSON_Delete(root);
	return EXIT_SUCCESS;
} // nii_savejnii()
#endif //#ifdef myEnableJNIFTI

int nii_saveForeign(char *niiFilename, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts, struct TDICOMdata d, struct TDTI4D *dti4D, int numDTI) {
	if (opts.saveFormat == kSaveFormatMGH)
		return nii_saveMGH(niiFilename, hdr, im, opts, d, dti4D, numDTI);
	#ifdef myEnableJNIFTI
	else if (opts.saveFormat == kSaveFormatJNII || opts.saveFormat == kSaveFormatBNII)
		return nii_savejnii(niiFilename, hdr, im, opts, d, dti4D, numDTI);
	#endif
	return nii_saveNRRD(niiFilename, hdr, im, opts, d, dti4D, numDTI);
}// nii_saveForeign()

#endif

void removeSclSlopeInter(struct nifti_1_header *hdr, unsigned char *img) {
	//NRRD does not have scl_slope scl_inter. Adjust data if possible
	// https://discourse.slicer.org/t/preserve-image-rescale-and-slope-when-saving-in-nrrd-file/13357
	if (isSameFloat(hdr->scl_inter, 0.0) && isSameFloat(hdr->scl_slope, 1.0))
		return;
	if ((!isSameFloat(fmod(hdr->scl_inter, 1.0f), 0.0)) || (!isSameFloat(fmod(hdr->scl_slope, 1.0f), 0.0)))
		return;
	int nVox = 1;
	for (int i = 1; i < 8; i++)
		if (hdr->dim[i] > 1)
			nVox = nVox * hdr->dim[i];
	if (hdr->datatype == DT_INT16) {
		int16_t *img16 = (int16_t *)img;
		int16_t mn, mx;
		mn = img16[0];
		mx = mn;
		for (int i = 0; i < nVox; i++) {
			mn = min(mn, img16[i]);
			mx = max(mx, img16[i]);
		}
		float v = (mn * hdr->scl_slope) + hdr->scl_inter;
		if ((v < -32768) || (v > 32767))
			return;
		v = (mx * hdr->scl_slope) + hdr->scl_inter;
		if ((v < -32768) || (v > 32767))
			return;
		for (int i = 0; i < nVox; i++)
			img16[i] = round((img16[i] * hdr->scl_slope) + hdr->scl_inter);
		hdr->scl_slope = 1.0;
		hdr->scl_inter = 0.0;
		return;
	}
	if (hdr->datatype == DT_UINT16) {
		uint16_t *img16 = (uint16_t *)img;
		uint16_t mn, mx;
		mn = img16[0];
		mx = mn;
		for (int i = 0; i < nVox; i++) {
			mn = min(mn, img16[i]);
			mx = max(mx, img16[i]);
		}
		float v = (mn * hdr->scl_slope) + hdr->scl_inter;
		if ((v < 0) || (v > 65535))
			return;
		v = (mx * hdr->scl_slope) + hdr->scl_inter;
		if ((v < 0) || (v > 65535))
			return;
		for (int i = 0; i < nVox; i++)
			img16[i] = round((img16[i] * hdr->scl_slope) + hdr->scl_inter);
		hdr->scl_slope = 1.0;
		hdr->scl_inter = 0.0;
		return;
	}
	//printWarning("NRRD unable to record scl_slope/scl_inter %g/%g\n", hdr->scl_slope, hdr->scl_inter);
}

int nii_saveNII(char *niiFilename, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts, struct TDICOMdata d) {
#ifdef USING_R
	ImageList *images = (ImageList *)opts.imageList;
    if (opts.isImageInMemory) {
        hdr.vox_offset = 352;
        // Extract the basename from the full file path
        char *start = niiFilename + strlen(niiFilename);
        while (start >= niiFilename && *start != '/' && *start != kPathSeparator)
            start--;
        std::string name(++start);
        nifti_image *image = nifti_convert_nhdr2nim(hdr, niiFilename);
        if (image == NULL)
            return EXIT_FAILURE;
        image->data = (void *)im;
        images->append(image, name);
        free(image);
        return EXIT_SUCCESS;
    }
#else
	if (opts.isOnlyBIDS)
		return EXIT_SUCCESS;
	if (opts.saveFormat != kSaveFormatNIfTI) {
		struct TDTI4D *dti4D = (struct TDTI4D *)malloc(sizeof(struct TDTI4D));
		int ret = nii_saveForeign(niiFilename, hdr, im, opts, d, dti4D, 0);
		free(dti4D);
		return ret;
	}
#endif
	hdr.vox_offset = 352;
	size_t imgsz = nii_ImgBytes(hdr);
	if (imgsz < 1) {
		printMessage("Error: Image size is zero bytes %s\n", niiFilename);
		return EXIT_FAILURE;
	}
#ifndef myDisableGzSizeLimits
	//see https://github.com/rordenlab/dcm2niix/issues/124
	uint64_t kMaxPigz = 4294967264;
//https://stackoverflow.com/questions/5272825/detecting-64bit-compile-in-c
#ifndef UINTPTR_MAX
	uint64_t kMaxGz = 2147483647;
#elif UINTPTR_MAX == 0xffffffff
	uint64_t kMaxGz = 2147483647;
#elif UINTPTR_MAX == 0xffffffffffffffff
	uint64_t kMaxGz = kMaxPigz;
#else
	compiler error : unable to determine is 32 or 64 bit
#endif
#ifndef myDisableZLib
	if ((opts.isGz) && (strlen(opts.pigzname) < 1) && ((imgsz + hdr.vox_offset) >= kMaxGz)) { //use internal compressor
		printWarning("Saving uncompressed data: internal compressor unable to process such large files.\n");
		if ((imgsz + hdr.vox_offset) < kMaxPigz)
			printWarning(" Hint: using external compressor (pigz) should help.\n");
	} else if ((opts.isGz) && (strlen(opts.pigzname) < 1) && ((imgsz + hdr.vox_offset) < kMaxGz)) { //use internal compressor
		if (!opts.isSaveNativeEndian)
			swapEndian(&hdr, im, true); //byte-swap endian (e.g. little->big)
		writeNiiGz(niiFilename, hdr, im, imgsz, opts.gzLevel, false);
#ifdef USING_R
		images->appendPath(std::string(niiFilename) + ".nii.gz");
#endif
		if (!opts.isSaveNativeEndian)
			swapEndian(&hdr, im, false); //unbyte-swap endian (e.g. big->little)
		return EXIT_SUCCESS;
	}
#endif
#endif
	char fname[2048] = {""};
	strcpy(fname, niiFilename);
	strcat(fname, ".nii");
#if defined(_WIN64) || defined(_WIN32)
	if ((opts.isGz) && (opts.isPipedGz))
		printWarning("The 'optimal' piped gz is only available for Unix\n");
#else //if windows else Unix
	if ((opts.isGz) && (opts.isPipedGz) && (strlen(opts.pigzname) > 0)) {
		//piped gz
		if (opts.isVerbose)
			printMessage(" Optimal piped gz will fail if pigz version < 2.3.4.\n");
		char command[768];
		strcpy(command, "\"");
		strcat(command, opts.pigzname);
		if ((opts.gzLevel > 0) && (opts.gzLevel < 12)) {
			char newstr[256];
			snprintf(newstr, 256, "\" -n -f -%d > \"", opts.gzLevel);
			//749 snprintf(newstr, 256, "\" -n -f -%d > '", opts.gzLevel);
			strcat(command, newstr);
		} else
			strcat(command, "\" -n -f > \""); //current versions of pigz (2.3) built on Windows can hang if the filename is included, presumably because it is not finding the path characters ':\'
			//749 strcat(command, "\" -n -f > '"); //current versions of pigz (2.3) built on Windows can hang if the filename is included, presumably because it is not finding the path characters ':\'
		strcat(command, fname);
		//issue749 single not double quotes so $ character does not cause issues
		//749 strcat(command, ".gz'"); //add quotes in case spaces in filename 'pigz "c:\my dir\img.nii"'
		strcat(command, ".gz\""); //add quotes in case spaces in filename 'pigz "c:\my dir\img.nii"'
		if (opts.isVerbose)
			printMessage("Compress: %s\n", command);
		FILE *pigzPipe;
		if ((pigzPipe = popen(command, "w")) == NULL) {
			printError("Unable to open pigz pipe\n");
			return EXIT_FAILURE;
		}
		if (!opts.isSaveNativeEndian)
			swapEndian(&hdr, im, true); //byte-swap endian (e.g. little->big)
		fwrite(&hdr, sizeof(hdr), 1, pigzPipe);
		uint32_t pad = 0;
		fwrite(&pad, sizeof(pad), 1, pigzPipe);
		fwrite(&im[0], imgsz, 1, pigzPipe);
		pclose(pigzPipe);
		if (!opts.isSaveNativeEndian)
			swapEndian(&hdr, im, false); //unbyte-swap endian (e.g. big->little)
		return EXIT_SUCCESS;
	}
#endif

#ifndef USING_DCM2NIIXFSWRAPPER
	FILE *fp = fopen(fname, "wb");
	if (!fp)
		return EXIT_FAILURE;
	if (!opts.isSaveNativeEndian)
		swapEndian(&hdr, im, true); //byte-swap endian (e.g. little->big)
	fwrite(&hdr, sizeof(hdr), 1, fp);
	uint32_t pad = 0;
	fwrite(&pad, sizeof(pad), 1, fp);
	fwrite(&im[0], imgsz, 1, fp);
	fclose(fp);

	if (!opts.isSaveNativeEndian)
		swapEndian(&hdr, im, false); //unbyte-swap endian (e.g. big->little)
#endif

#ifdef USING_R
	images->appendPath(fname);
#else
	if ((opts.isGz) && (strlen(opts.pigzname) > 0)) {
#ifndef myDisableGzSizeLimits
		if ((imgsz + hdr.vox_offset) > kMaxPigz) {
			printWarning("Saving uncompressed data: image too large for pigz.\n");
			return EXIT_SUCCESS;
		}
#endif
		return pigz_File(fname, opts, imgsz);
	}
#endif
	return EXIT_SUCCESS;
} // nii_saveNII()

int nii_saveNIIx(char *niiFilename, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts) {
	struct TDICOMdata dcm = clear_dicom_data();
	return nii_saveNII(niiFilename, hdr, im, opts, dcm);
}

int nii_saveNII3D(char *niiFilename, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts, struct TDICOMdata d) {
	//save 4D series as sequence of 3D volumes
	struct nifti_1_header hdr1 = hdr;
	int nVol = 1;
	for (int i = 4; i < 8; i++) {
		if (hdr.dim[i] > 1)
			nVol = nVol * hdr.dim[i];
		hdr1.dim[i] = 0;
	}
	hdr1.dim[0] = 3; //save as 3D file
	size_t imgsz = nii_ImgBytes(hdr1);
	size_t pos = 0;
	char fname[2048] = {""};
	char zeroPad[PATH_MAX] = {""};
	double fnVol = nVol;
	int zeroPadLen = (1 + log10(fnVol));
	snprintf(zeroPad, PATH_MAX, "%%s_%%0%dd", zeroPadLen);
	for (int i = 1; i <= nVol; i++) {
		snprintf(fname, 2048, zeroPad, niiFilename, i);
		if (nii_saveNII(fname, hdr1, (unsigned char *)&im[pos], opts, d) == EXIT_FAILURE)
			return EXIT_FAILURE;
		pos += imgsz;
	}
	return EXIT_SUCCESS;
} // nii_saveNII3D()

void nii_storeIntegerScaleFactor(int scale, struct nifti_1_header *hdr) {
	//appends NIfTI header description field with " isN" where N is integer scaling
	char newstr[256];
	snprintf(newstr, 256, " is%d", scale);
	if ((strlen(newstr) + strlen(hdr->descrip)) < 80)
		strcat(hdr->descrip, newstr);
}

int int12toint16(int U12) {
	return (short)(U12 & 0xFFF) - ((U12 & 0x800) << 1);
}

void nii_mask12bit(unsigned char *img, struct nifti_1_header *hdr, bool isSigned) {
	//https://github.com/rordenlab/dcm2niix/issues/251
	if (hdr->datatype != DT_INT16)
		return;
	int dim3to7 = 1;
	for (int i = 3; i < 8; i++)
		if (hdr->dim[i] > 1)
			dim3to7 = dim3to7 * hdr->dim[i];
	int nVox = hdr->dim[1] * hdr->dim[2] * dim3to7;
	if (nVox < 1)
		return;
	int16_t *img16 = (int16_t *)img;
	//issue 688
	if (isSigned) {
		for (int i = 0; i < nVox; i++)
			img16[i] = int12toint16(img16[i]); //signed 12 bit data ranges from 0..4095, any other values are overflow
	
	} else {
		for (int i = 0; i < nVox; i++)
			img16[i] = img16[i] & 4095; //12 bit data ranges from 0..4095, any other values are overflow
	}
}

unsigned char * nii_uint16toFloat32(unsigned char *img, struct nifti_1_header *hdr, int isVerbose) {
	if (hdr->datatype != DT_UINT16)
		return img;
	int dim3to7 = 1;
	for (int i = 3; i < 8; i++)
		if (hdr->dim[i] > 1)
			dim3to7 = dim3to7 * hdr->dim[i];
	int nVox = hdr->dim[1] * hdr->dim[2] * dim3to7;
	if (nVox < 1)
		return img;
	unsigned short *img16 = (unsigned short *)img;
	unsigned char *imOut = (unsigned char *)malloc(nVox * 4); // *4 as 32-bits per voxel, sizeof(float) )
	float *imOut32 = (float *)imOut;
	for (int i = 0; i < nVox; i++)
		imOut32[i] = (hdr->scl_slope * img16[i]) + hdr->scl_inter;
	free(img);
	hdr->scl_slope = 1.0;
	hdr->scl_inter = 1.0;
	hdr->datatype = DT_FLOAT32;
	hdr->bitpix = 32;
	if (isVerbose)
		printMessage("Converted uint16 to float32\n");
	return imOut;
} // nii_uint16toFloat32()

void nii_scale16bitSigned(unsigned char *img, struct nifti_1_header *hdr, int isVerbose) {
	//lossless scaling of INT16 data: e.g. input with range -100...3200 and scl_slope=1
	// will be stored as -1000...32000 with scl_slope 0.1
	if (hdr->datatype != DT_INT16)
		return;
	int dim3to7 = 1;
	for (int i = 3; i < 8; i++)
		if (hdr->dim[i] > 1)
			dim3to7 = dim3to7 * hdr->dim[i];
	int nVox = hdr->dim[1] * hdr->dim[2] * dim3to7;
	if (nVox < 1)
		return;
	int16_t *img16 = (int16_t *)img;
	int16_t max16 = img16[0];
	int16_t min16 = max16;
	for (int i = 0; i < nVox; i++) {
		if (img16[i] < min16)
			min16 = img16[i];
		if (img16[i] > max16)
			max16 = img16[i];
	}
	int kMx = 32000; //actually 32767 - maybe a bit of padding for interpolation ringing
	int scale = kMx / (int)max16;
	if (abs(min16) > max16)
		scale = kMx / (int)abs(min16);
	if (scale < 2) {
		if (isVerbose)
			printMessage("Sufficient 16-bit range: raw %d..%d\n", min16, max16);
		return; //already uses dynamic range
	}
	hdr->scl_slope = hdr->scl_slope / scale;
	for (int i = 0; i < nVox; i++)
		img16[i] = img16[i] * scale;
	printMessage("Maximizing 16-bit range: raw %d..%d is%d\n", min16, max16, scale);
	nii_storeIntegerScaleFactor(scale, hdr);
}

void nii_scale16bitUnsigned(unsigned char *img, struct nifti_1_header *hdr, int isVerbose) {
	//lossless scaling of UINT16 data: e.g. input with range 0...3200 and scl_slope=1
	// will be stored as 0...64000 with scl_slope 0.05
	if (hdr->datatype != DT_UINT16)
		return;
	int dim3to7 = 1;
	for (int i = 3; i < 8; i++)
		if (hdr->dim[i] > 1)
			dim3to7 = dim3to7 * hdr->dim[i];
	int nVox = hdr->dim[1] * hdr->dim[2] * dim3to7;
	if (nVox < 1)
		return;
	uint16_t *img16 = (uint16_t *)img;
	uint16_t max16 = img16[0];
	for (int i = 0; i < nVox; i++)
		if (img16[i] > max16)
			max16 = img16[i];
	int kMx = 64000; //actually 65535 - maybe a bit of padding for interpolation ringing
	int scale = kMx / (int)max16;
	if (scale < 2) {
		if (isVerbose > 0)
			printMessage("Sufficient unsigned 16-bit range: raw max %d\n", max16);
		return; //already uses dynamic range
	}
	hdr->scl_slope = hdr->scl_slope / scale;
	for (int i = 0; i < nVox; i++)
		img16[i] = img16[i] * scale;
	printMessage("Maximizing 16-bit range: raw max %d is%d\n", max16, scale);
	nii_storeIntegerScaleFactor(scale, hdr);
}

#define UINT16_TO_INT16_IF_LOSSLESS
#ifdef UINT16_TO_INT16_IF_LOSSLESS
void nii_check16bitUnsigned(unsigned char *img, struct nifti_1_header *hdr, int isVerbose) {
	//default NIfTI 16-bit is signed, set to unusual 16-bit unsigned if required...
	if (hdr->datatype != DT_UINT16)
		return;
	int dim3to7 = 1;
	for (int i = 3; i < 8; i++)
		if (hdr->dim[i] > 1)
			dim3to7 = dim3to7 * hdr->dim[i];
	int nVox = hdr->dim[1] * hdr->dim[2] * dim3to7;
	if (nVox < 1)
		return;
	unsigned short *img16 = (unsigned short *)img;
	unsigned short max16 = img16[0];
	//clock_t start = clock();
	for (int i = 0; i < nVox; i++)
		if (img16[i] > max16)
			max16 = img16[i];
	//printMessage("max16= %d vox=%d %fms\n",max16, nVox, ((double)(clock()-start))/1000);
	if (max16 > 32767) {
		if (isVerbose > 0)
			printMessage("Note: 16-bit UNSIGNED integer image. Some tools will convert to 32-bit.\n");
	} else {
		hdr->datatype = DT_INT16;
		printMessage("UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338\n");
	}
} //nii_check16bitUnsigned()
#else
void nii_check16bitUnsigned(unsigned char *img, struct nifti_1_header *hdr, int isVerbose) {
	if (hdr->datatype != DT_UINT16)
		return;
	if (isVerbose < 1)
		return;
	printMessage("Note: 16-bit UNSIGNED integer image. Some tools will convert to 32-bit.\n");
}
#endif

//void reportPos(struct TDICOMdata d1) {
//	printMessage("Instance\t%d\t0020,0032\t%g\t%g\t%g\n", d1.imageNum, d1.patientPosition[1],d1.patientPosition[2],d1.patientPosition[3]);
//}

int siemensCtKludge(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata dcmList[]) {
	//Siemens CT bug: when a user draws an open object graphics object onto a 2D slice this is appended as an additional image,
	//regardless of slice position. These images do not report number of positions in the volume, so we need tedious leg work to detect
	uint64_t indx0 = dcmSort[0].indx;
	if ((nConvert < 2) || (dcmList[indx0].manufacturer != kMANUFACTURER_SIEMENS) || (!isSameFloat(dcmList[indx0].TR, 0.0f)))
		return nConvert;
	float prevDx = 0.0;
	for (int i = 1; i < nConvert; i++) {
		float dx = intersliceDistance(dcmList[indx0], dcmList[dcmSort[i].indx]);
		if ((!isSameFloat(dx, 0.0f)) && (dx < prevDx)) {
			//for (int j = 1; j < nConvert; j++)
			//	reportPos(dcmList[dcmSort[j].indx]);
			printMessage("Slices skipped: image position not sequential, admonish your vendor (Siemens OOG?)\n");
			return i;
		}
		prevDx = dx;
	}
	return nConvert; //all images in sequential order
} // siemensCtKludge()

void adjustOriginForNegativeTilt(struct nifti_1_header *hdr, float shiftPxY) {
	if (hdr->sform_code > 0) {
		// Adjust the srow_* offsets using srow_y
		hdr->srow_x[3] -= shiftPxY * hdr->srow_y[0];
		hdr->srow_y[3] -= shiftPxY * hdr->srow_y[1];
		hdr->srow_z[3] -= shiftPxY * hdr->srow_y[2];
	}
	if (hdr->qform_code > 0) {
		// Adjust the quaternion offsets using quatern_* and pixdim
		mat44 mat = nifti_quatern_to_mat44(hdr->quatern_b, hdr->quatern_c, hdr->quatern_d,
			hdr->qoffset_x, hdr->qoffset_y, hdr->qoffset_z,
			hdr->pixdim[1], hdr->pixdim[2], hdr->pixdim[3], hdr->pixdim[0]);
		hdr->qoffset_x -= shiftPxY * mat.m[1][0];
		hdr->qoffset_y -= shiftPxY * mat.m[1][1];
		hdr->qoffset_z -= shiftPxY * mat.m[1][2];
	}
}

unsigned char *nii_saveNII3DtiltFloat32(char *niiFilename, struct nifti_1_header *hdr, unsigned char *im, struct TDCMopts opts, struct TDICOMdata d, float *sliceMMarray, float gantryTiltDeg, int manufacturer) {
	//correct for gantry tilt - http://www.mathworks.com/matlabcentral/fileexchange/24458-dicom-gantry-tilt-correction
	if (opts.isOnlyBIDS)
		return im;
	if (gantryTiltDeg == 0.0)
		return im;
	struct nifti_1_header hdrIn = *hdr;
	int nVox2DIn = hdrIn.dim[1] * hdrIn.dim[2];
	if ((nVox2DIn < 1) || (hdrIn.dim[0] != 3) || (hdrIn.dim[3] < 3))
		return im;
	if (hdrIn.datatype != DT_FLOAT32) {
		printMessage("Only able to correct gantry tilt for 16-bit integer or 32-bit float data with at least 3 slices.");
		return im;
	}
	printMessage("Gantry Tilt Correction is new: please validate conversions\n");
	float GNTtanPx = tan(gantryTiltDeg / (180 / M_PI)) / hdrIn.pixdim[2]; //tangent(degrees->radian)
//unintuitive step: reverse sign for negative gantry tilt, therefore -27deg == +27deg (why @!?#)
// seen in http://www.mathworks.com/matlabcentral/fileexchange/28141-gantry-detector-tilt-correction/content/gantry2.m
// also validated with actual data...
#ifndef newTilt
	if (manufacturer == kMANUFACTURER_PHILIPS) //see 'Manix' example from Osirix
		GNTtanPx = -GNTtanPx;
	else if ((manufacturer == kMANUFACTURER_SIEMENS) && (gantryTiltDeg > 0.0))
		GNTtanPx = -GNTtanPx;
	else if (manufacturer == kMANUFACTURER_GE)
		; //do nothing
	else if (gantryTiltDeg < 0.0)
		GNTtanPx = -GNTtanPx; //see Toshiba examples from John Muschelli
#endif //newTilt
	float *imIn32 = (float *)im;
	//create new output image: larger due to skew
	// compute how many pixels slice must be extended due to skew
	int s = hdrIn.dim[3] - 1; //top slice
	float maxSliceMM = fabs(s * hdrIn.pixdim[3]);
	if (sliceMMarray != NULL)
		maxSliceMM = fabs(sliceMMarray[s]);
	int pxOffset = ceil(fabs(GNTtanPx * maxSliceMM));
	// printMessage("Tilt extends slice by %d pixels", pxOffset);
	hdr->dim[2] = hdr->dim[2] + pxOffset;
	// When there is negative tilt, the image origin must be adjusted for the padding that will be added.
	if (GNTtanPx < 0) {
		// printMessage("Adjusting origin for %d pixels padding (float)\n", pxOffset);
		adjustOriginForNegativeTilt(hdr, pxOffset);
	}
	int nVox2D = hdr->dim[1] * hdr->dim[2];
	unsigned char *imOut = (unsigned char *)malloc(nVox2D * hdrIn.dim[3] * 4); // *4 as 32-bits per voxel, sizeof(float) );
	float *imOut32 = (float *)imOut;
	//set surrounding voxels to padding (if present) or darkest observed value
	bool hasPixelPaddingValue = !isnan(d.pixelPaddingValue);
	float pixelPaddingValue;
	if (hasPixelPaddingValue) {
		pixelPaddingValue = d.pixelPaddingValue;
	} else {
		// Find darkest pixel value. Note that `hasPixelPaddingValue` remains false so that the darkest value
		// will not trigger nearest neighbor interpolation below when this value is found in the image.
		pixelPaddingValue = imIn32[0];
		for (int v = 0; v < (nVox2DIn * hdrIn.dim[3]); v++)
			if (imIn32[v] < pixelPaddingValue)
				pixelPaddingValue = imIn32[v];
	}
	for (int v = 0; v < (nVox2D * hdrIn.dim[3]); v++)
		imOut32[v] = pixelPaddingValue;
	//copy skewed voxels
	for (int s = 0; s < hdrIn.dim[3]; s++) { //for each slice
		float sliceMM = s * hdrIn.pixdim[3];
		if (sliceMMarray != NULL)
			sliceMM = sliceMMarray[s]; //variable slice thicknesses
		//sliceMM -= mmMidZ; //adjust so tilt relative to middle slice
		if (GNTtanPx < 0)
			sliceMM -= maxSliceMM;
		float Offset = GNTtanPx * sliceMM;
		float fracHi = ceil(Offset) - Offset; //ceil not floor since rI=r-Offset not rI=r+Offset
		float fracLo = 1.0f - fracHi;
		for (int r = 0; r < hdr->dim[2]; r++) { //for each row of output
			float rI = (float)r - Offset;		//input row
			if ((rI >= 0.0) && (rI < hdrIn.dim[2])) {
				int rLo = floor(rI);
				int rHi = rLo + 1;
				if (rHi >= hdrIn.dim[2])
					rHi = rLo;
				rLo = (rLo * hdrIn.dim[1]) + (s * nVox2DIn); //offset to start of row below
				rHi = (rHi * hdrIn.dim[1]) + (s * nVox2DIn); //offset to start of row above
				int rOut = (r * hdrIn.dim[1]) + (s * nVox2D); //offset to output row
				for (int c = 0; c < hdrIn.dim[1]; c++) { //for each column
					float valLo = (float)imIn32[rLo + c];
					float valHi = (float)imIn32[rHi + c];
					if (hasPixelPaddingValue && (valLo == pixelPaddingValue || valHi == pixelPaddingValue)) {
						// https://github.com/rordenlab/dcm2niix/issues/262 - Use nearest neighbor interpolation
						// when at least one of the values is padding.
						imOut32[rOut + c] = fracHi >= 0.5 ? valHi : valLo;
					} else {
						imOut32[rOut + c] = round(valLo * fracLo + valHi * fracHi);
					}
				} //for c (each column)
			} //rI (input row) in range
		} //for r (each row)
	} //for s (each slice)*/
	free(im);
	if (sliceMMarray != NULL)
		return imOut; //we will save after correcting for variable slice thicknesses
	char niiFilenameTilt[2048] = {""};
	strcat(niiFilenameTilt, niiFilename);
	strcat(niiFilenameTilt, "_Tilt");
	nii_saveNII3D(niiFilenameTilt, *hdr, imOut, opts, d);
	return imOut;
} // nii_saveNII3DtiltFloat32()

unsigned char *nii_saveNII3Dtilt(char *niiFilename, struct nifti_1_header *hdr, unsigned char *im, struct TDCMopts opts, struct TDICOMdata d, float *sliceMMarray, float gantryTiltDeg, int manufacturer) {
	//correct for gantry tilt - http://www.mathworks.com/matlabcentral/fileexchange/24458-dicom-gantry-tilt-correction
	if (opts.isOnlyBIDS)
		return im;
	if (gantryTiltDeg == 0.0)
		return im;
	struct nifti_1_header hdrIn = *hdr;
	int nVox2DIn = hdrIn.dim[1] * hdrIn.dim[2];
	if ((nVox2DIn < 1) || (hdrIn.dim[0] != 3) || (hdrIn.dim[3] < 3))
		return im;
	if (hdrIn.datatype == DT_FLOAT32)
		return nii_saveNII3DtiltFloat32(niiFilename, hdr, im, opts, d, sliceMMarray, gantryTiltDeg, manufacturer);
	if (hdrIn.datatype != DT_INT16) {
		printMessage("Only able to correct gantry tilt for 16-bit integer data with at least 3 slices.");
		return im;
	}
	printMessage("Gantry Tilt Correction is new: please validate conversions\n");
	float GNTtanPx = tan(gantryTiltDeg / (180 / M_PI)) / hdrIn.pixdim[2]; //tangent(degrees->radian)
//unintuitive step: reverse sign for negative gantry tilt, therefore -27deg == +27deg (why @!?#)
// seen in http://www.mathworks.com/matlabcentral/fileexchange/28141-gantry-detector-tilt-correction/content/gantry2.m
// also validated with actual data...
#ifndef newTilt
	if (manufacturer == kMANUFACTURER_PHILIPS) //see 'Manix' example from Osirix
		GNTtanPx = -GNTtanPx;
	else if ((manufacturer == kMANUFACTURER_SIEMENS) && (gantryTiltDeg > 0.0))
		GNTtanPx = -GNTtanPx;
	else if (manufacturer == kMANUFACTURER_GE)
		; //do nothing
	else if (gantryTiltDeg < 0.0)
		GNTtanPx = -GNTtanPx; //see Toshiba examples from John Muschelli
#endif //newTilt
	short *imIn16 = (short *)im;
	//create new output image: larger due to skew
	// compute how many pixels slice must be extended due to skew
	int s = hdrIn.dim[3] - 1; //top slice
	float maxSliceMM = fabs(s * hdrIn.pixdim[3]);
	if (sliceMMarray != NULL)
		maxSliceMM = fabs(sliceMMarray[s]);
	int pxOffset = ceil(fabs(GNTtanPx * maxSliceMM));
	// printMessage("Tilt extends slice by %d pixels", pxOffset);
	hdr->dim[2] = hdr->dim[2] + pxOffset;

	// When there is negative tilt, the image origin must be adjusted for the padding that will be added.
	if (GNTtanPx < 0) {
		// printMessage("Adjusting origin for %d pixels padding (short)\n", pxOffset);
		adjustOriginForNegativeTilt(hdr, pxOffset);
	}
	int nVox2D = hdr->dim[1] * hdr->dim[2];
	unsigned char *imOut = (unsigned char *)malloc(nVox2D * hdrIn.dim[3] * 2); // *2 as 16-bits per voxel, sizeof( short) );
	short *imOut16 = (short *)imOut;
	//set surrounding voxels to padding (if present) or darkest observed value
	bool hasPixelPaddingValue = !isnan(d.pixelPaddingValue);
	short pixelPaddingValue;
	if (hasPixelPaddingValue) {
		pixelPaddingValue = (short)round(d.pixelPaddingValue);
	} else {
		// Find darkest pixel value. Note that `hasPixelPaddingValue` remains false so that the darkest value
		// will not trigger nearest neighbor interpolation below when this value is found in the image.
		pixelPaddingValue = imIn16[0];
		for (int v = 0; v < (nVox2DIn * hdrIn.dim[3]); v++)
			if (imIn16[v] < pixelPaddingValue)
				pixelPaddingValue = imIn16[v];
	}
	for (int v = 0; v < (nVox2D * hdrIn.dim[3]); v++)
		imOut16[v] = pixelPaddingValue;
	//copy skewed voxels
	for (int s = 0; s < hdrIn.dim[3]; s++) { //for each slice
		float sliceMM = s * hdrIn.pixdim[3];
		if (sliceMMarray != NULL)
			sliceMM = sliceMMarray[s]; //variable slice thicknesses
		//sliceMM -= mmMidZ; //adjust so tilt relative to middle slice
		if (GNTtanPx < 0)
			sliceMM -= maxSliceMM;
		float Offset = GNTtanPx * sliceMM;
		float fracHi = ceil(Offset) - Offset; //ceil not floor since rI=r-Offset not rI=r+Offset
		float fracLo = 1.0f - fracHi;
		for (int r = 0; r < hdr->dim[2]; r++) { //for each row of output
			float rI = (float)r - Offset;		//input row
			if ((rI >= 0.0) && (rI < hdrIn.dim[2])) {
				int rLo = floor(rI);
				int rHi = rLo + 1;
				if (rHi >= hdrIn.dim[2])
					rHi = rLo;
				rLo = (rLo * hdrIn.dim[1]) + (s * nVox2DIn); //offset to start of row below
				rHi = (rHi * hdrIn.dim[1]) + (s * nVox2DIn); //offset to start of row above
				int rOut = (r * hdrIn.dim[1]) + (s * nVox2D); //offset to output row
				for (int c = 0; c < hdrIn.dim[1]; c++) { //for each row
					short valLo = imIn16[rLo + c];
					short valHi = imIn16[rHi + c];
					if (hasPixelPaddingValue && (valLo == pixelPaddingValue || valHi == pixelPaddingValue)) {
						// https://github.com/rordenlab/dcm2niix/issues/262 - Use nearest neighbor interpolation
						// when at least one of the values is padding.
						imOut16[rOut + c] = fracHi >= 0.5 ? valHi : valLo;
					} else {
						imOut16[rOut + c] = round((((float)valLo) * fracLo) + ((float)valHi) * fracHi);
					}
				} //for c (each column)
			} //rI (input row) in range
		} //for r (each row)
	} //for s (each slice)*/
	free(im);
	if (sliceMMarray != NULL)
		return imOut; //we will save after correcting for variable slice thicknesses
	char niiFilenameTilt[2048] = {""};
	strcat(niiFilenameTilt, niiFilename);
	strcat(niiFilenameTilt, "_Tilt");
	nii_saveNII3D(niiFilenameTilt, *hdr, imOut, opts, d);
	return imOut;
} // nii_saveNII3Dtilt()

int nii_saveNII3Deq(char *niiFilename, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts, struct TDICOMdata d, float *sliceMMarray) {
	//convert image with unequal slice distances to equal slice distances
	//sliceMMarray = 0.0 3.0 6.0 12.0 22.0 <- ascending distance from first slice
	if (opts.isOnlyBIDS)
		return EXIT_SUCCESS;
	int nVox2D = hdr.dim[1] * hdr.dim[2];
	if ((nVox2D < 1) || (hdr.dim[0] != 3) || (hdr.dim[3] < 3))
		return EXIT_FAILURE;
	if ((hdr.datatype != DT_FLOAT32) && (hdr.datatype != DT_UINT8) && (hdr.datatype != DT_RGB24) && (hdr.datatype != DT_INT16)) {
		printMessage("Only able to make equidistant slices from 8,16,24-bit integer or 32-bit float image data.");
		return EXIT_FAILURE;
	}
	float mn = sliceMMarray[1] - sliceMMarray[0];
	for (int i = 1; i < hdr.dim[3]; i++) {
		float dx = sliceMMarray[i] - sliceMMarray[i - 1];
		if ((dx < mn) && (!isSameFloat(dx, 0.0))) // <- allow slice direction to reverse
			mn = sliceMMarray[i] - sliceMMarray[i - 1];
	}
	if (mn <= 0.0f) {
		printMessage("Unable to equalize slice distances: slice order not consistently ascending:\n");
		printMessage("dx=[0");
		for (int i = 1; i < hdr.dim[3]; i++)
			printMessage(" %g", sliceMMarray[i - 1]);
		printMessage("]\n");
		printMessage(" Recompiling with '-DmyInstanceNumberOrderIsNotSpatial' might help.\n");
		return EXIT_FAILURE;
	}
	int slices = hdr.dim[3];
	slices = (int)ceil((sliceMMarray[slices - 1] - 0.5 * (sliceMMarray[slices - 1] - sliceMMarray[slices - 2])) / mn); //-0.5: fence post
	if (slices > (hdr.dim[3] * 2)) {
		slices = 2 * hdr.dim[3];
		mn = (sliceMMarray[hdr.dim[3] - 1]) / (slices - 1);
	}
	//printMessage("-->%g mn slices %d orig %d\n", mn, slices, hdr.dim[3]);
	if (slices < 3)
		return EXIT_FAILURE;
	struct nifti_1_header hdrX = hdr;
	hdrX.dim[3] = slices;
	hdrX.pixdim[3] = mn;
	if ((hdr.pixdim[3] != 0.0) && (hdr.pixdim[3] != hdrX.pixdim[3])) {
		float Scale = hdrX.pixdim[3] / hdr.pixdim[3];
		//to do: do I change srow_z or srow_x[2], srow_y[2], srow_z[2],
		hdrX.srow_z[0] = hdr.srow_z[0] * Scale;
		hdrX.srow_z[1] = hdr.srow_z[1] * Scale;
		hdrX.srow_z[2] = hdr.srow_z[2] * Scale;
	}
	unsigned char *imX;
	if (hdr.datatype == DT_FLOAT32) {
		float *im32 = (float *)im;
		imX = (unsigned char *)malloc((nVox2D * slices) * 4); //sizeof(float)
		float *imX32 = (float *)imX;
		for (int s = 0; s < slices; s++) {
			float sliceXmm = s * mn;	//distance from first slice
			int sliceXi = (s * nVox2D); //offset for this slice
			int sHi = 0;
			while ((sHi < (hdr.dim[3] - 1)) && (sliceMMarray[sHi] < sliceXmm))
				sHi += 1;
			int sLo = sHi - 1;
			if (sLo < 0)
				sLo = 0;
			float mmHi = sliceMMarray[sHi];
			float mmLo = sliceMMarray[sLo];
			sLo = sLo * nVox2D;
			sHi = sHi * nVox2D;
			if ((mmHi == mmLo) || (sliceXmm > mmHi)) { //select only from upper slice TPX
				//for (int v=0; v < nVox2D; v++)
				// imX16[sliceXi+v] = im16[sHi+v];
				memcpy(&imX32[sliceXi], &im32[sHi], nVox2D * sizeof(float)); //memcpy( dest, src, bytes)
			} else {
				float fracHi = (sliceXmm - mmLo) / (mmHi - mmLo);
				float fracLo = 1.0 - fracHi;
				//weight between two slices
				for (int v = 0; v < nVox2D; v++)
					imX32[sliceXi + v] = round(((float)im32[sLo + v] * fracLo) + (float)im32[sHi + v] * fracHi);
			}
		}
	} else if (hdr.datatype == DT_INT16) {
		short *im16 = (short *)im;
		imX = (unsigned char *)malloc((nVox2D * slices) * 2); //sizeof( short) );
		short *imX16 = (short *)imX;
		for (int s = 0; s < slices; s++) {
			float sliceXmm = s * mn;	//distance from first slice
			int sliceXi = (s * nVox2D); //offset for this slice
			int sHi = 0;
			while ((sHi < (hdr.dim[3] - 1)) && (sliceMMarray[sHi] < sliceXmm))
				sHi += 1;
			int sLo = sHi - 1;
			if (sLo < 0)
				sLo = 0;
			float mmHi = sliceMMarray[sHi];
			float mmLo = sliceMMarray[sLo];
			sLo = sLo * nVox2D;
			sHi = sHi * nVox2D;
			if ((mmHi == mmLo) || (sliceXmm > mmHi)) { //select only from upper slice TPX
				//for (int v=0; v < nVox2D; v++)
				// imX16[sliceXi+v] = im16[sHi+v];
				memcpy(&imX16[sliceXi], &im16[sHi], nVox2D * sizeof(unsigned short)); //memcpy( dest, src, bytes)
			} else {
				float fracHi = (sliceXmm - mmLo) / (mmHi - mmLo);
				float fracLo = 1.0 - fracHi;
				//weight between two slices
				for (int v = 0; v < nVox2D; v++)
					imX16[sliceXi + v] = round(((float)im16[sLo + v] * fracLo) + (float)im16[sHi + v] * fracHi);
			}
		}
	} else {
		if (hdr.datatype == DT_RGB24)
			nVox2D = nVox2D * 3;
		imX = (unsigned char *)malloc((nVox2D * slices) * 2); //sizeof( short) );
		for (int s = 0; s < slices; s++) {
			float sliceXmm = s * mn;	//distance from first slice
			int sliceXi = (s * nVox2D); //offset for this slice
			int sHi = 0;
			while ((sHi < (hdr.dim[3] - 1)) && (sliceMMarray[sHi] < sliceXmm))
				sHi += 1;
			int sLo = sHi - 1;
			if (sLo < 0)
				sLo = 0;
			float mmHi = sliceMMarray[sHi];
			float mmLo = sliceMMarray[sLo];
			sLo = sLo * nVox2D;
			sHi = sHi * nVox2D;
			if ((mmHi == mmLo) || (sliceXmm > mmHi)) { //select only from upper slice TPX
				memcpy(&imX[sliceXi], &im[sHi], nVox2D); //memcpy( dest, src, bytes)
			} else {
				float fracHi = (sliceXmm - mmLo) / (mmHi - mmLo);
				float fracLo = 1.0 - fracHi; //weight between two slices
				for (int v = 0; v < nVox2D; v++)
					imX[sliceXi + v] = round(((float)im[sLo + v] * fracLo) + (float)im[sHi + v] * fracHi);
			}
		}
	}
	char niiFilenameEq[2048] = {""};
	strcat(niiFilenameEq, niiFilename);
	strcat(niiFilenameEq, "_Eq");
	nii_saveNII3D(niiFilenameEq, hdrX, imX, opts, d);
	free(imX);
	return EXIT_SUCCESS;
} // nii_saveNII3Deq()

float PhilipsPreciseVal(float lPV, float lRS, float lRI, float lSS) {
	if ((lRS * lSS) == 0) //avoid divide by zero
		return 0.0;
	else
		return (lPV * lRS + lRI) / (lRS * lSS);
}

void PhilipsPrecise(struct TDICOMdata *d, bool isPhilipsFloatNotDisplayScaling, struct nifti_1_header *h, int verbose) {
	if (d->manufacturer != kMANUFACTURER_PHILIPS)
		return; //not Philips
	if (d->isScaleVariesEnh)
		return; //issue363 rescaled before slice reordering
	/*
	if (!isSameFloatGE(0.0, d->RWVScale)) { //https://github.com/rordenlab/dcm2niix/issues/493
		h->scl_slope = d->RWVScale;
		h->scl_inter = d->RWVIntercept;
		printMessage("Using RWVSlope:RWVIntercept = %g:%g\n",d->RWVScale,d->RWVIntercept);
		printMessage(" Philips Scaling Values RS:RI:SS = %g:%g:%g (see PMC3998685)\n",d->intenScale,d->intenIntercept,d->intenScalePhilips);
		if (verbose == 0) return;
		printMessage("Potential Alternative Intensity Scalings\n");
		printMessage(" R = raw value, P = precise value, D = displayed value\n");
		printMessage(" RS = rescale slope, RI = rescale intercept, SS = scale slope\n");
		printMessage(" D = R * RS + RI , P = D/(RS * SS)\n");
		return;
	}*/
	if (d->intenScalePhilips == 0)
		return; //no Philips Precise
	//we will report calibrated "FP" values http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998685/
	float l0 = PhilipsPreciseVal(0, d->intenScale, d->intenIntercept, d->intenScalePhilips);
	float l1 = PhilipsPreciseVal(1, d->intenScale, d->intenIntercept, d->intenScalePhilips);
	float intenScaleP = d->intenScale;
	float intenInterceptP = d->intenIntercept;
	if (l0 != l1) {
		intenInterceptP = l0;
		intenScaleP = l1 - l0;
	}
	if (isSameFloat(d->intenIntercept, intenInterceptP) && isSameFloat(d->intenScale, intenScaleP))
		return; //same result for both methods: nothing to do or report!
	printMessage("Philips Scaling Values RS:RI:SS = %g:%g:%g (see PMC3998685)\n", d->intenScale, d->intenIntercept, d->intenScalePhilips);
	if (verbose > 0) {
		printMessage(" R = raw value, P = precise value, D = displayed value\n");
		printMessage(" RS = rescale slope, RI = rescale intercept, SS = scale slope\n");
		printMessage(" D = R * RS + RI; P = D/(RS * SS)\n");
		printMessage(" D scl_slope:scl_inter = %g:%g\n", d->intenScale, d->intenIntercept);
		printMessage(" P scl_slope:scl_inter = %g:%g\n", intenScaleP, intenInterceptP);
	}
	//#define myUsePhilipsPrecise
	if (isPhilipsFloatNotDisplayScaling) {
		if (verbose > 0)
			printMessage(" Using P values ('-p n ' for D values)\n");
		//to change DICOM:
		//d->intenScale = intenScaleP;
		//d->intenIntercept = intenInterceptP;
		//to change NIfTI
		h->scl_slope = intenScaleP;
		h->scl_inter = intenInterceptP;
		d->intenScalePhilips = 0; //so we never run this TWICE!
	} else if (verbose > 0)
		printMessage(" Using D values ('-p y ' for P values)\n");
} //PhilipsPrecise()

void smooth1D(int num, double *im) {
	if (num < 3)
		return;
	double *src = (double *)malloc(sizeof(double) * num);
	memcpy(&src[0], &im[0], num * sizeof(double)); //memcpy( dest, src, bytes)
	double frac = 0.25;
	for (int i = 1; i < (num - 1); i++)
		im[i] = (src[i - 1] * frac) + (src[i] * frac * 2) + (src[i + 1] * frac);
	free(src);
} // smooth1D()

int nii_saveCrop(char *niiFilename, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts, struct TDICOMdata d) {
	//remove excess neck slices - assumes output of nii_setOrtho()
	if (opts.isOnlyBIDS)
		return EXIT_SUCCESS;
	int nVox2D = hdr.dim[1] * hdr.dim[2];
	if ((nVox2D < 1) || (fabs(hdr.pixdim[3]) < 0.001) || (hdr.dim[0] != 3) || (hdr.dim[3] < 128))
		return EXIT_FAILURE;
	if ((hdr.datatype != DT_INT16) && (hdr.datatype != DT_UINT16)) {
		printMessage("Only able to crop 16-bit volumes.");
		return EXIT_FAILURE;
	}
	short *im16 = (short *)im;
	unsigned short *imu16 = (unsigned short *)im;
	float kThresh = 0.09; //more than 9% of max brightness
	int ventralCrop = 0;
	//find max value for each slice
	int slices = hdr.dim[3];
	double *sliceSums = (double *)malloc(sizeof(double) * slices);
	double maxSliceVal = 0.0;
	for (int i = (slices - 1); i >= 0; i--) {
		sliceSums[i] = 0;
		int sliceStart = i * nVox2D;
		if (hdr.datatype == DT_UINT16)
			for (int j = 0; j < nVox2D; j++)
				sliceSums[i] += imu16[j + sliceStart];
		else
			for (int j = 0; j < nVox2D; j++)
				sliceSums[i] += im16[j + sliceStart];
		if (sliceSums[i] > maxSliceVal)
			maxSliceVal = sliceSums[i];
	}
	if (maxSliceVal <= 0) {
		free(sliceSums);
		return EXIT_FAILURE;
	}
	smooth1D(slices, sliceSums);
	for (int i = 0; i < slices; i++)
		sliceSums[i] = sliceSums[i] / maxSliceVal; //so brightest slice has value 1
	//dorsal crop: eliminate slices with more than 5% brightness
	int dorsalCrop;
	for (dorsalCrop = (slices - 1); dorsalCrop >= 1; dorsalCrop--)
		if (sliceSums[dorsalCrop - 1] > kThresh)
			break;
	if (dorsalCrop <= 1) {
		free(sliceSums);
		return EXIT_FAILURE;
	}
	const double kMaxDVmm = 169.0;
	ventralCrop = dorsalCrop - round(kMaxDVmm / hdr.pixdim[3]);
	if (ventralCrop < 0)
		ventralCrop = 0;
	//apply crop
	printMessage(" Cropping from slice %d to %d (of %d)\n", ventralCrop, dorsalCrop, slices);
	struct nifti_1_header hdrX = hdr;
	slices = dorsalCrop - ventralCrop + 1;
	hdrX.dim[3] = slices;
	//translate origin to account for missing slices
	hdrX.srow_x[3] += hdr.srow_x[2] * ventralCrop;
	hdrX.srow_y[3] += hdr.srow_y[2] * ventralCrop;
	hdrX.srow_z[3] += hdr.srow_z[2] * ventralCrop;
	//convert data
	unsigned char *imX;
	imX = (unsigned char *)malloc((nVox2D * slices) * 2); //sizeof( short) );
	short *imX16 = (short *)imX;
	for (int s = 0; s < slices; s++) {
		int sIn = s + ventralCrop;
		int sOut = s;
		sOut = sOut * nVox2D;
		sIn = sIn * nVox2D;
		memcpy(&imX16[sOut], &im16[sIn], nVox2D * sizeof(unsigned short)); //memcpy( dest, src, bytes)
	}
	char niiFilenameCrop[2048] = {""};
	strcat(niiFilenameCrop, niiFilename);
	strcat(niiFilenameCrop, "_Crop");
	const int returnCode = nii_saveNII3D(niiFilenameCrop, hdrX, imX, opts, d);
	free(imX);
	return returnCode;
} // nii_saveCrop()

double dicomTimeToSec(double dicomTime) {
	//convert HHMMSS to seconds, 135300.024 -> 135259.731 are 0.293 sec apart
	char acqTimeBuf[64];
	snprintf(acqTimeBuf, sizeof acqTimeBuf, "%+013.5f", (double)dicomTime);
	int ahour, amin;
	double asec;
	int count = 0;
	sscanf(acqTimeBuf, "%3d%2d%lf%n", &ahour, &amin, &asec, &count);
	if (!count)
		return -1;
	return (ahour * 3600) + (amin * 60) + asec;
}

double acquisitionTimeDifference(struct TDICOMdata *d1, struct TDICOMdata *d2) {
	if (d1->acquisitionDate != d2->acquisitionDate)
		return -1; //to do: scans running across midnight
	double sec1 = dicomTimeToSec(d1->acquisitionTime);
	double sec2 = dicomTimeToSec(d2->acquisitionTime);
	//printMessage("%g\n",d2->acquisitionTime);
	if ((sec1 < 0) || (sec2 < 0))
		return -1;
	return (sec2 - sec1);
}

void checkDateTimeOrder(struct TDICOMdata *d, struct TDICOMdata *d1) {
	if (d->acquisitionDate < d1->acquisitionDate)
		return; //d1 occurred on later date
	if (d->acquisitionTime <= d1->acquisitionTime)
		return; //d1 occurred on later (or same) time
	if (d->imageNum > d1->imageNum)
		printWarning("Images not sorted in ascending instance number (0020,0013)\n");
	else
		printWarning("Images sorted by instance number [0020,0013](%d..%d), but AcquisitionTime [0008,0032] suggests a different order (%g..%g) \n", d->imageNum, d1->imageNum, d->acquisitionTime, d1->acquisitionTime);
}

void checkSliceTiming(struct TDICOMdata *d, struct TDICOMdata *d1, int verbose, int isForceSliceTimeHHMMSS) {
	//detect images with slice timing errors. https://github.com/rordenlab/dcm2niix/issues/126
	//modified 20190704: this function now ensures all slice times are in msec
	if ((d->TR < 0.0) || (d->CSA.sliceTiming[0] < 0.0))
		return; //no slice timing
	if (d->manufacturer == kMANUFACTURER_PHILIPS)
		return; //Philips does not provide slice timing details in DICOM
	if (d->manufacturer == kMANUFACTURER_GE)
		return; //compute directly from Protocol Block
	if (d->modality == kMODALITY_PT)
		return; //issue407
	int nSlices = 0;
	while ((nSlices < kMaxEPI3D) && (d->CSA.sliceTiming[nSlices] >= 0.0))
		nSlices++;
	if (nSlices < 2)
		return;
	if (d->CSA.sliceTiming[kMaxEPI3D - 1] < -1.0) //the value -2.0 is used as a flag for negative MosaicRefAcqTimes in checkSliceTimes(), see issue 271
		printWarning("Adjusting for negative MosaicRefAcqTimes (issue 271).\n");
	bool isSliceTimeHHMMSS = (d->manufacturer == kMANUFACTURER_UIH);
	if (isForceSliceTimeHHMMSS)
		isSliceTimeHHMMSS = true;
	//if (d->isXA10A) isSliceTimeHHMMSS = true; //for XA10 use TimeAfterStart 0x0021,0x1104 -> Siemens de-identification can corrupt acquisition ties https://github.com/rordenlab/dcm2niix/issues/236
	if (isSliceTimeHHMMSS) { //handle midnight crossing
		for (int i = 0; i < nSlices; i++)
			d->CSA.sliceTiming[i] = dicomTimeToSec(d->CSA.sliceTiming[i]);
		float minT = d->CSA.sliceTiming[0];
		float maxT = minT;
		for (int i = 0; i < nSlices; i++) {
			if (d->CSA.sliceTiming[i] < minT)
				minT = d->CSA.sliceTiming[i];
			if (d->CSA.sliceTiming[i] < maxT)
				maxT = d->CSA.sliceTiming[i];
		}
		//printf("%d %g ---> %g..%g\n", nSlices, d->TR, minT, maxT);
		float kMidnightSec = 86400;
		float kNoonSec = 43200;
		if ((maxT - minT) > kNoonSec) { //volume started before midnight but ended next day!
			//identify and fix 'Cinderella error' where clock resets at midnight: untested
			printWarning("Acquisition crossed midnight: check slice timing\n");
			for (int i = 0; i < nSlices; i++)
				if (d->CSA.sliceTiming[i] > kNoonSec)
					d->CSA.sliceTiming[i] = d->CSA.sliceTiming[i] - kMidnightSec;
			minT = d->CSA.sliceTiming[0];
			for (int i = 0; i < nSlices; i++)
				if (d->CSA.sliceTiming[i] < minT)
					minT = d->CSA.sliceTiming[i];
		}
		for (int i = 0; i < nSlices; i++)
			d->CSA.sliceTiming[i] = d->CSA.sliceTiming[i] - minT;
	} //XA10/UIH: HHMMSS -> Sec
	float minT = d->CSA.sliceTiming[0];
	float maxT = minT;
	for (int i = 0; i < kMaxEPI3D; i++) {
		if (d->CSA.sliceTiming[i] < 0.0)
			break;
		if (d->CSA.sliceTiming[i] < minT)
			minT = d->CSA.sliceTiming[i];
		if (d->CSA.sliceTiming[i] > maxT)
			maxT = d->CSA.sliceTiming[i];
	}
	if (isSliceTimeHHMMSS) //convert HHMMSS to msec
		for (int i = 0; i < kMaxEPI3D; i++)
			d->CSA.sliceTiming[i] = dicomTimeToSec(d->CSA.sliceTiming[i]) * 1000.0;
	float TRms = d->TR; //d->TR in msec!
	if ((minT != maxT) && (maxT <= TRms)) {
		if (verbose != 0)
			printMessage("Slice timing range appears reasonable (range %g..%g, TR=%g ms)\n", minT, maxT, TRms);
		return; //looks fine
	}
	if ((minT == maxT) && (d->is3DAcq))
		return; //fine: 3D EPI
	if ((minT == maxT) && (d->CSA.multiBandFactor == d->CSA.mosaicSlices))
		return; //fine: all slices single excitation
	if ((strlen(d->seriesDescription) > 0) && (strstr(d->seriesDescription, "SBRef") != NULL))
		return; //fine: single-band calibration data, the slice timing WILL exceed the TR
	if (verbose > 1)
		printMessage("Slice timing range of first volume: range %g..%g, TR=%g ms)\n", minT, maxT, TRms);
	//check if 2nd image has valid slice timing
	float minT1 = d1->CSA.sliceTiming[0];
	float maxT1 = minT1;
	for (int i = 0; i < nSlices; i++) {
		//if (d1->CSA.sliceTiming[i] < 0.0) break;
		if (d1->CSA.sliceTiming[i] < minT1)
			minT1 = d1->CSA.sliceTiming[i];
		if (d1->CSA.sliceTiming[i] > maxT1)
			maxT1 = d1->CSA.sliceTiming[i];
	}
	if (verbose > 1)
		printMessage("Slice timing range of 2nd volume: range %g..%g, TR=%g ms)\n", minT, maxT, TRms);
	if ((minT1 < maxT1) && (minT1 > 0.0) && ((maxT1 - minT1) <= TRms)) { //issue 429: 2nd volume may not start from zero
		for (int i = 0; i < nSlices; i++)
			d1->CSA.sliceTiming[i] -= minT1;
		maxT1 -= minT1;
		minT1 -= minT1;
	}
	if ((minT1 < 0.0) && (d->rtia_timerGE >= 0.0))
		return; //use rtia timer
	if (minT1 < 0.0) { //https://github.com/neurolabusc/MRIcroGL/issues/31
		if (d->isDerived) { //slice timing not relevant for derived data, values mangled with Siemens XA30
			d->CSA.sliceTiming[0] = -1.0;
			return;
		}
		if (d->modality == kMODALITY_MR)
			printWarning("Siemens MoCo? Bogus slice timing (range %g..%g, TR=%g seconds)\n", minT1, maxT1, TRms);
		return;
	}
	if ((minT1 == maxT1) || (maxT1 >= TRms)) { //both first and second image corrupted
		printWarning("Slice timing appears corrupted (range %g..%g, TR=%g ms)\n", minT1, maxT1, TRms);
		return;
	}
	//1st image corrupted, but 2nd looks ok - substitute values from 2nd image
	for (int i = 0; i < kMaxEPI3D; i++) {
		d->CSA.sliceTiming[i] = d1->CSA.sliceTiming[i];
		if (d1->CSA.sliceTiming[i] < 0.0)
			break;
	}
	d->CSA.multiBandFactor = d1->CSA.multiBandFactor;
	printMessage("CSA slice timing based on 2nd volume, 1st volume corrupted (CMRR bug, range %g..%g, TR=%g ms)\n", minT, maxT, TRms);
} //checkSliceTiming()

void setMultiBandFactor(int dim3, uint64_t indx0, struct TDICOMdata *dcmList) {
		float mn = dcmList[indx0].CSA.sliceTiming[0];
		//first pass: find minimum
		for (int v = 0; v < dim3; v++)
			mn = fminf(dcmList[indx0].CSA.sliceTiming[v],mn);
		//second pass: all times relative to min (i.e. make min = 0)
		int mb = 0;
		for (int v = 0; v < dim3; v++) {
			dcmList[indx0].CSA.sliceTiming[v] -= mn;
			if (isSameFloatGE(dcmList[indx0].CSA.sliceTiming[v], 0.0))
				mb++;
		}
		if ((dcmList[indx0].CSA.multiBandFactor < 2) && (mb > 1) && (mb < dim3))
			dcmList[indx0].CSA.multiBandFactor = mb;
} // setMultiBandFactor()

void sliceTimingXA(struct TDCMsort *dcmSort, struct TDICOMdata *dcmList, struct nifti_1_header *hdr, int verbose, const char *filename, int nConvert) {
	//Siemens XA10 slice timing
	// Ignore first volume: For an example of erroneous first volume timing, see series 10 (Functional_w_SMS=3) https://github.com/rordenlab/dcm2niix/issues/240
	// an alternative would be to use 0018,9074 - this would need to be converted from DT to Secs, and is scrambled if de-identifies data see enhanced de-identified series 26 from issue 236
	uint64_t indx0 = dcmSort[0].indx; //first volume
	if ((!dcmList[indx0].isXA10A) || (hdr->dim[3] < 1) || (hdr->dim[4] < 1))
		return;
	if ((nConvert == (hdr->dim[3] * hdr->dim[4])) && (hdr->dim[3] < (kMaxEPI3D - 1)) && (hdr->dim[3] > 1)) {
		//XA11 2D classic: nb XA30 in `MFSPLIT` will save each 3D volume from 4D timeseries as a unique series number!
		for (int v = 0; v < hdr->dim[3]; v++)
			dcmList[indx0].CSA.sliceTiming[v] = dcmList[dcmSort[v].indx].CSA.sliceTiming[0];
		setMultiBandFactor(hdr->dim[3], indx0, dcmList);
	} else if ((nConvert == (hdr->dim[4])) && (hdr->dim[3] < (kMaxEPI3D - 1)) && (hdr->dim[3] > 1) && (hdr->dim[4] > 1)) {
		//XA10 mosaics - these are missing a lot of information
		//get slice timing from second volume
		for (int v = 0; v < hdr->dim[3]; v++)
			dcmList[indx0].CSA.sliceTiming[v] = dcmList[dcmSort[1].indx].CSA.sliceTiming[v];
		setMultiBandFactor(hdr->dim[3], indx0, dcmList);
		return; //we have subtracted min
	}
	//issue429: subtract min
	float mn = dcmList[indx0].CSA.sliceTiming[0];
	for (int v = 0; v < hdr->dim[3]; v++)
		mn = min(mn, dcmList[indx0].CSA.sliceTiming[v]);
	if (isSameFloatGE(mn, 0.0))
		return;
	for (int v = 0; v < hdr->dim[3]; v++)
		dcmList[indx0].CSA.sliceTiming[v] -= mn;
} //sliceTimingXA()

void sliceTimeGE(struct TDICOMdata *d, int mb, int dim3, float TR, bool isInterleaved, float geMajorVersion, bool is27r3, float groupDelaysec) {
	//mb : multiband factor
	//dim3 : number of slices in volume
	//TRsec : repetition time in seconds
	//isInterleaved : interleaved or sequential slice order
	//geMajorVersion: version, e.g. 29.0
	//is27r3 : software release 27.0 R03 or later
	float sliceTiming[kMaxEPI3D];
	//multiband can be fractional! 'extra' slices discarded
	int nExcitations = ceil(float(dim3) / float(mb));
	if ((mb > 1) && (geMajorVersion < 26.0)) {
		printWarning("Unable to determine slice times for early GE HyperBand.\n");
		d->CSA.sliceTiming[0] = -1;
		return;
	}
	if ((mb > 1) && (!is27r3) && ((nExcitations % 2) == 0) ) { //number of slices divided by MB factor should is Even
			nExcitations ++; //https://osf.io/q4d53/wiki/home/; Figure 3 of https://pubmed.ncbi.nlm.nih.gov/26308571/
		}
	//int nDiscardedSlices = (nExcitations * mb) - dim3;
	float secPerSlice = (TR - groupDelaysec) / (nExcitations);
	if (!isInterleaved) {
		for (int i = 0; i < nExcitations; i++)
			sliceTiming[i] = i * secPerSlice;
	} else {
		int nOdd = (nExcitations - 1) / 2;
		for (int i = 0; i < nExcitations; i++) {
			if (i % 2 == 0) //ODD slices since we index from 0!
				sliceTiming[i] = (i / 2) * secPerSlice;
			else
				sliceTiming[i] = (nOdd + ((i + 1) / 2)) * secPerSlice;
		} //for each slice
		if ((mb > 1) && (is27r3) && (isInterleaved) && (nExcitations > 2) && ((nExcitations % 2) == 0)) {
			float tmp = sliceTiming[nExcitations - 1];
			sliceTiming[nExcitations - 1] = sliceTiming[nExcitations - 3];
			sliceTiming[nExcitations - 3] = tmp;
			//printf("SWAP!\n");
		}
	} //if interleaved
	for (int i = 0; i < dim3; i++)
		sliceTiming[i] = sliceTiming[i % nExcitations];
//#define testSliceTimesGE //note that early GE HyperBand sequences reported single-band values in x0021x105E
#ifdef testSliceTimesGE
	float maxErr = 0.0;
	for (int i = 0; i < dim3; i++)
		maxErr = max(maxErr, fabs(sliceTiming[i] - d->CSA.sliceTiming[i]));
	if ((d->CSA.sliceTiming[0] >= 0.0) && (maxErr > 1.0)) { //allow a 1.0 msec tolerance for rounding
		printMessage("GE estimated slice times differ from reported (max error: %g)\n", maxErr);
		printMessage("Slice\tEstimated\tReported\n");
		for (int i = 0; i < dim3; i++) {
			printMessage("%d %g %g\n", i, sliceTiming[i], d->CSA.sliceTiming[i]);
			maxErr = max(maxErr, fabs(sliceTiming[i] - d->CSA.sliceTiming[i]));
		}
	}
#endif
	for (int i = 0; i < dim3; i++)
		d->CSA.sliceTiming[i] = sliceTiming[i];
} // sliceTimeGE()

void readSoftwareVersionsGE(char softwareVersionsGE[], int verbose, char geVersionPrefix[], float *geMajorVersion, int *geMajorVersionInt, int *geMinorVersionInt, int *geReleaseVersionInt, bool *is27r3) {
	// softwareVersionsGE
	//	"27\LX\MR Software release:RX27.0_R02_1831.a" -> 27
	//	"28\LX\MR29.1_EA_2039.g" -> 29
	//  "30\LX\SIGNA_LX1.MR30.0_R01_2236.d" -> 30; see issue 634
	// geVersionPrefix
	//	RX27.0_R02_1831.a -> RX
	//	MR29.1_EA_2039.g -> MR
	// geMajorVersion
	//	RX27.0_R02_1831.a -> 27.0
	//	MR29.1_EA_2039.g -> 29.1
	// geMajorVersionInt
	//	RX27.0_R02_1831.a -> 27
	//	MR29.1_EA_2039.g -> 29
	// geMinorVersionInt
	//	RX27.0_R02_1831.a -> 0
	//	MR29.1_EA_2039.g -> 1
	// geReleaseVersionInt
	//	EA->0, R01->1, R02->2, R03->4
	//	RX27.0_R02_1831.a -> 2
	//	MR29.1_EA_2039.g -> 0
	int len = 0;
	bool ismatched = false;
	int substrlen = 0;

	// If softwareVersionsGE is 30\LX\SIGNA_LX1.MR30.0_R01_2236.d; see issue 634
	char *sepStart = strstr(softwareVersionsGE, "SIGNA_LX1");
	if (ismatched == false) {
		if (sepStart != NULL) {
			ismatched = true;
			substrlen = strlen("SIGNA_LX1");
			sepStart += substrlen+1;
		}
	}
	// If softwareVersionsGE is 27\LX\MR Software release:RX27.0_R02_1831.a
	if (ismatched == false) {
		sepStart = strstr(softwareVersionsGE, "MR Software release");
		if (sepStart != NULL) {
			ismatched = true;
			substrlen = strlen("MR Software release");
			sepStart += substrlen+1;
		}
	}
	// If softwareVersionsGE is 28\LX\MR29.1_EA_2039.g
	if (ismatched == false) {
		sepStart = strrchr(softwareVersionsGE, '\\');
		if (sepStart != NULL) {
			ismatched = true;
			sepStart += 1;
		}
	}
	len = 11; // RX27.0_R02_
	char *versionString = (char *)malloc(sizeof(char) * len);
	versionString[len - 1] = 0;
	memcpy(versionString, sepStart, len);
	char c1, c2, c3, c4;
	// RX27.0_R02_ or MR29.1_EA_2
	sscanf(versionString, "%c%c%d.%d_%c%c%d", &c1, &c2, geMajorVersionInt, geMinorVersionInt, &c3, &c4, geReleaseVersionInt);
	memcpy(geVersionPrefix, &c1, 1);
	memcpy(geVersionPrefix + 1, &c2, 1);
	if ((c3 == 'E') && (c4 == 'A')) {
		*geReleaseVersionInt = 0;
	}
	free(versionString);
	*geMajorVersion = (float)*geMajorVersionInt + (float)0.1 * (float)*geMinorVersionInt;
	*is27r3 = ((*geMajorVersion >= 27.1) || ((*geMajorVersionInt == 27) && (*geReleaseVersionInt >= 3)));
	if (verbose > 1) {
		printMessage("GE Software VersionSting: %s\n", softwareVersionsGE);
		printMessage("GE Software VersionPrefix: %s\n", geVersionPrefix);
		printMessage("GE Software MajorVersion: %d\n", *geMajorVersionInt);
		printMessage("GE Software MinorVersion: %d\n", *geMinorVersionInt);
		printMessage("GE Software ReleaseVersion: %d\n", *geReleaseVersionInt);
		printMessage("GE Software is27r3: %d\n", *is27r3);
	}
} // readSoftwareVersionsGE()

void sliceTimingGE_Testx0021x105E(struct TDICOMdata *d, struct TDCMopts opts, struct nifti_1_header *hdr, struct TDCMsort *dcmSort, struct TDICOMdata *dcmList) {
	if ((!opts.isTestx0021x105E) || (hdr->dim[3] < 2) || (hdr->dim[4] < 1))
		return;
	if (d->rtia_timerGE <= 0.0) {
		printMessage("DICOM images do not report RTIA timer(0021,105E)\n");
		return;
	}
	int j = hdr->dim[3];
	float sliceTiming[kMaxEPI3D];
	float mn = INFINITY;
	for (int v = 0; v < hdr->dim[3]; v++) {
		sliceTiming[v] = dcmList[dcmSort[v + j].indx].rtia_timerGE;
		mn = min(mn, sliceTiming[v]);
	}
	if (mn < 0.0)
		return;
	float mxErr = 0.0;
	for (int v = 0; v < hdr->dim[3]; v++) {
		sliceTiming[v] = (sliceTiming[v] - mn) * 1000.0; //subtract offset, convert sec -> ms
		mxErr = max(mxErr, float(fabs(sliceTiming[v] - d->CSA.sliceTiming[v])));
	}
	printMessage("Slice Timing Error between calculated and RTIA timer(0021,105E): %gms\n", mxErr);
	if ((mxErr < 1.0) && (opts.isVerbose < 1))
		return;
	for (int v = 0; v < hdr->dim[3]; v++)
		printMessage("\t%g\t%g\n", d->CSA.sliceTiming[v], sliceTiming[v]);
}

void reportProtocolBlockGE(struct TDICOMdata *d, const char *filename, int isVerbose) {
#ifdef myReadGeProtocolBlock
	if ((d->manufacturer != kMANUFACTURER_GE) || (d->modality != kMODALITY_MR))
		return;
	if ((d->protocolBlockStartGE < 1) || (d->protocolBlockLengthGE < 19)) {
		//if (isVerbose)
		printWarning("Missing GE protocol data block (0025,101B)\n");
		return;
	}
	int viewOrderGE = -1;
	int sliceOrderGE = -1;
	int mbAccel = -1;
	int nSlices = -1;
	float groupDelay = 0.0;
	char ioptGE[3000] = "";
	char seqName[kDICOMStr] = "";
	geProtocolBlock(filename, d->protocolBlockStartGE, d->protocolBlockLengthGE, isVerbose, &sliceOrderGE, &viewOrderGE, &mbAccel, &nSlices, &groupDelay, ioptGE, seqName);
	//if (strlen(d->procedureStepDescription) < 2)
	//	strcpy(d->procedureStepDescription, seqName);
	strcat(d->procedureStepDescription, seqName); //issue790
#endif
} //bidsGE

void setBidsSiemens(struct TDICOMdata *d, int nConvert, int isVerbose, const char *filename) {
	char seqDetails[kDICOMStrLarge] = "";
	char acqStr[kDICOMStrLarge] = "";
	char preAcqStr[kDICOMStrLarge] = "";
	float inv1 = NAN;
	float inv2 = NAN;
	bool isDualTI = false;
	int lContrasts = 0; //detect me-mprage
	#ifdef myReadAsciiCsa
	if ((d->CSA.SeriesHeader_offset > 0) && (d->CSA.SeriesHeader_length > 0)) {
		float pf = 1.0f; //partial fourier
		float shimSetting[8];
		char protocolName[kDICOMStrLarge], fmriExternalInfo[kDICOMStrLarge], coilID[kDICOMStrLarge], consistencyInfo[kDICOMStrLarge], coilElements[kDICOMStrLarge], wipMemBlock[kDICOMStrExtraLarge];
		TCsaAscii csaAscii;
		siemensCsaAscii(filename, &csaAscii, d->CSA.SeriesHeader_offset, d->CSA.SeriesHeader_length, shimSetting, coilID, consistencyInfo, coilElements, seqDetails, fmriExternalInfo, protocolName, wipMemBlock);
		inv1 = csaAscii.alTI[0] / 1000.0;
		inv2 = csaAscii.alTI[1] / 1000.0;
		lContrasts = csaAscii.lContrasts;
		//If parameter lInvContrasts exists in the protocol, a value of 1 indicates MPRAGE and a value of 2 MP2RAGE. Note that lInvContrasts is different from lContrasts and that only lInvContrasts must be considered.
		//If parameter lInvContrasts does not exist, then the presence of alTI[1] indicates that this is an MP2RAGE protocol. An MPRAGE protocol will only contain alTI[0].
		if (csaAscii.lInvContrasts == 1) //explicitly reports one TI
			inv2 = NAN;
		if ((!isnan(inv1)) && (!isnan(inv2)) && (inv1 > 0.0) && (inv2 > 0.0))
			isDualTI = true;

	}
	#endif // myReadAsciiCsa
	char *dataTypeBIDS = d->CSA.bidsDataType;
	strcpy(dataTypeBIDS, "");
	char *suffixBIDS = d->CSA.bidsEntitySuffix;
	strcpy(suffixBIDS, "");
	char modalityBIDS[kDICOMStrLarge]  = ""; //T1w, bold, dwi
	char recBIDS[kDICOMStrLarge]  = ""; //_desc-preproc
	if (d->manufacturer != kMANUFACTURER_SIEMENS)
		return;
	bool isReportEcho = true; //do not report _echo for PD/T2 pair or fieldmap
	bool isMultiEcho = false;
	bool isDerived = d->isDerived; //report phase encoding direction
	bool isDirLabel = false;
	bool isPart = false;
	if (d->isHasPhase)
		isPart = true;
	bool isAddSeriesToRun = true; //except phasemap, where phasediff and magnitude have different series numbers but must share acq 
	char seqName[kDICOMStrLarge];
	strcpy(seqName, d->sequenceName);
	if (strlen(d->sequenceName) < 2) //e.g. XA uses 0018,9005 while VE uses 0018,0024
		strcpy(seqName, d->pulseSequenceName);
	if (strlen(seqDetails) < 2)
		strcpy(seqDetails, seqName);
	if (strstr(d->imageType, "DERIVED")) {
		isDerived = true; //to do: respond to derived images
	}
	if (d->modality != kMODALITY_MR)
		return;
	if (((d->xyzDim[3] < 2) && (nConvert < 1)) || (d->isLocalizer)) { //need nConvert or nifti header
		strcpy(dataTypeBIDS, "discard");
		strcpy(modalityBIDS, "localizer");
	} else if (strstr(seqDetails,"b1map")) {
		//issue 751 nb both T1 and b1map can use tfl base
		//https://bids-specification.readthedocs.io/en/stable/appendices/qmri.html#tb1tfl-and-tb1rfm-specific-notes
		strcpy(dataTypeBIDS, "fmap");
		strcpy(modalityBIDS, "TB1TFL");
		if ((strstr(d->imageType, "FLIP ANGLE MAP")) || (strstr(d->imageType, "FLIP ANGLE MAP")))
			strcpy(preAcqStr, "famp");
		else
			strcpy(preAcqStr, "anat");
	} else if ((strstr(seqDetails, "tfl") != NULL) || (strstr(seqDetails, "mp2rage") != NULL) || (strstr(seqDetails, "wip925") != NULL)) { //prog_mprage
		strcpy(dataTypeBIDS, "anat");
		if (isDualTI)
			strcpy(modalityBIDS, "MP2RAGE");
		else { //bizarrely mprage can populate both alTI[0] alTI[1] see dcm_qa_xa30
			strcpy(modalityBIDS, "T1w");
			//bork inv2 = NAN;
		}
		if (strstr(d->imageType, "T1 MAP") != NULL) {
			strcpy(modalityBIDS, "T1map");
			isDualTI = false; //issue 750 derived from two images
		}
		if (strstr(d->imageType, "_UNI") != NULL) {
			isDualTI = false; //issue 750 derived from two images
			strcpy(modalityBIDS, "UNIT1");
			if (strstr(d->imageComments, "DENOISED IMAGE") != NULL)
				strcat(recBIDS, "denoise");
		}
		isDerived = false; //issue750 Siemens E11 considers UNIT1 derived, but BIDS does not
	} else if ((d->CSA.numDti > 0) || (strstr(seqDetails, "_diff") != NULL) || (strstr(seqDetails, "resolve") != NULL) || (strstr(seqDetails, "PtkSmsVB13ADwDualSpinEchoEpi") != NULL) || (strstr(seqDetails, "ep2d_stejskal_386") != NULL)) { //prog_diff
		strcpy(dataTypeBIDS, "dwi");
		strcpy(modalityBIDS, "dwi");
		if (strstr(d->seriesDescription, "_SBRef") != NULL)
			strcpy(modalityBIDS, "sbref");
		//if seriesDesc trace", "fa", "adc"  isDerived = true;
		isDirLabel = true;
	} else if ((strstr(seqDetails, "fairest")) || (strstr(seqDetails, "_asl") != NULL) || (strstr(seqDetails, "_pasl") != NULL) || (strstr(seqDetails, "pcasl") != NULL) || (strstr(seqDetails, "PCASL") != NULL)) { //prog_asl
		strcpy(dataTypeBIDS, "perf");
		strcpy(modalityBIDS, "asl");
		if (strstr(d->seriesDescription, "_m0") != NULL)
			strcpy(modalityBIDS, "m0scan");
	} else if (strstr(d->pulseSequenceName, "spcR") != NULL) {
		strcpy(dataTypeBIDS, "anat");
		strcpy(modalityBIDS, "T2w");
	} else if (strstr(seqDetails, "tse_vfl") != NULL) { //prog_tse_vfl
		strcpy(dataTypeBIDS, "anat");
		if ((strstr(seqDetails, "spcir") != NULL) || (strstr(d->sequenceName, "spcir") != NULL))
			strcpy(modalityBIDS, "FLAIR");
		else
			strcpy(modalityBIDS, "T2w");
	} else if (strstr(seqDetails, "tse") != NULL) { //prog_tse
		isReportEcho = false; //do not report _echo for T2/PDw pair
		strcpy(dataTypeBIDS, "anat");
		if (strstr(d->sequenceName, "tir") != NULL)
			strcpy(modalityBIDS, "FLAIR");
		if ((strstr(d->sequenceName, "tse2d") != NULL) || (strstr(d->pulseSequenceName, "tse2d") != NULL)) {
			if (d->TE < 50)
				strcpy(modalityBIDS, "PDw");
			else
				strcpy(modalityBIDS, "T2w");
		}
	} else if ((strstr(seqDetails, "ep2d_ase") != NULL)) { //prog_ep2d_se
		// oxygen extraction fraction(OEF) Asymmetric Spin Echo (ASE)
		//printWarning("BIDS does not yet specify `ase` data\n");
		//n.b. we do not specify dataTypeBIDS as not yet defined
		strcpy(modalityBIDS, "oef_ase");
	} else if ((strstr(seqDetails, "ep2d_se") != NULL)) { //prog_ep2d_se
		strcpy(dataTypeBIDS, "fmap");
		strcpy(modalityBIDS, "epi");
		isDirLabel = true;
	} else if ((strstr(seqDetails, "gre_field_mapping") != NULL)) { //prog_fmap
		isReportEcho = false; //echo encoded in "_magnitude"
		isAddSeriesToRun = false;
		isPart = false;
		strcpy(dataTypeBIDS, "fmap");
		if (d->isHasPhase)
			strcpy(modalityBIDS, "phasediff");
		if (d->isHasMagnitude)
			snprintf(modalityBIDS, kDICOMStrLarge - strlen(modalityBIDS), "magnitude%d", d->echoNum);
		//printf("magnitude%d\n", d->echoNum);
	//} else if (( seqName,"_tfl2d1") == 0) || (strcmp(dcmList[indx].sequenceName, "_fl3d1_ns") == 0) || (strcmp(dcmList[indx].sequenceName, "_fl2d1"
	} else if ((strstr(seqDetails, "\\trufi") != NULL) || (strstr(seqName, "fl3d1_ns") != NULL) || (strstr(seqName, "fl2d1") != NULL) || (strstr(seqName, "tfl2d1") != NULL)) { //localizers
		strcpy(dataTypeBIDS, "discard");
		strcpy(modalityBIDS, "localizer");
	} else if ((strstr(seqName, "fl3d1r") != NULL) || (strstr(seqName, "fl2d1") != NULL) || (strstr(seqName, "tfl2d1") != NULL)) { //localizers
		//nb ToF fl3d1r_ts fl3d1r_t70 fl3d1r7t but check for fl3d1r SWI
		strcpy(dataTypeBIDS, "anat");
		strcpy(modalityBIDS, "angio");
	} else if (strstr(seqDetails, "ep_seg_fid") != NULL) {
		//n.b. large echoTrainLength even for single echo acquisition
		strcpy(dataTypeBIDS, "anat");
		strcpy(modalityBIDS, "T2starw");
		isPart = true;
		if (strstr(d->seriesDescription, "mIP") != NULL) { //derived minimum intensity
			strcpy(dataTypeBIDS, "discard");
			strcpy(modalityBIDS, "mIP");
		}
		if (strstr(d->seriesDescription, "SWI_Images") != NULL) { //derived SWI
			strcpy(dataTypeBIDS, "discard");
			strcpy(modalityBIDS, "SWI_Images");
		}
	} else if (strstr(seqDetails, "gre") != NULL) { //prog_gre
		//printf("GRE T2starw or if MEGRE\n");
		strcpy(dataTypeBIDS, "anat");
		strcpy(modalityBIDS, "T2starw");
		if ((d->echoNum > 1) || (lContrasts > 1)) {
			strcpy(modalityBIDS, "MEGRE");
			isMultiEcho = true;
		}
		isPart = true;
	} else if ((strstr(seqDetails, "AALScout") != NULL) || (strstr(seqDetails, "haste") != NULL)) { //localizer: unused
		strcpy(dataTypeBIDS, "discard");
		strcpy(modalityBIDS, "localizer");
	} else if ((strstr(seqDetails, "_bold")) || (strstr(seqDetails, "pace"))
		|| (strstr(d->imageType, "FMRI")) || (strstr(seqDetails, "ep2d_fid"))) { //prog_bold
		//n.b. "Space" is not "pace"
		strcpy(dataTypeBIDS, "func");
		strcpy(modalityBIDS, "bold");
		isDirLabel = true;
		char* p = strstr(d->protocolName, "func_");
		if (p == d->protocolName)
		//todo issue753 infer task from d->protocolName
		if (strstr(d->seriesDescription, "_SBRef") != NULL)
			strcpy(modalityBIDS, "sbref");
	} else if (strstr(d->sequenceName, "*epse2d") != NULL) {
		//pepolar?
		strcpy(dataTypeBIDS, "fmap");
		strcpy(modalityBIDS, "epi");
		isDirLabel = true;
	}
	strcpy(acqStr, "_acq-");
	strcat(acqStr, preAcqStr);
	int len = strlen(seqName);
	if (len > 0) {
		for (int i = 0; i < len; i++) {
			char ch = seqName[i];
			if (ch == '*') continue;
			if ((ch >= '0' && ch <= '9') || (ch >= 'a' && ch <= 'z') || (ch >= 'A' && ch <= 'Z'))
				strncat(acqStr, &ch, 1);
			if (isdigit(ch)) break;
		}
	} //len > 0
	if (d->accelFactPE > 1)
		snprintf(acqStr + strlen(acqStr), kDICOMStrLarge - strlen(acqStr), "p%d", (int)round(d->accelFactPE));
	if (d->CSA.multiBandFactor > 1)
		snprintf(acqStr + strlen(acqStr), kDICOMStrLarge - strlen(acqStr), "m%d", (int)round(d->CSA.multiBandFactor));
	strcat(suffixBIDS, acqStr);
	//add _rec
	// https://bids-specification.readthedocs.io/en/stable/05-derivatives/02-common-data-types.html#common-file-level-metadata-fields
	if (strlen(recBIDS) > 0) {
		strcat(suffixBIDS, "_rec-");
		strcat(suffixBIDS, recBIDS);
	}
	//add dir
	//nb for func dir comes before echo
	int phPos = d->CSA.phaseEncodingDirectionPositive;
	if (isDirLabel) {
		char dirLabel[kDICOMStrLarge]  = "_dir-";
		if (d->phaseEncodingRC == 'C') {
			if (phPos)
				strcat(dirLabel, "AP");
			else
				strcat(dirLabel, "PA");
		} else {
			if (phPos)
				strcat(dirLabel, "RL");
			else
				strcat(dirLabel, "LR");
		}
		strcat(suffixBIDS, dirLabel);
	}
	//add run
	if (isAddSeriesToRun)
		snprintf(suffixBIDS + strlen(suffixBIDS), kDICOMStrLarge - strlen(suffixBIDS), "_run-%ld", d->seriesNum);
	//add echo
	if (isReportEcho)
		if ((d->echoNum > 1) || (isMultiEcho) || ((d->isMultiEcho) && (d->echoNum > 0)))
			snprintf(suffixBIDS + strlen(suffixBIDS), kDICOMStrLarge - strlen(suffixBIDS), "_echo-%d", d->echoNum);
	//add inv
	// https://bids-specification.readthedocs.io/en/stable/appendices/entities.html#inv
	if (isDualTI) {
		//n.b. Siemens uses alTI[0]/alTI[1] for inversion times: alTI[2] used by ASL
		int invIdx = 1;
		if (isSameFloatGE(d->TI, inv2))
			invIdx = 2;
		snprintf(suffixBIDS + strlen(suffixBIDS), kDICOMStrLarge - strlen(suffixBIDS), "_inv-%d", invIdx);
	}
	//add part
	if (isPart) {
		if (d->isHasPhase)
			strcat(suffixBIDS, "_part-phase");
		if (d->isHasMagnitude)
			strcat(suffixBIDS, "_part-mag");
	}
	if (strlen(modalityBIDS) > 0) {
		strcat(suffixBIDS, "_");
		strcat(suffixBIDS, modalityBIDS);
	}
	if ((isVerbose > 0) || (strlen(dataTypeBIDS) < 1))
		printf("::autoBids:Siemens CSAseqFname:'%s' pulseSeq:'%s' seqName:'%s'\n", 
			seqDetails, d->pulseSequenceName, d->sequenceName);
	if (isDerived)
		strcpy(dataTypeBIDS, "derived");
	//bork - ARC data follows
	/*
	if (strstr(dataTypeBIDS, "dwi")) {
		if (strstr(d->protocolName, "12 dirs"))
			strcpy(dataTypeBIDS, "discard");
	}
	if (strstr(dataTypeBIDS, "fmap"))
		strcpy(dataTypeBIDS, "discard");
	if (strstr(dataTypeBIDS, "perf"))
		strcpy(dataTypeBIDS, "discard");
	if (strstr(dataTypeBIDS, "func")) {
		if (d->TR > 9999) {
			if (nConvert < 60)
				strcpy(dataTypeBIDS, "discard");
			strcpy(d->CSA.bidsTask, "naming40");
		} else {
			if (!strcasestr(d->protocolName, "REST"))
				strcpy(dataTypeBIDS, "discard");
		}
		if (nConvert < 10)
			strcpy(dataTypeBIDS, "discard");
	}*/
} // setBidsSiemens()

void setBidsPhilips(struct TDICOMdata *d, int nConvert, int isVerbose) {
	if (d->manufacturer != kMANUFACTURER_PHILIPS)
		return;
	char *dataTypeBIDS = d->CSA.bidsDataType;
	strcpy(dataTypeBIDS, "");
	char *suffixBIDS = d->CSA.bidsEntitySuffix;
	strcpy(suffixBIDS, "");
	if (d->modality != kMODALITY_MR)
		return;
	char seqName[kDICOMStr] = "";
	strcpy(seqName, d->sequenceVariant);
	char modalityBIDS[kDICOMStrLarge]  = ""; //_acq-FL3p2m2
	bool isReportEcho = true;
	bool isDirLabel = false; //report phase encoding direction
	bool isDerived = d->isDerived; //report phase encoding direction
	bool isAddSeriesToRun = true;
	bool isPart = false;
	//d->pulseSequenceName, d->scanningSequence, d->sequenceVariant)
	if (((d->xyzDim[3] < 4) && (nConvert < 4)) || (d->isLocalizer)) {
		strcpy(dataTypeBIDS, "discard");
		strcpy(modalityBIDS, "localizer");
	} else if (strstr(seqName, "MP") != NULL) {
		strcpy(dataTypeBIDS, "anat");
		strcpy(modalityBIDS, "T1w");
	} else if ((d->isDiffusion) && (strstr(seqName, "SK") != NULL) && (strstr(d->scanningSequence, "SE") != NULL) ) {
		strcpy(dataTypeBIDS, "dwi");
		strcpy(modalityBIDS, "dwi");
	} else if (strstr(d->imageType, "PERFUSION") != NULL) {
		//scanSeq:'GR' seqVariant:'SK'
		strcpy(dataTypeBIDS, "perf");
		strcpy(modalityBIDS, "asl");
	} else if ((strstr(d->pulseSequenceName, "SEEPI") != NULL) && (!d->isDiffusion) && (strstr(seqName, "SK") != NULL) && (strstr(d->scanningSequence, "SE") != NULL) )  {
		//pepolar? d->pulseSequenceName
		isAddSeriesToRun = false;
		strcpy(dataTypeBIDS, "fmap");
		strcpy(modalityBIDS, "epi");
		printWarning("Unable to estimate BIDS `_dir` for fmap epi as Philips DICOMs do not report phase encoding polarity\n");
		isDirLabel = true;
	} else if ((!d->isDiffusion) && (strstr(seqName, "SK") != NULL) && (strstr(d->scanningSequence, "SE") != NULL) ) {
		strcpy(dataTypeBIDS, "anat");
		if (false)//((strstr(d->scanningSequence, "IR") != NULL))
			strcpy(modalityBIDS, "FLAIR");
		else if (d->TE < 40)
			strcpy(modalityBIDS, "PDw");
		else
			strcpy(modalityBIDS, "T2w");
	} else if ((strstr(seqName, "SK") != NULL) && (strstr(d->scanningSequence, "IR") != NULL) ) {
		strcpy(dataTypeBIDS, "anat");
		strcpy(modalityBIDS, "FLAIR");
	} else if ((strstr(d->imageType, "PERFUSION") != NULL) && (strstr(d->pulseSequenceName, "FEEPI") != NULL) && (strstr(seqName, "SK") != NULL) && (strstr(d->scanningSequence, "GR") != NULL) ) {
		strcpy(dataTypeBIDS, "perf");
		strcpy(modalityBIDS, "asl");
	} else if (((d->rawDataRunNumber >= 1)  || (strstr(d->pulseSequenceName, "FEEPI") != NULL)) && (strstr(seqName, "SK") != NULL) && (strstr(d->scanningSequence, "GR") != NULL) ) {
		//nb older Philips data does not record EPI so use 2005,1063 fMRIStatusIndication
		strcpy(dataTypeBIDS, "func");
		strcpy(modalityBIDS, "bold");
		isDirLabel = true;
	} else if ((strstr(seqName, "SS") != NULL) && (strstr(d->scanningSequence, "GR") != NULL) ) {
		strcpy(dataTypeBIDS, "anat");
		strcpy(modalityBIDS, "T2starw");
		isPart = true;
	} else if ((d->isRealIsPhaseMapHz) && (strstr(seqName, "SS") != NULL) && (strstr(d->scanningSequence, "RM") != NULL)) {
		//https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#expressing-the-mr-protocol-intent-for-fieldmaps
		//isRealIsPhaseMapHz for 'Case 3: Direct field mapping'
		//sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_fieldmap.nii[.gz]
		//sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude.nii[.gz]
		isReportEcho = false;
		strcpy(dataTypeBIDS, "fmap");
		if (d->isHasReal)
			strcpy(modalityBIDS, "fieldmap");
		else
			strcpy(modalityBIDS, "magnitude");
	} else if ((strstr(seqName, "SP") != NULL) && (strstr(d->scanningSequence, "GR") != NULL)) {
		//issue 753 need to distinguish different types of phase map see Levitas example B0_DTI_MED_RES
		// https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#case-3-direct-field-mapping
		printWarning("Unable to distinguish Philips fieldmaps: phase difference, two phase/magnitude, direct fieldmapping.");
		isReportEcho = false;
		strcpy(dataTypeBIDS, "fmap");
		if (d->isHasPhase)
			strcpy(modalityBIDS, "phasediff");
		else if (d->echoTrainLength < 2) 
			snprintf(modalityBIDS, kDICOMStrLarge - strlen(modalityBIDS), "magnitude%d", d->echoNum);

		if (d->echoTrainLength > 1) {
			if (d->isHasPhase)
				snprintf(modalityBIDS, kDICOMStrLarge - strlen(modalityBIDS), "phase%d", d->echoNum);
			else if (d->isHasImaginary)
				snprintf(modalityBIDS, kDICOMStrLarge - strlen(modalityBIDS), "imaginary%d", d->echoNum);
			else if (d->isHasReal)
				snprintf(modalityBIDS, kDICOMStrLarge - strlen(modalityBIDS), "real%d", d->echoNum);
			else
				snprintf(modalityBIDS, kDICOMStrLarge - strlen(modalityBIDS), "magnitude%d", d->echoNum);
		}
	}
	//add acq- 
	char acqStr[kDICOMStrLarge] = "";
	strcat(acqStr, "_acq-");
	int len = strlen(seqName);
	if (len > 0) {
		for (int i = 0; i < len; i++) {
			char ch = seqName[i];
			if ((ch >= '0' && ch <= '9') || (ch >= 'a' && ch <= 'z') || (ch >= 'A' && ch <= 'Z'))
				strncat(acqStr, &ch, 1);
		}
	} //len > 0
	len = strlen(d->scanningSequence);
	if (len > 0) {
		for (int i = 0; i < len; i++) {
			char ch = d->scanningSequence[i];
			if ((ch >= '0' && ch <= '9') || (ch >= 'a' && ch <= 'z') || (ch >= 'A' && ch <= 'Z'))
				strncat(acqStr, &ch, 1);
		}
	} //len > 0
	len = strlen(d->pulseSequenceName);
	if (len > 0) {
		for (int i = 0; i < len; i++) {
			char ch = d->pulseSequenceName[i];
			if ((ch >= '0' && ch <= '9') || (ch >= 'a' && ch <= 'z') || (ch >= 'A' && ch <= 'Z'))
				strncat(acqStr, &ch, 1);
		}
	} //len > 0
	if (d->triggerDelayTime > 1.0) //report post-label delays for MultiPhase ASL
		snprintf(acqStr + strlen(acqStr), kDICOMStrLarge - strlen(acqStr), "t%d", (int)roundf(d->triggerDelayTime));
	if (d->accelFactPE > 1.0) //n.b. Philips can have fractional sense, so multiply by 10 so x2.3 -> "p23"
		snprintf(acqStr + strlen(acqStr), kDICOMStrLarge - strlen(acqStr), "p%d", (int)round(10.0 * d->accelFactPE));
	if (d->CSA.multiBandFactor > 1)
		snprintf(acqStr + strlen(acqStr), kDICOMStrLarge - strlen(acqStr), "m%d", (int)round(d->CSA.multiBandFactor));
	//snprintf(acqStr + strlen(acqStr), kDICOMStrLarge - strlen(acqStr), "s%ld", d->seriesNum);
	strcat(suffixBIDS, acqStr);
	//add run
	if (isAddSeriesToRun)
		snprintf(suffixBIDS + strlen(suffixBIDS), kDICOMStrLarge - strlen(suffixBIDS), "_run-%ld", d->seriesNum);
	//add echo
	if (isReportEcho)
		if ((d->echoNum > 1) || ((d->isMultiEcho) && (d->echoNum > 0)))
			snprintf(suffixBIDS + strlen(suffixBIDS), kDICOMStrLarge - strlen(suffixBIDS), "_echo-%d", d->echoNum);
	//add part
	if (isPart) {
		if (d->isHasPhase)
			strcat(suffixBIDS, "_part-phase");
		if (d->isHasMagnitude)
			strcat(suffixBIDS, "_part-mag");
	}
	//finish suffix
	if (strlen(modalityBIDS) > 0) {
		strcat(suffixBIDS,"_");
		strcat(suffixBIDS,modalityBIDS);
	}
	//if ((isVerbose > 0) || (strlen(dataTypeBIDS) < 1))
	//if (isVerbose > 0)
		printf("::autoBids:Philips pulseSeq:'%s' scanSeq:'%s' seqVariant:'%s'\n", 
			d->pulseSequenceName, d->scanningSequence, d->sequenceVariant);
	if (isDerived)
		strcpy(dataTypeBIDS, "derived");
} //setBidsPhilips()

void setBidsGE(struct TDICOMdata *d, int nConvert, int isVerbose, const char *filename) {
	char seqName[kDICOMStrLarge] = "";
	strcat(seqName, d->phaseEncodingDirectionDisplayedUIH); //prefer InternalPulseSequenceName (0019,109e) 
	if (strlen(seqName) < 1) //fall back PulseSequenceName (0019,109c)
		strcat(seqName, d->pulseSequenceName);
	char *dataTypeBIDS = d->CSA.bidsDataType;
	strcpy(dataTypeBIDS, "");
	char *suffixBIDS = d->CSA.bidsEntitySuffix;
	strcpy(suffixBIDS, "");
	char modalityBIDS[kDICOMStrLarge]  = ""; //T1w, bold, dwi
	bool isDirLabel = false; //report phase encoding direction
	bool isDerived = d->isDerived; //report phase encoding direction
	bool isAddSeriesToRun = true;
	bool isReportEcho = true; //fieldmaps do not include _echo-
	bool isPart = false;
	bool isEPSE = strstr(d->scanningSequence, "EP\\SE") != NULL;
	bool isEPGR = strstr(d->scanningSequence, "EP\\GR") != NULL;
	bool isGR = isEPGR || (strstr(seqName, "GRE"));

	#ifdef myReadGeProtocolBlock
	//research mode EP\RM does not discriminate between SE and GE (EP\SE and EP||GR)
	//solution: check procedureStepDescription
	//if (strstr(d->scanningSequence, "EP\\RM")) {
	reportProtocolBlockGE(d, filename, isVerbose);
	if (strstr(d->procedureStepDescription, "Gradient Echo")) {
		isGR = true;
		if (strstr(d->scanningSequence, "EP\\RM"))
			isEPGR = true;
	}
	if (strstr(d->procedureStepDescription, "Spin Echo")) {
		if (strstr(d->scanningSequence, "EP\\RM"))
			isEPSE = true;
	}
	#endif
	int nVol = 1;
	if (d->locationsInAcquisition > 0)
		nVol = nConvert / d->locationsInAcquisition;
	if (((d->xyzDim[3] < 2) && (nConvert < 4)) || (d->isLocalizer)) {
		strcpy(dataTypeBIDS, "discard");
		strcpy(modalityBIDS, "localizer");
	} else if (strstr(d->seriesDescription, "3 Plane Loc")) {
		strcpy(dataTypeBIDS, "discard");
		strcpy(modalityBIDS, "localizer");
		isReportEcho = false;
	} else if ((d->isRealIsPhaseMapHz) || (strstr(seqName, "B0map")) || (strstr( d->pulseSequenceName, "3db0map"))) {
		//case sensitivity: B0Map vs 3db0map
		isReportEcho = false;
		isAddSeriesToRun = false;
		strcpy(dataTypeBIDS, "fmap");
		strcpy(modalityBIDS, "magnitude");
		if (d->isRealIsPhaseMapHz)
			strcpy(modalityBIDS, "fieldmap");
	} else if ((d->isMultiEcho) && (!isEPGR) && (isGR)) {
		//detect EFGRE3D "STAGE 24" sequence, see 7T 29.1 example
		// not sure if STAGE is always multiecho: strstr(d->seriesDescription, "STAGE")
		// bids validator 8/2023 complains about multi-echo T2star
		strcpy(dataTypeBIDS, "anat");
		strcpy(modalityBIDS, "T2starw");
		isPart = true;
	} else if (strcmp( seqName, "EFGRE3D") == 0) { 
		//3D gradient echo
		strcpy(dataTypeBIDS, "anat");
		strcpy(modalityBIDS, "T1w");
	} else if (strstr( seqName, "3dradial") && strstr( d->scanningSequence, "GR\\IR")) { 
		//Silenz anatomical
		strcpy(dataTypeBIDS, "anat");
		strcpy(modalityBIDS, "T1w");

	} else if (strstr( seqName, "FSE")) { 
		//"3DFSE" or "FSE" fast spin echo
		strcpy(dataTypeBIDS, "anat");
		if (strstr(d->scanningSequence, "IR"))
			strcpy(modalityBIDS, "FLAIR");
		else if (d->TE < 40)
			strcpy(modalityBIDS, "PDw");
		else
			strcpy(modalityBIDS, "T2w");
		//BIDS validator does not allow "_echo-2", rather PDw/T2w
		isReportEcho = false;
	} else if ((strcmp( seqName, "2DFAST") == 0) && (strstr(d->seriesDescription, "STAR"))) { 
		strcpy(dataTypeBIDS, "anat");
		strcpy(modalityBIDS, "T2starw");
		isPart = true;
	} else if (strstr(seqName, "asl")) {
		strcpy(dataTypeBIDS, "perf");
		strcpy(modalityBIDS, "asl");
	} else if (((isEPSE) && (!d->isDiffusion)) || ((strstr(d->seriesDescription, "fieldmap")) && (strstr(seqName, "EPI")))) { 
		//this is typically just a EP\SE b=0 DWI scan, so we need to rely on series description
		//https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#case-4-multiple-phase-encoded-directions-pepolar
		strcpy(dataTypeBIDS, "fmap");
		strcpy(modalityBIDS, "epi");
		isDirLabel = true;
	} else if (strstr(seqName, "LoopingStar")) {
		//silent fMRI
		d->is3DAcq = true; //bold without slicetiming
		strcpy(dataTypeBIDS, "func");
		strcpy(modalityBIDS, "bold");
	} else if (isEPGR) {
		//n.b. test BEFORE fieldmap to detect EPI
		strcpy(dataTypeBIDS, "func");
		strcpy(modalityBIDS, "bold");
		isDirLabel = true;
	} else if ((strstr(seqName, "EPI")) && (d->isDiffusion)) { 
		//nb Gradient Echo images can report b=0: scanSeq:'EP\GR' seqName:'29.1 fMRI/DTI' stepDesc:'29.1 fMRI/DTI' 
		strcpy(dataTypeBIDS, "dwi");
		strcpy(modalityBIDS, "dwi");
		isDirLabel = true;
	} else if (strstr(seqName, "tof")) {
		strcpy(dataTypeBIDS, "anat");
		strcpy(modalityBIDS, "angio");
	}
	if ((strstr(d->scanningSequence, "EP\\SE")) || (strstr(d->scanningSequence, "EP\\RM")))
		isDirLabel = true;
	//add _acq-
	char acqStr[kDICOMStrLarge] = "";
	strcat(acqStr, "_acq-");
	//ScanningSequence discriminates tagged and untagged ASL (RM vs RMIR)
	int len = strlen(seqName);
	if (len > 0) {
		for (int i = 0; i < len; i++) {
			char ch = seqName[i];
			if ((ch >= '0' && ch <= '9') || (ch >= 'a' && ch <= 'z') || (ch >= 'A' && ch <= 'Z'))
				strncat(acqStr, &ch, 1);
			//if (isdigit(ch)) break; // do not use, unlike Siemens digit can come at start 3DFSE or end EFGRE3D
		}
	} //len > 0
	if (d->accelFactPE > 1) //if in-plane acceleration
		snprintf(acqStr + strlen(acqStr), kDICOMStrLarge - strlen(acqStr), "p%d", (int)round(d->accelFactPE));
	if (d->CSA.multiBandFactor > 1) //if multiband
		snprintf(acqStr + strlen(acqStr), kDICOMStrLarge - strlen(acqStr), "m%d", (int)round(d->CSA.multiBandFactor));
	//snprintf(acqStr + strlen(acqStr), kDICOMStrLarge - strlen(acqStr), "s%ld", d->seriesNum);
	if (strlen(acqStr) > 4)
		strcat(suffixBIDS, acqStr);
	//add _dir-
	if (isDirLabel) {
		char dirLabel[kDICOMStrLarge]  = "_dir-";
		if (d->phaseEncodingRC == 'C') {
			if (d->phaseEncodingGE == kGE_PHASE_ENCODING_POLARITY_UNFLIPPED)
				strcat(dirLabel, "AP");
			else
				strcat(dirLabel, "PA");
		} else {
			if (d->phaseEncodingGE == kGE_PHASE_ENCODING_POLARITY_UNFLIPPED)
				strcat(dirLabel, "LR");
			else
				strcat(dirLabel, "RL");
		}
		strcat(suffixBIDS, dirLabel);
	}
	//add run
	if (isAddSeriesToRun)
		snprintf(suffixBIDS + strlen(suffixBIDS), kDICOMStrLarge - strlen(suffixBIDS), "_run-%ld", d->seriesNum);
	//add _echo-
	if (isReportEcho)
		if ((d->echoNum > 1) || ((d->isMultiEcho) && (d->echoNum > 0)))
			snprintf(suffixBIDS + strlen(suffixBIDS), kDICOMStrLarge - strlen(suffixBIDS), "_echo-%d", d->echoNum);
	//add part
	if (isPart) {
		if (d->isHasImaginary)
			strcat(suffixBIDS, "_part-imag");
		if (d->isHasReal)
			strcat(suffixBIDS, "_part-real");
		if (d->isHasPhase)
			strcat(suffixBIDS, "_part-phase");
		if (d->isHasMagnitude)
			strcat(suffixBIDS, "_part-mag");
	}
	//finish suffix
	if (strlen(modalityBIDS) > 0) {
		strcat(suffixBIDS,"_");
		strcat(suffixBIDS,modalityBIDS);
	}
	if ((isVerbose > 0) || (strlen(dataTypeBIDS) < 1))
		printf("::autoBids:GE usedSeqName:'%s' seqName:'%s' internalSeqName:'%s' seriesDesc:'%s' scanSeq:'%s' stepDesc:'%s' bidsData:'%s' bidsSuffix:'%s'\n", 
			seqName, d->pulseSequenceName, d->phaseEncodingDirectionDisplayedUIH, d->seriesDescription, d->scanningSequence, d->procedureStepDescription, dataTypeBIDS, suffixBIDS);
	if (isDerived)
		strcpy(dataTypeBIDS, "derived");
} // setBidsGE()

bool setBids(struct TDICOMdata *d, const char *filename, int nConvert, int isVerbose) {
	if (d->modality == kMODALITY_PT) {
		strcpy(d->CSA.bidsDataType, "PET");
		strcpy(d->CSA.bidsEntitySuffix, "PET");
		return true;
	}
	if (d->modality == kMODALITY_CT) {
		strcpy(d->CSA.bidsDataType, "CT");
		strcpy(d->CSA.bidsEntitySuffix, "CT");
		return true;
	}
	if (d->manufacturer == kMANUFACTURER_SIEMENS)
		setBidsSiemens(d, nConvert, isVerbose, filename);
	if (d->manufacturer == kMANUFACTURER_PHILIPS)
		setBidsPhilips(d, nConvert, isVerbose);
	if (d->manufacturer == kMANUFACTURER_GE)
		setBidsGE(d, nConvert, isVerbose, filename);
	return ((!strstr(d->CSA.bidsDataType, "discard")) && (!strstr(d->CSA.bidsDataType, "derived")));
	//printf("%s\\%s\n", d->CSA.bidsDataType, d->CSA.bidsEntitySuffix);
}

void sliceTimingGE(struct TDICOMdata *d, const char *filename, struct TDCMopts opts, struct nifti_1_header *hdr, struct TDCMsort *dcmSort, struct TDICOMdata *dcmList) {
	//we can often read GE slice timing from TriggerTime (0018,1060) or RTIA Timer (0021,105E)
	// if both of these methods fail, we can often guess based on slice order stored in the Private Protocol Data Block (0025,101B)
	// this is referred to as "rescue" as we only know the TR, not the TA. So assumes continuous scans with no gap
	if (d->manufacturer != kMANUFACTURER_GE)
		return;
	if ((d->is3DAcq) || (d->isLocalizer) || (hdr->dim[4] < 2))
		return; //no need for slice times
	if (hdr->dim[3] < 2)
		return;
	if ((d->protocolBlockStartGE < 128) || (d->protocolBlockLengthGE < 10)) {
		d->CSA.sliceTiming[0] = -1;
		printWarning("Unable to determine GE Slice timing, no Protocol Data Block GE (0025,101B): %s\n", filename);
		return;
	}
	//start version check:
	float geMajorVersion = 0;
	int geMajorVersionInt = 0, geMinorVersionInt = 0, geReleaseVersionInt = 0;
	char geVersionPrefix[3] = "";
	bool is27r3 = false;
	readSoftwareVersionsGE(d->softwareVersions, opts.isVerbose, geVersionPrefix, &geMajorVersion, &geMajorVersionInt, &geMinorVersionInt, &geReleaseVersionInt, &is27r3);
	//readSoftwareVersionsGE(&geMajorVersion);
	/*
	//used for oldSliceTimingGE
	if (!opts.isIgnorex0021x105E) {
		if ((geMajorVersionInt >= 28) && (d->CSA.sliceTiming[0] >= 0.0)) {
			//if (opts.isVerbose > 1)
			printMessage("GEversion %.1f, slice timing from DICOM (0021,105E).\n", geMajorVersion);
			return; //trust slice timings for versions > 27, see issue 336
		}
	}*/
	//end: version check
	if ((d->maxEchoNumGE > 0) && (d->internalepiVersionGE != 2)) // GE non-Diffusion only
		printWarning("GE sequence with %d echoes. See issue 359\n", d->maxEchoNumGE);
	if ((d->protocolBlockStartGE < 1) || (d->protocolBlockLengthGE < 19))
		return;
#ifdef myReadGeProtocolBlock
	//GE final desperate attempt to determine slice order
	// GE does not provide a good estimate for TA: here we use TR, which will be wrong for sparse designs
	// Also, unclear what happens if slice order is flipped
	// Therefore, we warning the user that we are guessing
	int viewOrderGE = -1;
	int sliceOrderGE = -1;
	int mbAccel = -1;
	int nSlices = -1;
	float groupDelay = 0.0;
	char seqStr[kDICOMStr] = "";
	char ioptGE[3000] = "";
	//printWarning("Using GE Protocol Data Block for BIDS data (beware: new feature)\n");
	int ok = geProtocolBlock(filename, d->protocolBlockStartGE, d->protocolBlockLengthGE, 0, &sliceOrderGE, &viewOrderGE, &mbAccel, &nSlices, &groupDelay, ioptGE, seqStr);
	if (ok != EXIT_SUCCESS) {
		d->CSA.sliceTiming[0] = -1;
		printWarning("Unable to estimate slice times: issue decoding GE protocol block.\n");
		return;
	}
	mbAccel = max(mbAccel, 1);
	if (nSlices != hdr->dim[3]) //redundant with locationsInAcquisition check?
		printWarning("Missing DICOMs, number of slices estimated (%d) differs from Protocol Block (0025,101B) report (%d).\n", hdr->dim[3], nSlices);
	d->CSA.multiBandFactor = max(d->CSA.multiBandFactor, mbAccel);
	bool isInterleaved = true;
	groupDelay *= 1000.0; //sec -> ms
	//
	// Estimate GE Slice Time only for EPI Multi-Phase (epi) or EPI fMRI/BrainWave (epiRT)
	//
	// BrainWave (epiRT)
	if (d->epiVersionGE >= kGE_EPI_PEPOLAR_FWD)
		printWarning("GE ABCD pepolar research sequence handling is experimental\n");//
	else if ((d->epiVersionGE == 1) || (strstr(ioptGE, "FMRI") != NULL)) { //-1 = not epi, 0 = epi, 1 = epiRT
		isInterleaved = (sliceOrderGE != 0);
		d->epiVersionGE = 1;
		d->internalepiVersionGE = 1; // 'EPI'(gradient echo)/'EPI2'(spin echo)
		if (!isSameFloatGE(groupDelay, d->groupDelay))
			printWarning("With epiRT (i.e. FMRI option), Group delay reported in private tag (0043,107C = %g) and Protocol Block (0025,101B = %g) differ.\n", d->groupDelay, groupDelay);
	}
	// EPI Multi-Phase (epi)
	else if ((d->epiVersionGE == 0) || (strstr(ioptGE, "MPh") != NULL)) { //-1 = not epi, 0 = epi, 1 = epiRT
		d->epiVersionGE = 0;
		d->internalepiVersionGE = 1; // 'EPI'(gradient echo)/'EPI2'(spin echo)
		if (groupDelay > 0) {
			d->TR += groupDelay;
			d->groupDelay = groupDelay;
		}
		// EPI Multi-Phase (epi) with Variable Delays (Unsupported)
		if (groupDelay < -0.5) {
			printWarning("SliceTiming Unsupported: GE Multi-Phase EPI with Variable Delays\n");
			d->CSA.sliceTiming[0] = -1;
			return;
		}
	}
	// Diffusion (see issue 635)
	else if ((d->epiVersionGE == 2) || (d->internalepiVersionGE == 2) || (strstr(ioptGE, "DIFF") != NULL)) {
		// diffusion gradient cycling OFF
		if (opts.diffCyclingModeGE >= 0)
			d->diffCyclingModeGE = opts.diffCyclingModeGE;
		if ((d->diffCyclingModeGE == kGE_DIFF_CYCLING_SPOFF) || (d->diffCyclingModeGE == kGE_DIFF_CYCLING_OFF))
			is27r3 = false;
		else if (d->diffCyclingModeGE == kGE_DIFF_CYCLING_ALLTR) {
			printWarning("Unable to compute slice times for GE Diffusion:Cycling\n");
			d->CSA.sliceTiming[0] = -1.0;
			return;
		}
		// TO DO: support 2TR/3TR cycling mode
		else if (d->diffCyclingModeGE == kGE_DIFF_CYCLING_2TR) {
			printWarning("Unable to compute slice times for GE Diffusion:2TR-Cycling\n");
			d->CSA.sliceTiming[0] = -1.0;
			return;
		}
		else if (d->diffCyclingModeGE == kGE_DIFF_CYCLING_3TR) {
			printWarning("Unable to compute slice times for GE Diffusion:3TR-Cyclin\n");
			d->CSA.sliceTiming[0] = -1.0;
			return;
		}
		else {
			printWarning("Unable to compute slice times for GE Diffusion\n");
			d->CSA.sliceTiming[0] = -1.0;
			return;
		}
	}
	// Others (Unsupported)
	else {
		printWarning("Unable to compute slice times for this GE dataset\n");
		d->CSA.sliceTiming[0] = -1.0;
		return;
	}
	if (opts.isVerbose > 1) {
		printMessage("GEiopt: %s, groupDelay (%g), internalepiVersionGE (%d), epiVersionGE(%d)\n", ioptGE, groupDelay, d->internalepiVersionGE, d->epiVersionGE);
		printMessage("GEversion %s%.1f_R0%d, TRms %g, interleaved %d, multiband %d, groupdelayms %g\n", geVersionPrefix, geMajorVersion, geReleaseVersionInt, d->TR, isInterleaved, d->CSA.multiBandFactor, d->groupDelay);
	}
	sliceTimeGE(d, d->CSA.multiBandFactor, hdr->dim[3], d->TR, isInterleaved, geMajorVersion, is27r3, d->groupDelay);
	sliceTimingGE_Testx0021x105E(d, opts, hdr, dcmSort, dcmList);
#endif
} //sliceTimingGE()

void reverseSliceTiming(struct TDICOMdata *d, int verbose, int nSL) {
	if ((d->CSA.protocolSliceNumber1 == 0) || ((d->CSA.protocolSliceNumber1 == 1)))
		return; //slices not flipped
	if (d->is3DAcq)
		return; //no need for slice times
	if (d->CSA.sliceTiming[0] < 0.0)
		return; //no slice times
	if (nSL > kMaxEPI3D)
		return;
	if (nSL < 2)
		return;
	if (verbose)
		printMessage("Slices were spatially flipped, so slice times are flipped\n");
	d->CSA.protocolSliceNumber1 = 0;
	float sliceTiming[kMaxEPI3D];
	for (int i = 0; i < nSL; i++)
		sliceTiming[i] = d->CSA.sliceTiming[i];
	for (int i = 0; i < nSL; i++)
		d->CSA.sliceTiming[i] = sliceTiming[(nSL - 1) - i];
}

int sliceTimingSiemens2D(struct TDCMsort *dcmSort, struct TDICOMdata *dcmList, struct nifti_1_header *hdr, int verbose, const char *filename, int nConvert) {
	//only for Siemens 2D images, use acquisitionTime
	uint64_t indx0 = dcmSort[0].indx; //first volume
	if (!(dcmList[indx0].manufacturer == kMANUFACTURER_SIEMENS))
		return 0;
	if (dcmList[indx0].is3DAcq)
		return 0; //no need for slice times
	if (dcmList[indx0].CSA.sliceTiming[0] >= 0.0)
		return 0; //slice times calculated
	if (dcmList[indx0].CSA.mosaicSlices > 1)
		return 0;
	if (nConvert != (hdr->dim[3] * hdr->dim[4]))
		return 0;
	if (hdr->dim[3] > (kMaxEPI3D - 1))
		return 0;
	int nZero = 0; //infer multiband: E11C may not populate kPATModeText
	for (int v = 0; v < hdr->dim[3]; v++) {
		dcmList[indx0].CSA.sliceTiming[v] = dcmList[dcmSort[v].indx].acquisitionTime; //nb format is HHMMSS we need to handle midnight-crossing and convert to ms, see checkSliceTiming()
		if (dcmList[indx0].CSA.sliceTiming[v] == dcmList[indx0].CSA.sliceTiming[0])
			nZero++;
	}
	if ((dcmList[indx0].CSA.multiBandFactor < 2) && (nZero > 1))
		dcmList[indx0].CSA.multiBandFactor = nZero;
	return 1;
}

void rescueSliceTimingSiemens(struct TDICOMdata *d, int verbose, int nSL, const char *filename) {
	if (d->is3DAcq)
		return; //no need for slice times
	if (d->CSA.multiBandFactor > 1)
		return; //pattern of multiband slice order unknown
	if (d->CSA.sliceTiming[0] >= 0.0)
		return; //slice times calculated
	if (d->CSA.mosaicSlices < 2)
		return; //20190807 E11C 2D (not mosaic) files do not report mosaicAcqTimes or multi-band factor.
	if (nSL < 2)
		return;
	if ((d->manufacturer != kMANUFACTURER_SIEMENS) || (d->CSA.SeriesHeader_offset < 1) || (d->CSA.SeriesHeader_length < 1))
		return;
#ifdef myReadAsciiCsa
	float shimSetting[8];
	char protocolName[kDICOMStrLarge], fmriExternalInfo[kDICOMStrLarge], coilID[kDICOMStrLarge], consistencyInfo[kDICOMStrLarge], coilElements[kDICOMStrLarge], pulseSequenceDetails[kDICOMStrLarge], wipMemBlock[kDICOMStrExtraLarge];
	TCsaAscii csaAscii;
	siemensCsaAscii(filename, &csaAscii, d->CSA.SeriesHeader_offset, d->CSA.SeriesHeader_length, shimSetting, coilID, consistencyInfo, coilElements, pulseSequenceDetails, fmriExternalInfo, protocolName, wipMemBlock);
	int ucMode = csaAscii.ucMode;
	if ((ucMode < 1) || (ucMode == 3) || (ucMode > 4))
		return;
	float trSec = d->TR / 1000.0;
	float delaySec = csaAscii.delayTimeInTR / 1000000.0;
	float taSec = trSec - delaySec;
	float sliceTiming[kMaxEPI3D];
	for (int i = 0; i < nSL; i++)
		sliceTiming[i] = i * taSec / nSL * 1000.0; //expected in ms
	if (ucMode == 1) //asc
		for (int i = 0; i < nSL; i++)
			d->CSA.sliceTiming[i] = sliceTiming[i];
	if (ucMode == 2) //desc
		for (int i = 0; i < nSL; i++)
			d->CSA.sliceTiming[i] = sliceTiming[(nSL - 1) - i];
	if (ucMode == 4) { //int
		int oddInc = 0; //for slices 1,3,5
		int evenInc = (nSL + 1) / 2; //for 4 slices 0,1,2,3 we will order [2,0,3,1] for 5 slices [0,3,1,4,2]
		if (nSL % 2 == 0) { //Siemens interleaved for acquisitions with odd number of slices https://www.mccauslandcenter.sc.edu/crnl/tools/stc
			oddInc = evenInc;
			evenInc = 0;
		}
		for (int i = 0; i < nSL; i++) {
			if (i % 2 == 0) { //odd slice 1,3,etc [indexed from 0]!
				d->CSA.sliceTiming[i] = sliceTiming[oddInc];
				//printf("%d %d\n", i, oddInc);
				oddInc += 1;
			} else { //even slice
				d->CSA.sliceTiming[i] = sliceTiming[evenInc];
				//printf("%d %d %d\n", i, evenInc, nSL);
				evenInc += 1;
			}
		}
	} //if ucMode == 3 int
	//dicm2nii provides sSliceArray.ucImageNumb - similar to protocolSliceNumber1
	//if asc_header(s, 'sSliceArray.ucImageNumb'), t = t(nSL:-1:1); end % rev-num
#endif
}

void sliceTimingUIH(struct TDCMsort *dcmSort, struct TDICOMdata *dcmList, struct nifti_1_header *hdr, int verbose, const char *filename, int nConvert) {
	uint64_t indx0 = dcmSort[0].indx; //first volume
	if (!(dcmList[indx0].manufacturer == kMANUFACTURER_UIH))
		return;
	if (nConvert != (hdr->dim[3] * hdr->dim[4]))
		return;
	if (hdr->dim[3] > (kMaxEPI3D - 1))
		return;
	if (hdr->dim[4] < 2)
		return;
	for (int v = 0; v < hdr->dim[3]; v++)
		dcmList[indx0].CSA.sliceTiming[v] = dcmList[dcmSort[v].indx].acquisitionTime; //nb format is HHMMSS we need to handle midnight-crossing and convert to ms, see checkSliceTiming()
}

/*
void oldSliceTimingGE(struct TDCMsort *dcmSort,struct TDICOMdata *dcmList, struct nifti_1_header * hdr, int verbose, const char * filename, int nConvert) {
	//GE check slice timing >>>
	uint64_t indx0 = dcmSort[0].indx; //first volume
	if (!(dcmList[indx0].manufacturer == kMANUFACTURER_GE)) return;
	bool GEsliceTiming_x0018x1060 = false;
	if ((hdr->dim[3] < (kMaxEPI3D-1)) && (hdr->dim[3] > 1) && (hdr->dim[4] > 1)) {
		//GE: 1st method for "epi" PSD
		//0018x1060 is defined in msec: http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,1060)
		//as of 20190704 dcm2niix expects sliceTiming to be encoded in msec for all vendors
		GEsliceTiming_x0018x1060 = true;
		for (int v = 0; v < hdr->dim[3]; v++) {
			if (dcmList[dcmSort[v].indx].CSA.sliceTiming[0] < 0)
				GEsliceTiming_x0018x1060 = false;
				dcmList[indx0].CSA.sliceTiming[v] = dcmList[dcmSort[v].indx].CSA.sliceTiming[0]; //ms 20190704
				//dcmList[indx0].CSA.sliceTiming[v] = dcmList[dcmSort[v].indx].CSA.sliceTiming[0] / 1000.0; //ms -> sec prior to 20190704
		}
		//printMessage(">>>>Reading GE slice timing from 0018,1060\n");
		//0018,1060 provides time at end of acquisition, not start...
		if (GEsliceTiming_x0018x1060) {
			float minT = dcmList[indx0].CSA.sliceTiming[0];
			float maxT = minT;
			for (int v = 0; v < hdr->dim[3]; v++)
				if (dcmList[indx0].CSA.sliceTiming[v] < minT)
					minT = dcmList[indx0].CSA.sliceTiming[v];
			for (int v = 0; v < hdr->dim[3]; v++)
				if (dcmList[indx0].CSA.sliceTiming[v] > maxT)
					maxT = dcmList[indx0].CSA.sliceTiming[v];
			for (int v = 0; v < hdr->dim[3]; v++)
				dcmList[indx0].CSA.sliceTiming[v] = dcmList[indx0].CSA.sliceTiming[v] - minT;
			if (isSameFloatGE(minT, maxT)) {
				//ABCD simulated GE DICOMs do not populate 0018,1060 correctly
				GEsliceTiming_x0018x1060 = false;
				dcmList[indx0].CSA.sliceTiming[0] = -1.0; //no valid slice times
			}
		} //adjust: first slice is time = 0.0
	} //GE slice timing from 0018,1060
	if ((!GEsliceTiming_x0018x1060) && (hdr->dim[3] < (kMaxEPI3D-1)) && (hdr->dim[3] > 1) && (hdr->dim[4] > 1)) {
		//printMessage(">>>>Reading GE slice timing from epiRT (0018,1060 did not work)\n");
		//GE: 2nd method for "epiRT" PSD
		//ignore bogus values of first volume https://neurostars.org/t/getting-missing-ge-information-required-by-bids-for-common-preprocessing/1357/6
		// this necessarily requires at last two volumes, hence dim[4] > 1
		int j = hdr->dim[3];
		//since first volume is bogus, we define the volume start time as the first slice in the second volume
		float minTime = dcmList[dcmSort[j].indx].rtia_timerGE;
		float maxTime = minTime;
		for (int v = 0; v < hdr->dim[3]; v++) {
			if (dcmList[dcmSort[v+j].indx].rtia_timerGE < minTime)
				minTime = dcmList[dcmSort[v+j].indx].rtia_timerGE;
			if (dcmList[dcmSort[v+j].indx].rtia_timerGE > maxTime)
				maxTime = dcmList[dcmSort[v+j].indx].rtia_timerGE;
		}
		//compare all slice times in 2nd volume to start time for this volume
		if (maxTime != minTime) {
			double scale2Sec = 1.0;
			if (dcmList[indx0].TR > 0.0) { //issue 286: determine units for rtia_timerGE
				//See https://github.com/rordenlab/dcm2niix/tree/master/GE
				// Nikadon's DV24 data stores RTIA Timer as seconds, issue 286 14_LX uses 1/10,000 sec
				// The slice timing should always be less than the TR (which is in ms)
				// Below we assume 1/10,000 of a sec if slice time is >90% and less than <100% of a TR
				// Will not work for sparse designs, but slice timing inappropriate for those datasets
				float maxSliceTimeFrac = (maxTime-minTime) / dcmList[indx0].TR; //should be slightly less than 1.0
				if ((maxSliceTimeFrac > 9.0) && (maxSliceTimeFrac < 10))
					scale2Sec = 1.0 / 10000.0;
				//printMessage(">> %g %g %g\n", maxSliceTimeFrac, scale2Sec, dcmList[indx0].TR);
			}
			double scale2ms = scale2Sec * 1000.0; //20190704: convert slice timing values to ms for all vendors
			for (int v = 0; v < hdr->dim[3]; v++)
				dcmList[indx0].CSA.sliceTiming[v] = (dcmList[dcmSort[v+j].indx].rtia_timerGE - minTime) * scale2ms;
			dcmList[indx0].CSA.sliceTiming[hdr->dim[3]] = -1;
			//detect multi-band
			int nZero = 0;
			for (int v = 0; v < hdr->dim[3]; v++)
				if (isSameFloatGE(dcmList[indx0].CSA.sliceTiming[hdr->dim[3]], 0.0))
					nZero ++;
			if ((nZero > 1) && (nZero < hdr->dim[3]) && ((hdr->dim[3] % nZero) == 0))
				dcmList[indx0].CSA.multiBandFactor = nZero;
			//report times
			if (verbose > 0) {
				printMessage("GE slice timing (sec)\n");
				printMessage("\tTime\tX\tY\tZ\tInstance\n");
				for (int v = 0; v < hdr->dim[3]; v++) {
					if (v == (hdr->dim[3]-1))
						printMessage("...\n");
					if ((v < 4) || (v == (hdr->dim[3]-1)))
						printMessage("\t%g\t%g\t%g\t%g\t%d\n", dcmList[indx0].CSA.sliceTiming[v] / 1000.0, dcmList[dcmSort[v+j].indx].patientPosition[1], dcmList[dcmSort[v+j].indx].patientPosition[2], dcmList[dcmSort[v+j].indx].patientPosition[3], dcmList[dcmSort[v+j].indx].imageNum);
				} //for v
			} //verbose > 1
		} //if maxTime != minTIme
	} //GE slice timing from 0021,105E
} //oldSliceTimingGE()
*/

int sliceTimingCore(struct TDCMsort *dcmSort, struct TDICOMdata *dcmList, struct nifti_1_header *hdr, int verbose, const char *filename, int nConvert, struct TDCMopts opts) {
	int sliceDir = 0;
	if (hdr->dim[3] < 2)
		return sliceDir;
	//uint64_t indx0 = dcmSort[0].indx;
	//uint64_t indx1 = dcmSort[1].indx;
	struct TDICOMdata *d0 = &dcmList[dcmSort[0].indx];
	uint64_t indx1 = dcmSort[0].indx;
	if (nConvert > 1) //use 2nd volume as CMRR bug can create bogus slice timing in first volume
		indx1 = dcmSort[1].indx;
	struct TDICOMdata *d1 = &dcmList[indx1];
	//oldSliceTimingGE(dcmSort, dcmList, hdr, verbose, filename, nConvert);
	sliceTimingUIH(dcmSort, dcmList, hdr, verbose, filename, nConvert);
	int isSliceTimeHHMMSS = sliceTimingSiemens2D(dcmSort, dcmList, hdr, verbose, filename, nConvert);
	sliceTimingXA(dcmSort, dcmList, hdr, verbose, filename, nConvert);
	checkSliceTiming(d0, d1, verbose, isSliceTimeHHMMSS);
	rescueSliceTimingSiemens(d0, verbose, hdr->dim[3], filename); //desperate attempts if conventional methods fail
	if (hdr->dim[3] > 1)
		sliceDir = headerDcm2Nii2(dcmList[dcmSort[0].indx], dcmList[indx1], hdr, true);
	//UNCOMMENT NEXT TWO LINES TO RE-ORDER MOSAIC WHERE CSA's protocolSliceNumber does not start with 1
	if (dcmList[dcmSort[0].indx].CSA.protocolSliceNumber1 > 1) {
		printWarning("Weird CSA 'ProtocolSliceNumber' (System/Miscellaneous/ImageNumbering reversed): VALIDATE SLICETIMING AND BVECS\n");
		//https://www.healthcare.siemens.com/siemens_hwem-hwem_ssxa_websites-context-root/wcm/idc/groups/public/@global/@imaging/@mri/documents/download/mdaz/nzmy/~edisp/mri_60_graessner-01646277.pdf
		//see https://github.com/neurolabusc/dcm2niix/issues/40
		sliceDir = -1; //not sure how to handle negative determinants?
	}
	if (sliceDir < 0) {
		if ((dcmList[dcmSort[0].indx].manufacturer == kMANUFACTURER_UIH) || (dcmList[dcmSort[0].indx].manufacturer == kMANUFACTURER_GE))
			dcmList[dcmSort[0].indx].CSA.protocolSliceNumber1 = -1;
	}
	sliceTimingGE(d0, filename, opts, hdr, dcmSort, dcmList);
	//ensure slice times have variability
	reverseSliceTiming(d0, verbose, hdr->dim[3]);
	bool allSame = true;
	for (int i = 0; i < hdr->dim[3]; i++)
		if (!isSameFloatGE(d0->CSA.sliceTiming[i], d0->CSA.sliceTiming[0]))
			allSame = false;
	if (allSame)
		d0->CSA.sliceTiming[0] = -1.0;
	return sliceDir;
} //sliceTiming()

void loadOverlay(char *imgname, unsigned char *img, int offset, int x, int y, int z) {
	int nvox = x * y * z;
	size_t imgszRead = (nvox + 7) >> 3; //overlay stored as 1 bit per voxel
	FILE *file = fopen(imgname, "rb");
	if (!file) {
		printError("Unable to open '%s'\n", imgname);
		return;
	}
	fseek(file, 0, SEEK_END);
	long fileLen = ftell(file);
	if (fileLen < (int)(imgszRead + offset)) {
		printWarning("File not large enough to store overlay: %s\n", imgname);
		return;
	}
	fseek(file, (long)offset, SEEK_SET);
	unsigned char *bImg = (unsigned char *)malloc(imgszRead);
	size_t sz = fread(bImg, 1, imgszRead, file);
	if (sz < imgszRead)
		printWarning("loadOverlay fread error.");
	//static unsigned char mask[] = {128, 64, 32, 16, 8, 4, 2, 1};
	static unsigned char mask[] = {1, 2, 4, 8, 16, 32, 64, 128};
	for (int i = 0; i < nvox; i++) {
		int byt = (i >> 3);
		int bit = (i % 8);
		img[i] = ((bImg[byt] & mask[bit]) != 0);
	}
	free(bImg);
	fclose(file);
	return;
} //loadOverlay()

int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata dcmList[], struct TSearchList *nameList, struct TDCMopts opts, struct TDTI4D *dti4D, int segVol) {
#if 0
#ifdef USING_DCM2NIIXFSWRAPPER
	double seriesNum = (double) dcmList[dcmSort[0].indx].seriesUidCrc;
	int segVolEcho = segVol;
	if ((dcmList[dcmSort[0].indx].echoNum > 1) && (segVolEcho <= 0))
		segVolEcho = dcmList[dcmSort[0].indx].echoNum + 1;
	if (segVolEcho > 0)
		seriesNum = seriesNum + ((double)segVolEcho - 1.0) / 10.0;

	if (!isSameDouble(opts.seriesNumber[0], seriesNum))
		return EXIT_SUCCESS;
#endif
#endif

	bool iVaries = intensityScaleVaries(nConvert, dcmSort, dcmList);
	float *sliceMMarray = NULL; //only used if slices are not equidistant
	uint64_t indx = dcmSort[0].indx;
	uint64_t indx0 = dcmSort[0].indx;
	//uint64_t indx1 = indx0;
	//if (nConvert > 1)
	//	indx1 = dcmSort[1].indx;
	uint64_t indxEnd = dcmSort[nConvert - 1].indx;
	dti4D->repetitionTimeInversion = 0.0; //only set for Siemens and GE 3D T1 "TR"
	dti4D->repetitionTimeExcitation = 0.0; //only set for Philips 3D T1 "TR"
	if (nConvert > 0) { //issue 616: not enhanced DICOMs: infer these arrays from multiple volumes
		dti4D->volumeOnsetTime[0] = -1;
		dti4D->decayFactor[0] = -1;
		dti4D->frameDuration[0] = -1;
		dti4D->frameReferenceTime[0] = -1;
	}
	if (strlen(dcmList[indx0].patientOrient) < 3)
		printWarning("Patient Position (0018,5100) not specified (issue 642).\n");
	if (dcmList[indx0].isQuadruped)
		printWarning("Anatomical Orientation Type (0010,2210) is QUADRUPED: rotate coordinates accordingly (issue 642)\n");
#ifdef newTilt //see issue 254
	if (((nConvert > 1) || (dcmList[indx0].xyzDim[3] > 1)) && ((dcmList[indx0].modality == kMODALITY_CT) || (dcmList[indx0].isXRay) || (dcmList[indx0].gantryTilt > 0.0))) { //issue372: enhanced DICOMs can also have gantry tilt
		dcmList[indx0].gantryTilt = computeGantryTiltPrecise(dcmList[indx0], dcmList[indxEnd], opts.isVerbose);
		if (isnan(dcmList[indx0].gantryTilt))
			return EXIT_FAILURE;
	}
#endif //newTilt see issue 254
	if (dcmList[indx0].isPrivateCreatorRemap)
		printWarning("PrivateCreator remapping detected. DICOMs are not archival quality (issue 435).\n");
	if (dcmList[indx0].isScaleVariesEnh) //issue363
		iVaries = true;
	if ((dcmList[indx].isXA10A) && (dcmList[indx].CSA.mosaicSlices < 0)) {
		printMessage("Siemens XA10 Mosaics are not primary images and lack vital data.\n");
		printMessage(" See https://github.com/rordenlab/dcm2niix/issues/236\n");
#ifdef mySaveXA10Mosaics
		int n;
		printMessage("INPUT REQUIRED FOR %s\n", dcmList[indx].imageBaseName);
		printMessage("PLEASE ENTER NUMBER OF SLICES IN MOSAIC:\n");
		scanf("%d", &n);
		for (int i = 0; i < nConvert; i++)
			dcmList[dcmSort[i].indx].CSA.mosaicSlices = n;
#endif
	}
	if (opts.isIgnoreDerivedAnd2D && dcmList[indx].isDerived) {
		printMessage("Ignoring derived image(s) of series %ld %s\n", dcmList[indx].seriesNum, nameList->str[indx]);
		return EXIT_SUCCESS;
	}
	if ((opts.isIgnoreDerivedAnd2D) && ((dcmList[indx].isLocalizer) || (strcmp(dcmList[indx].sequenceName, "_tfl2d1") == 0) || (strcmp(dcmList[indx].sequenceName, "_fl3d1_ns") == 0) || (strcmp(dcmList[indx].sequenceName, "_fl2d1") == 0))) {
		printMessage("Ignoring localizer (sequence '%s') of series %ld %s\n", dcmList[indx].sequenceName, dcmList[indx].seriesNum, nameList->str[indx]);
		return EXIT_SUCCESS;
	}
	if ((opts.isIgnoreDerivedAnd2D) && ((strcmp(dcmList[indx].sequenceName, "*tfl2d1") == 0) || (strcmp(dcmList[indx].sequenceName, "*fl3d1_ns") == 0) || (strcmp(dcmList[indx].sequenceName, "*fl2d1") == 0))) {
		printMessage("Ignoring localizer (sequence '%s') of series %ld %s\n", dcmList[indx].sequenceName, dcmList[indx].seriesNum, nameList->str[indx]);
		return EXIT_SUCCESS;
	} //issue398 old versions of dcm2niix converted "*" to "_" as it is an illegal filename, modern versions preserve
	if ((opts.isIgnoreDerivedAnd2D) && (nConvert < 2) && (dcmList[indx].CSA.mosaicSlices < 2) && (dcmList[indx].xyzDim[3] < 2)) {
		printMessage("Ignoring 2D image of series %ld %s\n", dcmList[indx].seriesNum, nameList->str[indx]);
		return EXIT_SUCCESS;
	}
	if (dcmList[indx].manufacturer == kMANUFACTURER_UNKNOWN)
		printWarning("Unable to determine manufacturer (0008,0070), so conversion is not tuned for vendor.\n");
#ifdef myForce3DPhaseRealImaginary //compiler option: segment each phase/real/imaginary map
	bool saveAs3D = dcmList[indx].isHasPhase || dcmList[indx].isHasReal || dcmList[indx].isHasImaginary;
#else
	bool saveAs3D = false;
#endif

#ifdef USING_DCM2NIIXFSWRAPPER
	mrifsStruct.tdicomData = dcmList[indx];  // first in sorted list dcmSort
#endif 

	struct nifti_1_header hdr0 =  {0};
	unsigned char *img = nii_loadImgXL(nameList->str[indx], &hdr0, dcmList[indx], iVaries, opts.compressFlag, opts.isVerbose, dti4D);
	if (strlen(opts.imageComments) > 0) {
		for (int i = 0; i < 24; i++)
			hdr0.aux_file[i] = 0; //remove dcm.imageComments
		snprintf(hdr0.aux_file, 24, "%s", opts.imageComments);
	}
	if (opts.isVerbose)
		printMessage("Converting %s\n", nameList->str[indx]);
	if (img == NULL)
		return EXIT_FAILURE;
	size_t imgsz = nii_ImgBytes(hdr0);
	unsigned char *imgM = (unsigned char *)malloc(imgsz * (uint64_t)nConvert);
	memcpy(&imgM[0], &img[0], imgsz);
	free(img);

#ifdef USING_DCM2NIIXFSWRAPPER
	printMessage("load Image %s\n", nameList->str[indx]);
#endif

	//printMessage(" %d %d %d %d %lu\n", hdr0.dim[1], hdr0.dim[2], hdr0.dim[3], hdr0.dim[4], (unsigned long)[imgM length]);
	bool isHasOverlay = dcmList[indx0].isHasOverlay;
	bool isDerived = dcmList[indx0].isDerived;
	if (nConvert > 1) {
		//next: detect trigger time see example https://www.slicer.org/wiki/Documentation/4.4/Modules/MultiVolumeExplorer
		double triggerDx = dcmList[dcmSort[nConvert - 1].indx].triggerDelayTime - dcmList[indx0].triggerDelayTime;
		if ((triggerDx > 0.0) && (dcmList[indx0].aslFlags == kASL_FLAG_NONE)) //issue 384, issue533
			dcmList[indx0].triggerDelayTime = triggerDx;
		//next: determine gantry tilt
		if (dcmList[indx0].gantryTilt != 0.0f)
			printWarning("Note these images have gantry tilt of %g degrees (manufacturer ID = %d)\n", dcmList[indx0].gantryTilt, dcmList[indx0].manufacturer);
		if (hdr0.dim[3] < 2) {
			//stack volumes with multiple acquisitions
			int nAcq = 1;
			//Next line works in theory, but fails with Siemens CT that saves pairs of slices as acquisitions, see example "testSiemensStackAcq"
			// nAcq = 1+abs( dcmList[dcmSort[nConvert-1].indx].acquNum-dcmList[indx0].acquNum);
			//therefore, the 'same position' is the most robust solution in the real world.
			if ((dcmList[indx0].manufacturer == kMANUFACTURER_SIEMENS) && (isSameFloat(dcmList[indx0].TR, 0.0f))) {
				nConvert = siemensCtKludge(nConvert, dcmSort, dcmList);
			}
			//resolve GE discrepancy between tags 0020,1002; 0021,104F; 0054,0081
			// e.g. T1 scans can be interpolated in the slice direction, so choose large number
			// EPI can report total number of slices (dim3*dim4), so choose smaller number
			if ((nAcq == 1) && (dcmList[indx0].locationsInAcquisitionConflict > 0) && ((nConvert % dcmList[indx0].locationsInAcquisitionConflict) == 0)) {
				//printMessage(" >>>%d %d %d %d\n", nAcq, nConvert, dcmList[indx0].locationsInAcquisitionConflict, dcmList[indx0].locationsInAcquisition);
				nAcq = 0;
				for (int i = 0; i < nConvert; i++)
					if (isSamePosition(dcmList[dcmSort[0].indx], dcmList[dcmSort[i].indx]))
						nAcq++;
				int nAcqConflict = nConvert / dcmList[indx0].locationsInAcquisitionConflict;
				if (nAcq == nAcqConflict) {
					printMessage("Resolved discrepancy between tags (0020,1002; 0021,104F; 0054,0081)\n");
					dcmList[indx0].locationsInAcquisition = dcmList[indx0].locationsInAcquisitionConflict;
				}
			}
			if ((nConvert > 1) && (nAcq == 1) && (dcmList[indx0].locationsInAcquisition > 0)) {
				if ((nConvert % dcmList[indx0].locationsInAcquisition) == 0)
					nAcq = nConvert / dcmList[indx0].locationsInAcquisition;
				else
					printMessage("DICOM images may be missing, expected %d spatial locations per volume, but found %d slices.\n", dcmList[indx0].locationsInAcquisition, nConvert);
			}
			//end validate number of spatial volumes: check that number of times a spatial position is repeated matches number of 3D volumes in 4D dataset
			int nSamePos = 0;
			for (int i = 0; i < nConvert; i++)
			if (isSamePosition(dcmList[dcmSort[0].indx], dcmList[dcmSort[i].indx]))
				nSamePos++;
			if ((nAcq < 2) && (nSamePos > 0)) nAcq = nSamePos;
			if (nAcq > nSamePos) { //issue556
				if ((dcmList[indx0].manufacturer == kMANUFACTURER_GE) && (dcmList[indx0].zThick > dcmList[indx0].xyzMM[3])) {
					int zipFactor = (int)roundf(dcmList[indx0].zThick / dcmList[indx0].xyzMM[3]);
					if (zipFactor > 1) {
						nAcq = nSamePos;
						dcmList[dcmSort[0].indx].interp3D = zipFactor;
					}
				}
			}
			if ((nAcq != nSamePos) && (!isDerived)) //Siemens Derived FA-RGB images have bogus spatial data
				printWarning("Expected %d volumes but found spatial position repeats %d times.\n", nAcq, nSamePos);
			//end validate number of spatial volumes
			if ((nAcq > 1) && ((nConvert / nAcq) > 1) && ((nConvert % nAcq) == 0)) {
				hdr0.dim[3] = nConvert / nAcq;
				hdr0.dim[4] = nAcq;
				hdr0.dim[0] = 4;
				if ((dcmList[indx0].locationsInAcquisition > 0) && (dcmList[indx0].locationsInAcquisition != hdr0.dim[3]))
					printMessage("DICOM images may be missing, expected %d spatial locations per volume, but found %d.\n", dcmList[indx0].locationsInAcquisition, hdr0.dim[3]);
			} else if ((dcmList[indx0].isXA10A) && (nConvert > nAcq) && (nAcq > 1)) {
				nAcq -= 1;
				hdr0.dim[3] = nConvert / nAcq;
				hdr0.dim[4] = nAcq;
				hdr0.dim[0] = 4;
				if ((nAcq > 1) && (nConvert != nAcq)) {
					printMessage("Slice positions repeated, but number of slices (%d) not divisible by number of repeats (%d): converting only complete volumes.\n", nConvert, nAcq);
				}
			} else {
				hdr0.dim[3] = nConvert;
				if ((nAcq > 1) && (nConvert != nAcq)) {
					printMessage("Slice positions repeated, but number of slices (%d) not divisible by number of repeats (%d): missing images?\n", nConvert, nAcq);
					if (dcmList[indx0].locationsInAcquisition > 0)
						printMessage("Hint: expected %d locations\n", dcmList[indx0].locationsInAcquisition);
				}
			}
			//next options removed: features now thoroughly detected in nii_loadDir()
			for (int i = 0; i < nConvert; i++) { //make sure 1st volume describes shared features
				if (dcmList[dcmSort[i].indx].isHasOverlay)
					isHasOverlay = true;
				if (dcmList[dcmSort[i].indx].isCoilVaries)
					dcmList[indx0].isCoilVaries = true;
				if (dcmList[dcmSort[i].indx].isMultiEcho)
					dcmList[indx0].isMultiEcho = true;
				if (dcmList[dcmSort[i].indx].isNonParallelSlices)
					dcmList[indx0].isNonParallelSlices = true;
				if (dcmList[dcmSort[i].indx].isHasPhase)
					dcmList[indx0].isHasPhase = true;
				if (dcmList[dcmSort[i].indx].isHasReal)
					dcmList[indx0].isHasReal = true;
				if (dcmList[dcmSort[i].indx].isHasImaginary)
					dcmList[indx0].isHasImaginary = true;
			}
			//next: detect variable inter-volume time https://github.com/rordenlab/dcm2niix/issues/184
			//if ((nConvert > 1) && ((dcmList[indx0].modality == kMODALITY_PT)|| (opts.isForceOnsetTimes))) {
			if ((nConvert > 1) && ((dcmList[indx0].modality == kMODALITY_PT) || ((opts.isForceOnsetTimes) && (dcmList[indx0].manufacturer != kMANUFACTURER_GE)))) {
				if (((dcmList[indx0].modality == kMODALITY_PT) && (dcmList[indx0].frameReferenceTime >= 0.0)) || (dcmList[dcmSort[0].indx].manufacturer == kMANUFACTURER_PHILIPS)) { //PT: issue 577
					ensureSequentialSlicePositions(hdr0.dim[3], hdr0.dim[4], dcmSort, dcmList, opts.isVerbose); //issue529
					indx0 = dcmSort[0].indx;
				}
				//printf("Bogo529\n"); return EXIT_SUCCESS;
				//note: GE 0008,0032 unreliable, see mb=6 data from sw27.0 20201026
				//issue 407
				int nTR = 0;
				for (int i = 0; i < nConvert; i++)
					if (isSamePosition(dcmList[indx0], dcmList[dcmSort[i].indx])) {
						dti4D->frameDuration[nTR] = dcmList[dcmSort[i].indx].frameDuration;
						dti4D->frameReferenceTime[nTR] = dcmList[dcmSort[i].indx].frameReferenceTime;
						nTR += 1;
						if (nTR >= kMaxDTI4D)
							break;
					}
				bool trVaries = false;
				bool dayVaries = false;
				float tr = -1.0;
				float mintr = 1000000;
				float maxtr = -1.0;
				float volumeTimeStartFirstStartLast = -1.0;
				int nVol = 0;
				uint64_t prevVolIndx = indx0;
				for (int i = 0; i < nConvert; i++)
					if (isSamePosition(dcmList[indx0], dcmList[dcmSort[i].indx])) {
						float trDiff = acquisitionTimeDifference(&dcmList[prevVolIndx], &dcmList[dcmSort[i].indx]);
						prevVolIndx = dcmSort[i].indx;
						nVol++;
						if (trDiff <= 0)
							continue;
						mintr = min(mintr, trDiff);
						maxtr = max(maxtr, trDiff);
						if (tr < 0)
							tr = trDiff;
						if (trDiff < 0)
							dayVaries = true;
						float trDiff0 = acquisitionTimeDifference(&dcmList[indx0], &dcmList[dcmSort[i].indx]);
						volumeTimeStartFirstStartLast = max(volumeTimeStartFirstStartLast, trDiff0);
					}
				float toleranceSec = 50.0 / 1000.0; //e.g. 50/1000 = 50ms
				if ((nVol > 1) && (volumeTimeStartFirstStartLast > 0.0)) {
					tr = volumeTimeStartFirstStartLast / (nVol - 1.0);
					if (fabs(tr - hdr0.pixdim[4]) > toleranceSec) {
						if (dcmList[indx0].numberOfAverages > 1.0) //e.g. Mediso will save averaged data
							tr = tr / dcmList[indx0].numberOfAverages;
						if (fabs(tr - hdr0.pixdim[4]) > toleranceSec) {
							if (hdr0.pixdim[4] > 0.0)
								printWarning("Discrepancy between reported (%gs) and estimated (%gs) repetition time (issue 560).\n", hdr0.pixdim[4], tr);
							if ((dcmList[indx0].isIR) && (dcmList[indx0].manufacturer != kMANUFACTURER_PHILIPS))
								dti4D->repetitionTimeInversion = hdr0.pixdim[4];
							else
								dti4D->repetitionTimeExcitation = hdr0.pixdim[4];
							hdr0.pixdim[4] = tr;
							dcmList[indx0].TR = tr * 1000.0; //as msec
						}
					}
				}
				if (dcmList[indx0].aslFlags != kASL_FLAG_NONE) { //issue533
					int nTR = 0;
					for (int i = 0; i < nConvert; i++) {
						if (isSamePosition(dcmList[indx0], dcmList[dcmSort[i].indx])) {
							dti4D->triggerDelayTime[nTR] = dcmList[dcmSort[i].indx].triggerDelayTime;
							nTR += 1;
							if (nTR >= kMaxDTI4D)
								break;
						}
					} //for each volume
				} //if ASL
				if ((maxtr - mintr) > toleranceSec)
					trVaries = true;
				if (trVaries) {
					if (dayVaries)
						printWarning("Seconds between volumes varies (perhaps run through midnight)\n");
					else
						printWarning("Seconds between volumes varies\n");
					//issue 407
					int nTR = 0;
					for (int i = 0; i < nConvert; i++)
						if (isSamePosition(dcmList[indx0], dcmList[dcmSort[i].indx])) {
							float trDiff = acquisitionTimeDifference(&dcmList[indx0], &dcmList[dcmSort[i].indx]);
							dti4D->volumeOnsetTime[nTR] = trDiff;
							dti4D->decayFactor[nTR] = dcmList[dcmSort[i].indx].decayFactor;
							nTR += 1;
							if (nTR >= kMaxDTI4D)
								break;
						}
					if (dcmList[indx0].modality != kMODALITY_PT)
						dti4D->decayFactor[0] = -1.0; //only for PET
					else
						hdr0.pixdim[4] = 0.0;
					// saveAs3D = true;
					// printWarning("Creating independent volumes as time between volumes varies\n");
					if (opts.isVerbose) {
						printMessage(" OnsetTime = [");
						for (int i = 0; i < nConvert; i++)
							if (isSamePosition(dcmList[indx0], dcmList[dcmSort[i].indx])) {
								float trDiff = acquisitionTimeDifference(&dcmList[indx0], &dcmList[dcmSort[i].indx]);
								printMessage(" %g", trDiff);
							}
						printMessage(" ]\n");
					}
				} //if trVaries
			} //if PET
			//next: detect variable inter-slice distance
			float dx = intersliceDistance(dcmList[dcmSort[0].indx], dcmList[dcmSort[1].indx]);
//#ifdef myInstanceNumberOrderIsNotSpatial
			if (!isSameFloat(dx, 0.0)) //only for XYZT, not TXYZ: perhaps run for swapDim3Dim4? Extremely rare anomaly
				if (!ensureSequentialSlicePositions(hdr0.dim[3], hdr0.dim[4], dcmSort, dcmList, opts.isVerbose))
					dx = intersliceDistance(dcmList[dcmSort[0].indx], dcmList[dcmSort[1].indx]);
			indx0 = dcmSort[0].indx;
//#endif
			bool dxVaries = false;
			for (int i = 1; i < nConvert; i++)
				if (!isSameFloatT(dx, intersliceDistance(dcmList[dcmSort[i - 1].indx], dcmList[dcmSort[i].indx]), kSliceTolerance))
					dxVaries = true;
			if (hdr0.dim[4] < 2) {
				if (dxVaries) {
					sliceMMarray = (float *)malloc(sizeof(float) * nConvert);
					sliceMMarray[0] = 0.0f;
					for (int i = 1; i < nConvert; i++)
						sliceMMarray[i] = intersliceDistance(dcmList[dcmSort[0].indx], dcmList[dcmSort[i].indx]);
					printWarning("Interslice distance varies in this volume (incompatible with NIfTI format).\n");
					if (opts.isVerbose) {
						printMessage("Dimensions %d %d %d %d nAcq %d nConvert %d\n", hdr0.dim[1], hdr0.dim[2], hdr0.dim[3], hdr0.dim[4], nAcq, nConvert);
						printMessage(" Distance from first slice:\n");
						printMessage("dx=[0");
						for (int i = 1; i < nConvert; i++)
							printMessage(" %g", sliceMMarray[i]);
						printMessage("]\n");
					}
#ifndef myInstanceNumberOrderIsNotSpatial
					//kludge to handle single volume without instance numbers (0020,0013), e.g. https://www.morphosource.org/Detail/MediaDetail/Show/media_id/8430
					bool isInconsistenSliceDir = false;
					int slicePositionRepeats = 1; //how many times is first position repeated
					if (nConvert > 2) {
						float dxPrev = intersliceDistance(dcmList[dcmSort[0].indx], dcmList[dcmSort[1].indx]);
						if (isSameFloatGE(dxPrev, 0.0))
							slicePositionRepeats++;
						for (int i = 2; i < nConvert; i++) {
							float dx = intersliceDistance(dcmList[dcmSort[0].indx], dcmList[dcmSort[i].indx]);
							if (dx < dxPrev)
								isInconsistenSliceDir = true;
							if (isSameFloatGE(dxPrev, 0.0))
								slicePositionRepeats++;
							dxPrev = dx;
						}
					}
					if ((isInconsistenSliceDir) && (slicePositionRepeats == 1)) {
						//printWarning("Slice order as defined by instance number not spatially sequential.\n");
						//printWarning("Attempting to reorder slices based on spatial position.\n");
						ensureSequentialSlicePositions(hdr0.dim[3], hdr0.dim[4], dcmSort, dcmList, opts.isVerbose);
						dx = intersliceDistance(dcmList[dcmSort[0].indx], dcmList[dcmSort[1].indx]);
						hdr0.pixdim[3] = dx;
						isInconsistenSliceDir = false;
						//code below duplicates prior code, could be written as modular function(s)
						indx0 = dcmSort[0].indx;
						//if (nConvert > 1)
						//	indx1 = dcmSort[1].indx;
						dxVaries = false;
						dx = intersliceDistance(dcmList[dcmSort[0].indx], dcmList[dcmSort[1].indx]);
						for (int i = 1; i < nConvert; i++)
							if (!isSameFloatT(dx, intersliceDistance(dcmList[dcmSort[i - 1].indx], dcmList[dcmSort[i].indx]), kSliceTolerance))
								dxVaries = true;
						for (int i = 1; i < nConvert; i++)
							sliceMMarray[i] = intersliceDistance(dcmList[dcmSort[0].indx], dcmList[dcmSort[i].indx]);
						//printf("dx=[");
						//for (int i = 1; i < nConvert; i++)
						//	printf("%g ", intersliceDistance(dcmList[dcmSort[0].indx],dcmList[dcmSort[i].indx]) );
						//printf("\n");
						isInconsistenSliceDir = false;
						int slicePositionRepeats = 1; //how many times is first position repeated
						if (nConvert > 2) {
							float dxPrev = intersliceDistance(dcmList[dcmSort[0].indx], dcmList[dcmSort[1].indx]);
							if (isSameFloatGE(dxPrev, 0.0))
								slicePositionRepeats++;
							for (int i = 2; i < nConvert; i++) {
								float dx = intersliceDistance(dcmList[dcmSort[0].indx], dcmList[dcmSort[i].indx]);
								if (dx < dxPrev)
									isInconsistenSliceDir = true;
								if (isSameFloatGE(dxPrev, 0.0))
									slicePositionRepeats++;
								dxPrev = dx;
							}
						}
						if (!dxVaries) {
							printMessage("Slice re-ordering resolved inter-slice distance variability.\n");
							free(sliceMMarray);
							sliceMMarray = NULL;
						}
					}
					if (isInconsistenSliceDir) {
						printMessage("Unable to equalize slice distances: slice order not consistently ascending.\n");
						printMessage("First spatial position repeated %d times\n", slicePositionRepeats);
						printError(" Recompiling with '-DmyInstanceNumberOrderIsNotSpatial' might help.\n");
						return EXIT_FAILURE;
					}
#endif
					int imageNumRange = 1 + abs(dcmList[dcmSort[nConvert - 1].indx].imageNum - dcmList[dcmSort[0].indx].imageNum);
					if ((imageNumRange > 1) && (imageNumRange != nConvert)) {
						if ((dcmList[dcmSort[0].indx].locationsInAcquisition > 0) && ((nConvert % dcmList[dcmSort[0].indx].locationsInAcquisition) != 0))
							printError("Missing images. Found %d images, expected %d slices per volume and instance number (0020,0013) ranges from %d to %d\n", nConvert, dcmList[dcmSort[0].indx].locationsInAcquisition, dcmList[dcmSort[0].indx].imageNum, dcmList[dcmSort[nConvert - 1].indx].imageNum);
						else
							printWarning("Missing images? Expected %d images, but instance number (0020,0013) ranges from %d to %d\n", nConvert, dcmList[dcmSort[0].indx].imageNum, dcmList[dcmSort[nConvert - 1].indx].imageNum);
						if (opts.isVerbose) {
							printMessage("instance=[");
							for (int i = 0; i < nConvert; i++) {
								printMessage(" %d", dcmList[dcmSort[i].indx].imageNum);
							}
							printMessage("]\n");
						}
					} //imageNum not sequential
				} //dx varies
			} //not 4D
			if ((hdr0.dim[4] > 0) && (dxVaries) && (dx == 0.0) && ((dcmList[dcmSort[0].indx].manufacturer == kMANUFACTURER_UNKNOWN) || (dcmList[dcmSort[0].indx].manufacturer == kMANUFACTURER_GE) || (dcmList[dcmSort[0].indx].manufacturer == kMANUFACTURER_PHILIPS))) { //Niels Janssen has provided GE sequential multi-phase acquisitions that also require swizzling
				swapDim3Dim4(hdr0.dim[3], hdr0.dim[4], dcmSort);
				dx = intersliceDistance(dcmList[dcmSort[0].indx], dcmList[dcmSort[1].indx]);
				if (opts.isVerbose)
					printMessage("Swizzling 3rd and 4th dimensions (XYTZ -> XYZT), assuming interslice distance is %f\n", dx);
			}
			if ((dx == 0.0) && (!dxVaries)) { //all images are the same slice - 16 Dec 2014
				printWarning("All images appear to be a single slice - please check slice/vector orientation\n");
				hdr0.dim[3] = 1;
				hdr0.dim[4] = nConvert;
				hdr0.dim[0] = 4;
			}
			if ((dx > 0) && (!isSameFloatGE(dx, hdr0.pixdim[3])))
				hdr0.pixdim[3] = dx;
			dcmList[dcmSort[0].indx].xyzMM[3] = dx; //16Sept2014 : correct DICOM for true distance between slice centers:
			// e.g. MCBI Siemens ToF 0018:0088 reports 16mm SpacingBetweenSlices, but actually 0.5mm
		} else if (hdr0.dim[4] < 2) {
			hdr0.dim[4] = nConvert;
			hdr0.dim[0] = 4;
		} else {
			hdr0.dim[5] = nConvert;
			hdr0.dim[0] = 5;
		}
		if (((dcmList[indx0].manufacturer == kMANUFACTURER_TOSHIBA) || (dcmList[indx0].manufacturer == kMANUFACTURER_CANON)) && (dcmList[indx0].CSA.numDti < 1) && (nConvert > 1) && (hdr0.dim[4] > 1)) {
			//TOSHIBA omits 0018,9087 from B=0 volumes in diffusion series. Since most diffusion series start with B=0 volume, this would cause us to detect a diffusion series
			for (int i = 1; i < nConvert; i++)
				if (dcmList[dcmSort[i].indx].CSA.numDti > 0)
					dcmList[indx0].CSA.numDti = 1;
		}
		//printMessage(" %d %d %d %d %lu\n", hdr0.dim[1], hdr0.dim[2], hdr0.dim[3], hdr0.dim[4], (unsigned long)[imgM length]);
		struct nifti_1_header hdrI;
		//double time = -1.0;
		if ((!opts.isOnlyBIDS) && (nConvert > 1)) {
			//for (int i = 0; i < nConvert; i++)
			//	printMessage("%d\t%s\n", i, nameList->str[indx]);
			//int iStart = 1;
			//if (isReorder) iStart = 0;
			//for (int i = 1; i < nConvert; i++) { //<- works except where ensureSequentialSlicePositions() changes 1st slice
			for (int i = 0; i < nConvert; i++) { //stack additional images
				indx = dcmSort[i].indx;
				//double time2 = dcmList[dcmSort[i].indx].acquisitionTime;
				//if (time != time2)
				//	printWarning("%g\n", time2);
				//time = time2;
				//if (headerDcm2Nii(dcmList[indx], &hdrI) == EXIT_FAILURE) return EXIT_FAILURE;
				img = nii_loadImgXL(nameList->str[indx], &hdrI, dcmList[indx], iVaries, opts.compressFlag, opts.isVerbose, dti4D);
				if (img == NULL)
					return EXIT_FAILURE;
				if ((hdr0.dim[1] != hdrI.dim[1]) || (hdr0.dim[2] != hdrI.dim[2]) || (hdr0.bitpix != hdrI.bitpix)) {
					printError("Image dimensions differ %s %s", nameList->str[dcmSort[0].indx], nameList->str[indx]);
					free(imgM);
					free(img);
					return EXIT_FAILURE;
				}
				memcpy(&imgM[(uint64_t)i * imgsz], &img[0], imgsz);
				free(img);

#ifdef USING_DCM2NIIXFSWRAPPER
				if (opts.isVerbose)
					printMessage("load Image #%d %s\n", i, nameList->str[indx]);
#endif
			}
		} //skip if we are only creating BIDS
		if (hdr0.dim[4] > 1) //for 4d datasets, last volume should be acquired before first
			checkDateTimeOrder(&dcmList[dcmSort[0].indx], &dcmList[dcmSort[nConvert - 1].indx]);
	}
	bool ok = setBids(&dcmList[indx0], nameList->str[dcmSort[0].indx], nConvert, opts.isVerbose);
	
	if (opts.isIgnoreDerivedAnd2D && !ok) {
		printMessage("Ignoring derived image(s) of series %ld %s\n", dcmList[indx].seriesNum, nameList->str[indx]);
		return EXIT_SUCCESS;
	}
	int sliceDir = sliceTimingCore(dcmSort, dcmList, &hdr0, opts.isVerbose, nameList->str[dcmSort[0].indx], nConvert, opts);
#ifdef myReportSliceFilenames
	if (sliceDir < 0) {
		for (int i = nConvert; i > 0; --i)
			printMessage("|%d|%s\n", i, nameList->str[dcmSort[i - 1].indx]);
	} else {
		for (int i = 0; i < nConvert; i++)
			printMessage("|%d|%s\n", i, nameList->str[dcmSort[i].indx]);
	}
#endif
	if (strlen(dcmList[dcmSort[0].indx].protocolName) < 1) //beware: tProtocolName can vary within a series "t1+AF8-mpr+AF8-ns+AF8-sag+AF8-p2+AF8-iso" vs "T1_mprage_ns_sag_p2_iso 1.0mm_192"
		rescueProtocolName(&dcmList[dcmSort[0].indx], nameList->str[dcmSort[0].indx]);
	//move before headerDcm2Nii2 checkSliceTiming(&dcmList[indx0], &dcmList[indx1]);
	char pathoutname[2048] = {""};
	if (nii_createFilename(dcmList[dcmSort[0].indx], pathoutname, opts) == EXIT_FAILURE) { //make sure call is subsequent to rescueProtocolName()
		free(imgM);
		return EXIT_FAILURE;
	}
	if (strlen(pathoutname) < 1) {
		free(imgM);
		return EXIT_FAILURE;
	}

#ifndef USING_DCM2NIIXFSWRAPPER 
	// skip converting if user has specified one or more series, but has not specified this one
	if (opts.numSeries > 0) { //issue453: moved to before saveBIDS
		int i = 0;
		double seriesNum = (double)dcmList[dcmSort[0].indx].seriesUidCrc;
		int segVolEcho = segVol;
		if ((dcmList[dcmSort[0].indx].echoNum > 1) && (segVolEcho <= 0))
			segVolEcho = dcmList[dcmSort[0].indx].echoNum + 1;
		if (segVolEcho > 0)
			seriesNum = seriesNum + ((double)segVolEcho - 1.0) / 10.0;
		for (; i < opts.numSeries; i++) {
			if (isSameDouble(opts.seriesNumber[i], seriesNum))
				break;
		}
		if (i == opts.numSeries)
			return EXIT_SUCCESS;
	}
#else
        double seriesNum = (double)dcmList[dcmSort[0].indx].seriesUidCrc;
        if (!isSameDouble(opts.seriesNumber[0], seriesNum))
            return EXIT_SUCCESS;
#endif

	if (opts.numSeries >= 0) //issue453
		nii_SaveBIDSX(pathoutname, dcmList[dcmSort[0].indx], opts, &hdr0, nameList->str[dcmSort[0].indx], dti4D);
	if (opts.isOnlyBIDS) {
		//note we waste time loading every image, however this ensures hdr0 matches actual output
#ifndef USING_DCM2NIIXFSWRAPPER
		free(imgM);
#endif
		return EXIT_SUCCESS;
	}
	if ((segVol >= 0) && (hdr0.dim[4] > 1)) {
		int inVol = hdr0.dim[4];
		int nVol = 0;
		for (int v = 0; v < inVol; v++)
			if (dti4D->gradDynVol[v] == segVol)
				nVol++;
		if (nVol < 1) {
			printError("Series %d does not exist\n", segVol);
			return EXIT_FAILURE;
		}
		size_t imgsz4D = imgsz;
		if (nVol < 2)
			hdr0.dim[0] = 3; //3D
		hdr0.dim[4] = 1;
		size_t imgsz3D = nii_ImgBytes(hdr0);
		unsigned char *img4D = (unsigned char *)malloc(imgsz4D);
		memcpy(&img4D[0], &imgM[0], imgsz4D);
		free(imgM);
		imgM = (unsigned char *)malloc(imgsz3D * nVol);
		int outVol = 0;
		for (int v = 0; v < inVol; v++) {
			if ((dti4D->gradDynVol[v] == segVol) && (outVol < nVol)) {
				memcpy(&imgM[outVol * imgsz3D], &img4D[v * imgsz3D], imgsz3D);
				outVol++;
			}
		}
		hdr0.dim[4] = nVol;
		imgsz = nii_ImgBytes(hdr0);
		free(img4D);
		saveAs3D = false;
	}
	// Prevent these DICOM files from being reused.
	for (int i = 0; i < nConvert; ++i)
		dcmList[dcmSort[i].indx].converted2NII = 1;
	if (opts.numSeries < 0) { //report series number but do not convert
		int segVolEcho = segVol;
		if ((dcmList[dcmSort[0].indx].echoNum > 1) && (segVolEcho <= 0))
			segVolEcho = dcmList[dcmSort[0].indx].echoNum + 1;
		if (segVolEcho >= 0) {
			printMessage("\t%u.%d\t%s\n", dcmList[dcmSort[0].indx].seriesUidCrc, segVolEcho - 1, pathoutname);
			//printMessage("\t%ld.%d\t%s\n", dcmList[dcmSort[0].indx].seriesNum, segVol-1, pathoutname);
		} else {
			printMessage("\t%u\t%s\n", dcmList[dcmSort[0].indx].seriesUidCrc, pathoutname);
			//printMessage("\t%ld\t%s\n", dcmList[dcmSort[0].indx].seriesNum, pathoutname);
		}
		printMessage(" %s\n", nameList->str[dcmSort[0].indx]);
		return EXIT_SUCCESS;
	}
	struct nifti_1_header hdrrx = hdr0;
	bool isFlipZ = false;
	if (sliceDir < 0) {
#ifdef USING_DCM2NIIXFSWRAPPER     // freesurfer fix dcm/261000-10-6?.dcm
		printMessage("***USING_DCM2NIIXFSWRAPPER***: skip nii_flipZ() when sliceDir < 0 (%s:%s:%d)\n", __FILE__, __func__, __LINE__);
#else
		isFlipZ = true;
		imgM = nii_flipZ(imgM, &hdr0);
		sliceDir = abs(sliceDir); //change this, we have flipped the image so GE DTI bvecs no longer need to be flipped!
#endif
	}
	nii_saveText(pathoutname, dcmList[dcmSort[0].indx], opts, &hdr0, nameList->str[indx]);
	int numADC = 0;
	int *volOrderIndex = nii_saveDTI(pathoutname, nConvert, dcmSort, dcmList, opts, sliceDir, dti4D, &numADC, hdr0.dim[4]);
	PhilipsPrecise(&dcmList[dcmSort[0].indx], opts.isPhilipsFloatNotDisplayScaling, &hdr0, opts.isVerbose);
	if ((dcmList[dcmSort[0].indx].bitsStored == 12) && (dcmList[dcmSort[0].indx].bitsAllocated == 16))
		nii_mask12bit(imgM, &hdr0, dcmList[dcmSort[0].indx].isSigned);
	if ((opts.saveFormat == kSaveFormatMGH) && (hdr0.datatype == DT_UINT16))
		imgM = nii_uint16toFloat32(imgM, &hdr0, opts.isVerbose);
	if ((opts.isMaximize16BitRange == kMaximize16BitRange_True) && (hdr0.datatype == DT_INT16)) {
		nii_scale16bitSigned(imgM, &hdr0, opts.isVerbose); //allow INT16 to use full dynamic range
	} else if ((opts.isMaximize16BitRange == kMaximize16BitRange_True) && (hdr0.datatype == DT_UINT16) && (!dcmList[dcmSort[0].indx].isSigned)) {
		nii_scale16bitUnsigned(imgM, &hdr0, opts.isVerbose); //allow UINT16 to use full dynamic range
	} else if ((opts.isMaximize16BitRange == kMaximize16BitRange_False) && (hdr0.datatype == DT_UINT16) && (!dcmList[dcmSort[0].indx].isSigned))
		nii_check16bitUnsigned(imgM, &hdr0, opts.isVerbose); //save UINT16 as INT16 if we can do this losslessly
	if ((dcmList[dcmSort[0].indx].isXA10A) && (nConvert > 1) && (nConvert == (hdr0.dim[3] * hdr0.dim[4])) )
		printWarning("Siemens XA exported as classic not enhanced DICOM (issue 236)\n");
#ifndef USING_DCM2NIIXFSWRAPPER
	printMessage("Convert %d DICOM as %s (%dx%dx%dx%d)\n", nConvert, pathoutname, hdr0.dim[1], hdr0.dim[2], hdr0.dim[3], hdr0.dim[4]);
#else
	printMessage( "Convert %d DICOM (%dx%dx%dx%d)\n",  nConvert, hdr0.dim[1],hdr0.dim[2],hdr0.dim[3],hdr0.dim[4]);
#endif
#ifndef USING_R
	fflush(stdout); //show immediately if run from MRIcroGL GUI
#endif
		//~ if (!dcmList[dcmSort[0].indx].isSlicesSpatiallySequentialPhilips)
	//~ 	nii_reorderSlices(imgM, &hdr0, dti4D);
	//hdr0.pixdim[3] = dxNoTilt;
	if ((hdr0.dim[3] < 2) && (!isnan(dcmList[dcmSort[0].indx].patientPosition[0])))
		printWarning("Check that 2D images are not mirrored.\n"); // isnan does not warn for non-spatial images (physio)
#ifndef USING_R
	else
		fflush(stdout); //GUI buffers printf, display all results
#endif
	//3D-EPI vs 3D SPACE/MPRAGE/ETC
	bool isFlipY = false;
	bool isSetOrtho = false;
	if ((opts.isRotate3DAcq) && (dcmList[dcmSort[0].indx].is3DAcq) && (!dcmList[dcmSort[0].indx].isEPI) && (hdr0.dim[3] > 1) && (hdr0.dim[0] < 4)) {
		bool isSliceEquidistant = true; //issue539
		if ((nConvert > 0)  && (sliceMMarray != NULL)){
			float dx = sliceMMarray[1] - sliceMMarray[0];
			float thr = fabs(dx) * 0.1;
			for (int i = 2; i < nConvert; i++)
				if (fabs(dx- (sliceMMarray[i]-sliceMMarray[i-1])) > (thr) ) {
					printWarning("Unable to rotate 3D volume: slices not equidistant: %g != %g\n", dx, sliceMMarray[i]-sliceMMarray[i-1]);
					isSliceEquidistant = false;
					break;
				}
		}
		if (isSliceEquidistant) {
			imgM = nii_setOrtho(imgM, &hdr0);
			isSetOrtho = true;
		}
	} else if (opts.isFlipY) { //(FLIP_Y) //(dcmList[indx0].CSA.mosaicSlices < 2) &&
		imgM = nii_flipY(imgM, &hdr0);
		isFlipY = true;
	} else
		printMessage("DICOM row order preserved: may appear upside down in tools that ignore spatial transforms\n");
	if ((dcmList[dcmSort[0].indx].epiVersionGE == kGE_EPI_PEPOLAR_REV) || (dcmList[dcmSort[0].indx].epiVersionGE == kGE_EPI_PEPOLAR_FWD_REV_FLIP) || (dcmList[dcmSort[0].indx].epiVersionGE == kGE_EPI_PEPOLAR_REV_FWD_FLIP)) {
		imgM = nii_flipImgY(imgM, &hdr0);
	}
	//begin: gantry tilt we need to save the shear in the transform
	mat44 sForm;
	LOAD_MAT44(sForm,
			hdr0.srow_x[0], hdr0.srow_x[1], hdr0.srow_x[2], hdr0.srow_x[3],
			hdr0.srow_y[0], hdr0.srow_y[1], hdr0.srow_y[2], hdr0.srow_y[3],
			hdr0.srow_z[0], hdr0.srow_z[1], hdr0.srow_z[2], hdr0.srow_z[3]);
	if (!isSameFloatGE(dcmList[indx0].gantryTilt, 0.0)) {
		float thetaRad = dcmList[indx0].gantryTilt * M_PI / 180.0;
		float c = cos(thetaRad);
		if (!isSameFloatGE(c, 0.0)) {
			mat33 shearMat;
			//gantry tilt formula changed with issue697
			/*printf("a=[%g %g %g %g; %g %g %g %g; %g %g %g %g; 0 0 0 1];\n",
				hdr0.srow_x[0], hdr0.srow_x[1], hdr0.srow_x[2], hdr0.srow_x[3],
				hdr0.srow_y[0], hdr0.srow_y[1], hdr0.srow_y[2], hdr0.srow_y[3],
				hdr0.srow_z[0], hdr0.srow_z[1], hdr0.srow_z[2], hdr0.srow_z[3]
			);*/
			hdr0.srow_y[2] = 0.0; //remove gantry tilt
			hdr0.srow_z[2] = hdr0.pixdim[3]; //retain distance between slices
			/*printf("b=[%g %g %g %g; %g %g %g %g; %g %g %g %g; 0 0 0 1];\n",
				hdr0.srow_x[0], hdr0.srow_x[1], hdr0.srow_x[2], hdr0.srow_x[3],
				hdr0.srow_y[0], hdr0.srow_y[1], hdr0.srow_y[2], hdr0.srow_y[3],
				hdr0.srow_z[0], hdr0.srow_z[1], hdr0.srow_z[2], hdr0.srow_z[3]
			);*/
			/*
			LOAD_MAT33(shearMat, 1.0, 0.0, 0.0,
					0.0, 1.0, sin(thetaRad) / c,
					0.0, 0.0, 1.0);
			mat33 s;
			LOAD_MAT33(s, hdr0.srow_x[0], hdr0.srow_x[1], hdr0.srow_x[2],
					hdr0.srow_y[0], hdr0.srow_y[1], hdr0.srow_y[2],
					hdr0.srow_z[0], hdr0.srow_z[1], hdr0.srow_z[2]);
			s = nifti_mat33_mul(shearMat, s);
			mat44 shearForm;
			LOAD_MAT44(shearForm, s.m[0][0], s.m[0][1], s.m[0][2], hdr0.srow_x[3],
					s.m[1][0], s.m[1][1], s.m[1][2], hdr0.srow_y[3],
					s.m[2][0], s.m[2][1], s.m[2][2], hdr0.srow_z[3]);
			setQSForm(&hdr0, shearForm, true);
			*/
		} //avoid div/0: cosine not zero
	} //if gantry tilt
	//end: gantry tilt we need to save the shear in the transform
	int returnCode = EXIT_FAILURE;
#ifndef myNoSave
	// Indicates success or failure of the (last) save
	if (opts.saveFormat != kSaveFormatNIfTI)
		removeSclSlopeInter(&hdr0, imgM);
	//printMessage(" x--> %d ----\n", nConvert);
	if (!opts.isRGBplanar) //save RGB as packed RGBRGBRGB... instead of planar RRR..RGGG..GBBB..B
		imgM = nii_planar2rgb(imgM, &hdr0, true); //NIfTI is packed while Analyze was planar
	if ((hdr0.dim[4] > 1) && (saveAs3D))
		returnCode = nii_saveNII3D(pathoutname, hdr0, imgM, opts, dcmList[dcmSort[0].indx]);
	else {
		if (volOrderIndex) //reorder volumes
			imgM = reorderVolumes(&hdr0, imgM, volOrderIndex);
		if ((opts.isIgnoreDerivedAnd2D) && (numADC > 0))
			printMessage("Ignoring derived diffusion image(s). Better isotropic and ADC maps can be generated later processing.\n");
		if ((!opts.isIgnoreDerivedAnd2D) && (numADC > 0)) { //ADC maps can disrupt analysis: save a copy with the ADC map, and another without
			char pathoutnameADC[2048] = {""};
			strcat(pathoutnameADC, pathoutname);
			strcat(pathoutnameADC, "_ADC");
			if (opts.isSave3D)
				nii_saveNII3D(pathoutnameADC, hdr0, imgM, opts, dcmList[dcmSort[0].indx]);
			else
				nii_saveNII(pathoutnameADC, hdr0, imgM, opts, dcmList[dcmSort[0].indx]);
		}
		if (isHasOverlay) { //each series can have up to 16 overlays, overlays may not be on all slices
			for (int j = 0; j < kMaxOverlay; j++) {
				bool isOverlay = false;
				for (int i = 0; i < nConvert; i++)
					if (dcmList[dcmSort[i].indx].overlayStart[j] > 0)
						isOverlay = true;
				if (!isOverlay)
					continue;
				char pathoutnameROI[2048] = {""};
				strcat(pathoutnameROI, pathoutname);
				char append[128] = {""};
				snprintf(append, 127, "_ROI%d", j + 1);
				strcat(pathoutnameROI, append);
				struct nifti_1_header hdrr = hdrrx;
				hdrr.dim[0] = 3;
				if (hdrr.dim[1] < 1)
					hdrr.dim[1] = 1;
				if (hdrr.dim[2] < 1)
					hdrr.dim[2] = 1;
				if (hdrr.dim[3] < 1)
					hdrr.dim[3] = 1;
				hdrr.dim[4] = 1;
				hdrr.bitpix = 8;
				hdrr.datatype = 2;
				hdrr.scl_inter = 0.0;
				hdrr.scl_slope = 1.0;
				int nvox = hdrr.dim[1] * hdrr.dim[2] * hdrr.dim[3];
				unsigned char *imgR = (unsigned char *)malloc(nvox);
				for (int v = 0; v < nvox; v++)
					imgR[v] = 0;
				if (nConvert == 1) {
					int indx = dcmSort[0].indx;
					loadOverlay(nameList->str[indx], imgR, dcmList[indx].overlayStart[j], hdrr.dim[1], hdrr.dim[2], hdrr.dim[3]);
				} else if (nConvert == hdrr.dim[3]) {
					for (int i = 0; i < nConvert; i++) {
						int indx = dcmSort[i].indx;
						if (dcmList[indx].overlayStart[j] > 0) {
							unsigned char *imgRS = imgR + (i * hdrr.dim[1] * hdrr.dim[2]);
							loadOverlay(nameList->str[indx], imgRS, dcmList[indx].overlayStart[j], hdrr.dim[1], hdrr.dim[2], 1);
						} //if overlay on slice
					} //for each volume
				} //
				if (isFlipZ)
					imgR = nii_flipZ(imgR, &hdrr);
				if (isSetOrtho)
					imgR = nii_setOrtho(imgR, &hdrr);
				if (isFlipY)
					imgR = nii_flipY(imgR, &hdrr);
				nii_saveNII(pathoutnameROI, hdrr, imgR, opts, dcmList[dcmSort[0].indx]);
			}
		}
		imgM = removeADC(&hdr0, imgM, numADC);
		if (iVaries)
			printMessage("Saving as 32-bit float (slope, intercept or bits allocated varies).\n");
#ifndef USING_R
		// divest does not support non-NIfTI formats, and requires only one
		// image per series, so skip this to avoid double-saving
		if (opts.saveFormat != kSaveFormatNIfTI)
			returnCode = nii_saveForeign(pathoutname, hdr0, imgM, opts, dcmList[dcmSort[0].indx], dti4D, dcmList[indx0].CSA.numDti);
		else if (opts.isSave3D)
			returnCode = nii_saveNII3D(pathoutname, hdr0, imgM, opts, dcmList[dcmSort[0].indx]);
		else
			returnCode = nii_saveNII(pathoutname, hdr0, imgM, opts, dcmList[dcmSort[0].indx]);
#endif
	}
#endif
	if (dcmList[indx0].gantryTilt != 0.0) {
		setQSForm(&hdr0, sForm, true);
		//if (dcmList[indx0].isResampled) { //we no detect based on image orientation https://github.com/rordenlab/dcm2niix/issues/253
		// printMessage("Tilt correction skipped: 0008,2111 reports RESAMPLED\n");
		//} else
		if (opts.isTiltCorrect) {
			imgM = nii_saveNII3Dtilt(pathoutname, &hdr0, imgM, opts, dcmList[dcmSort[0].indx], sliceMMarray, dcmList[indx0].gantryTilt, dcmList[indx0].manufacturer);
			strcat(pathoutname, "_Tilt");
		} else
			printMessage("Tilt correction skipped\n");
	}
	if ((sliceMMarray != NULL) &&  (!isSetOrtho)) {
		if (dcmList[indx0].isResampled) {
			printMessage("Slice thickness correction skipped: 0008,2111 reports RESAMPLED\n");
		} else
			returnCode = nii_saveNII3Deq(pathoutname, hdr0, imgM, opts, dcmList[dcmSort[0].indx], sliceMMarray);
		free(sliceMMarray);
	}
	//3D-EPI vs 3D SPACE/MPRAGE/ETC
	if ((opts.isRotate3DAcq) && (opts.isCrop) && (dcmList[indx0].is3DAcq) && (!dcmList[indx0].isEPI) && (hdr0.dim[3] > 1) && (hdr0.dim[0] < 4)) //for T1 scan: && (dcmList[indx0].TE < 25)
		returnCode = nii_saveCrop(pathoutname, hdr0, imgM, opts, dcmList[dcmSort[0].indx]);														//n.b. must be run AFTER nii_setOrtho()!
#ifdef USING_R
	// Note that for R, only one image should be created per series
	// Hence this extra test
	if (returnCode != EXIT_SUCCESS)
		returnCode = nii_saveNII(pathoutname, hdr0, imgM, opts, dcmList[dcmSort[0].indx]);
#endif

#ifdef USING_DCM2NIIXFSWRAPPER
	hdr0.vox_offset = 352;

	mrifsStruct.hdr0 = hdr0;
	mrifsStruct.imgsz = nii_ImgBytes(hdr0);
	mrifsStruct.imgM = imgM;

        mrifsStruct_vector.push_back(mrifsStruct);
#else  
	free(imgM);
#endif
	if (dcmList[dcmSort[0].indx].xyzDim[0] > 1)
		returnCode = kEXIT_INCOMPLETE_VOLUMES_FOUND; //issue515
	return returnCode; //EXIT_SUCCESS;
} // saveDcm2NiiCore()

int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata dcmList[], struct TSearchList *nameList, struct TDCMopts opts, struct TDTI4D *dti4D) {
#ifdef USING_DCM2NIIXFSWRAPPER
  memset(&mrifsStruct, 0, sizeof(mrifsStruct));

  int indx0 = dcmSort[0].indx;

  int len_dicomfile = strlen(nameList->str[indx0]);
  mrifsStruct.dicomfile = (char*)malloc(len_dicomfile+1);
  memset(mrifsStruct.dicomfile, 0, len_dicomfile+1);
  memcpy(mrifsStruct.dicomfile, nameList->str[indx0], len_dicomfile);

  if (opts.isDumpNotConvert) {
    mrifsStruct.tdicomData = dcmList[indx0];  // first in sorted list dcmSort
    mrifsStruct.dicomlst = new char*[nConvert];
    mrifsStruct.nDcm  = nConvert;

    dcmListDump(nConvert, dcmSort, dcmList, nameList, opts);

    mrifsStruct_vector.push_back(mrifsStruct);

    return 0;
  }
#endif
	//this wrapper does nothing if all the images share the same echo time and scale
	// however, it segments images when these properties vary
	uint64_t indx = dcmSort[0].indx;
	if ((!dcmList[indx].isScaleOrTEVaries) || (dcmList[indx].xyzDim[4] < 2))
		return saveDcm2NiiCore(nConvert, dcmSort, dcmList, nameList, opts, dti4D, -1);
	if ((dcmList[indx].xyzDim[4]) && (dti4D->sliceOrder[0] < 0)) {
		printError("Unexpected error for image with varying echo time or intensity scaling\n");
		return EXIT_FAILURE;
	}
	if ((nConvert == 1) && (dcmList[indx].manufacturer == kMANUFACTURER_PHILIPS))
		printWarning("Philips enhanced DICOMs (hint: export as classic DICOM)\n");
	int ret = EXIT_SUCCESS;
	//check for repeated echoes - count unique number of echoes
	//code below checks for multi-echoes - not required if maxNumberOfEchoes reported in PARREC
	int echoNum[kMaxDTI4D];
	int echo = 1;
	for (int i = 0; i < dcmList[indx].xyzDim[4]; i++)
		echoNum[i] = 0;
	echoNum[0] = 1;
	for (int i = 1; i < dcmList[indx].xyzDim[4]; i++) {
		for (int j = 0; j < i; j++)
			if (dti4D->TE[i] == dti4D->TE[j])
				echoNum[i] = echoNum[j];
		if (echoNum[i] == 0) {
			echo++;
			echoNum[i] = echo;
		}
	}
	if (echo > 1)
		dcmList[indx].isMultiEcho = true;
	//check for repeated volumes
	int series = 1;
	for (int i = 0; i < dcmList[indx].xyzDim[4]; i++)
		dti4D->gradDynVol[i] = 0;
	dti4D->gradDynVol[0] = 1;
	int dim3 = dcmList[indx].xyzDim[3];//vol2slice(int vol, int dim3)
	for (int i = 1; i < dcmList[indx].xyzDim[4]; i++) {
		int iv = (i * dim3); //intenIntercept and intenScale can vary within a volume
		for (int j = 0; j < i; j++) {
			int jv = (j * dim3);
			if (( (dcmList[indx].aslFlags != kASL_FLAG_NONE)  || isSameFloatGE(dti4D->triggerDelayTime[i], dti4D->triggerDelayTime[j])) && (dti4D->intenIntercept[iv] == dti4D->intenIntercept[jv]) && (dti4D->intenScale[iv] == dti4D->intenScale[jv]) && (dti4D->isReal[i] == dti4D->isReal[j]) && (dti4D->isImaginary[i] == dti4D->isImaginary[j]) && (dti4D->isPhase[i] == dti4D->isPhase[j]) && (dti4D->TE[i] == dti4D->TE[j]))
				dti4D->gradDynVol[i] = dti4D->gradDynVol[j];
		}
		if (dti4D->gradDynVol[i] == 0) {
			series++;
			dti4D->gradDynVol[i] = series;
		}
	}
	//bvec/bval saved for each series (real, phase, magnitude, imaginary) https://github.com/rordenlab/dcm2niix/issues/219
	TDTI4D dti4Ds = *dti4D;
	bool isHasDti = (dcmList[indx].CSA.numDti > 0);
	if ((isHasDti) && (dcmList[indx].CSA.numDti == dcmList[indx].xyzDim[4])) {
		int nDti = 0;
		for (int i = 0; i < dcmList[indx].xyzDim[4]; i++) {
			if (dti4D->gradDynVol[i] == 1) {
				dti4Ds.S[nDti].V[0] = dti4Ds.S[i].V[0];
				dti4Ds.S[nDti].V[1] = dti4Ds.S[i].V[1];
				dti4Ds.S[nDti].V[2] = dti4Ds.S[i].V[2];
				dti4Ds.S[nDti].V[3] = dti4Ds.S[i].V[3];
				nDti++;
			}
		}
		dcmList[indx].CSA.numDti = nDti;
	}
	//save each series
	bool isScaleVariesEnh = dcmList[indx].isScaleVariesEnh; //issue363: any variation in any image
	float intenScale = dcmList[indx].intenScale;
	float intenIntercept = dcmList[indx].intenIntercept;
	float intenScalePhilips = dcmList[indx].intenScalePhilips;
	float RWVIntercept = dcmList[indx].RWVIntercept;
	float RWVScale = dcmList[indx].RWVScale;
	for (int s = 1; s <= series; s++) {
		//issue461: assert these values as saveDcm2NiiCore modifies them when it applies Philips scaling
		dcmList[indx].intenScale = intenScale;
		dcmList[indx].intenIntercept = intenIntercept;
		dcmList[indx].intenScalePhilips = intenScalePhilips;
		dcmList[indx].RWVIntercept = RWVIntercept;
		dcmList[indx].RWVScale = RWVScale;
		//for (int i = 0; i < dcmList[indx].xyzDim[4]; i++) //for each volume
		//	printf("%g<<<!\n", dti4D->triggerDelayTime[i]);
		for (int i = 0; i < dcmList[indx].xyzDim[4]; i++) { //for each volume
			if (dti4D->gradDynVol[i] == s) {
				//dti4D->gradDynVol[i] = s;
				//nVol ++;
				dcmList[indx].TE = dti4D->TE[i];
				dcmList[indx].TR = dti4D->TR[i];
				//dcmList[indx].intenScale = dti4D->intenScale[i];
				//dcmList[indx].intenIntercept = dti4D->intenIntercept[i];
				//dcmList[indx].intenScalePhilips = dti4D->intenScalePhilips[i];
				//dcmList[indx].RWVScale = dti4D->RWVScale[i];
				//dcmList[indx].RWVIntercept = dti4D->RWVIntercept[i];
				dcmList[indx].isHasPhase = dti4D->isPhase[i];
				dcmList[indx].isHasReal = dti4D->isReal[i];
				dcmList[indx].isHasImaginary = dti4D->isImaginary[i];
				dcmList[indx].triggerDelayTime = dti4D->triggerDelayTime[i];
				dcmList[indx].isHasMagnitude = false;
				dcmList[indx].echoNum = echoNum[i];
				break;
			}
		}
		dcmList[indx].isScaleVariesEnh = false;
		if (isScaleVariesEnh) { //check if intensity scale varies for this particular output image, this will force 32-bit output
			int nz = 0;
			for (int i = 0; i < dcmList[indx].xyzDim[4]; i++) { //for each volume
				if (dti4D->gradDynVol[i] == s) {
					for (int z = 0; z < dcmList[indx].xyzDim[3]; z++) { //for each slice
						int ix = (i * dcmList[indx].xyzDim[3]) + z;
						dti4Ds.intenScale[nz] = dti4D->intenScale[ix];
						dti4Ds.intenIntercept[nz] = dti4D->intenIntercept[ix];
						dti4Ds.intenScalePhilips[nz] = dti4D->intenScalePhilips[ix];
						dti4Ds.RWVIntercept[nz] = dti4D->RWVIntercept[ix];
						dti4Ds.RWVScale[nz] = dti4D->RWVScale[ix];
						nz++;
					} //for z: each slice
				} //if series matches
			} //for each volume
			for (int i = 0; i < nz; i++) {
				if (dti4Ds.intenIntercept[i] != dti4Ds.intenIntercept[0])
					dcmList[indx].isScaleVariesEnh = true;
				if (dti4Ds.intenScale[i] != dti4Ds.intenScale[0])
					dcmList[indx].isScaleVariesEnh = true;
				if (dti4Ds.intenScalePhilips[i] != dti4Ds.intenScalePhilips[0])
					dcmList[indx].isScaleVariesEnh = true;
			}
			dcmList[indx].intenScale = dti4Ds.intenScale[0];
			dcmList[indx].intenIntercept = dti4Ds.intenIntercept[0];
			dcmList[indx].intenScalePhilips = dti4Ds.intenScalePhilips[0];
			dcmList[indx].RWVIntercept = dti4Ds.RWVIntercept[0];
			dcmList[indx].RWVScale = dti4Ds.RWVScale[0];
		}
		if (s > 1)
			dcmList[indx].CSA.numDti = 0; //only save bvec for first type (magnitude)
		int ret2 = saveDcm2NiiCore(nConvert, dcmSort, dcmList, nameList, opts, &dti4Ds, s);
		if (ret2 != EXIT_SUCCESS)
			ret = ret2; //return EXIT_SUCCESS only if ALL are successful
	}
	return ret;
} // saveDcm2Nii()

void fillTDCMsort(struct TDCMsort &tdcmref, const uint64_t indx, const struct TDICOMdata &dcmdata) {
	// Copy the relevant parts of dcmdata to tdcmref.
	tdcmref.indx = indx;
	//printf("series/image %d %d\n", dcmdata.seriesNum, dcmdata.imageNum);
	tdcmref.img = ((uint64_t)dcmdata.seriesNum << 32) + dcmdata.imageNum;
	for (int i = 0; i < MAX_NUMBER_OF_DIMENSIONS; ++i)
		tdcmref.dimensionIndexValues[i] = dcmdata.dimensionIndexValues[i];
	//lines below added to cope with extreme anonymization
	// https://github.com/rordenlab/dcm2niix/issues/211
	if (tdcmref.dimensionIndexValues[MAX_NUMBER_OF_DIMENSIONS - 1] != 0)
		return;
	//Since dimensionIndexValues are indexed from 1, 0 indicates unused
	// we leverage this as a hail mary attempt to distinguish images with identical series and instance numbers
	//See Correction Number CP-1242:
	// "Clarify in the description of dimension indices ... start from 1"
	// 0008,0032 stored as HHMMSS.FFFFFF, there are 86400000 ms per day
	// dimensionIndexValues stored as uint32, so encode acquisition time in ms
	uint32_t h = trunc(dcmdata.acquisitionTime / 10000.0);
	double tm = dcmdata.acquisitionTime - (h * 10000.0);
	uint32_t m = trunc(tm / 100.0);
	tm = tm - (m * 100.0);
	uint32_t ms = round(tm * 1000);
	ms += (h * 3600000) + (m * 60000);
	//printf("HHMMSS.FFFF %.5f -> %d ms\n", dcmdata.acquisitionTime, ms);
	tdcmref.dimensionIndexValues[MAX_NUMBER_OF_DIMENSIONS - 1] = ms;
} // fillTDCMsort()

int compareTDCMsort(void const *item1, void const *item2) {
	//for quicksort http://blog.ablepear.com/2011/11/objective-c-tuesdays-sorting-arrays.html
	struct TDCMsort const *dcm1 = (const struct TDCMsort *)item1;
	struct TDCMsort const *dcm2 = (const struct TDCMsort *)item2;
	//to do: detect duplicates with SOPInstanceUID (0008,0018) - accurate but slow text comparison
	int retval = 0; // tie
	if (dcm1->img < dcm2->img)
		retval = -1;
	else if (dcm1->img > dcm2->img)
		retval = 1;
	//printf("%d %d\n", dcm1->img, dcm2->img);
	//for(int i=0; i < MAX_NUMBER_OF_DIMENSIONS; i++)
	//	printf("%d %d\n", dcm1->dimensionIndexValues[i], dcm2->dimensionIndexValues[i]);
	if (retval != 0)
		return retval; //sorted images
	// Check the dimensionIndexValues (useful for enhanced DICOM 4D series).
	// ->img is basically behaving as a (seriesNum, imageNum) sort key
	// concatenated into a (large) integer for qsort. That is unwieldy when
	// dimensionIndexValues need to be compared, because the existence of
	// uint128_t, uint256_t, etc. is not guaranteed. This sorts by
	// (seriesNum, ImageNum, div[0], div[1], ...), or if you think of it as a
	// number, the dimensionIndexValues come after the decimal point.
	for (int i = 0; i < MAX_NUMBER_OF_DIMENSIONS; ++i) {
		if (dcm1->dimensionIndexValues[i] < dcm2->dimensionIndexValues[i])
			return -1;
		else if (dcm1->dimensionIndexValues[i] > dcm2->dimensionIndexValues[i])
			return 1;
	}
	return retval;
} //compareTDCMsort()

int isSameFloatDouble(double a, double b) {
	//Kludge for bug in 0002,0016="DIGITAL_JACKET", 0008,0070="GE MEDICAL SYSTEMS" DICOM data: Orient field (0020:0037) can vary 0.00604261 == 0.00604273 !!!
	// return (a == b); //niave approach does not have any tolerance for rounding errors
	return (fabs(a - b) <= 0.0001);
}

struct TWarnings { //generate a warning only once per set
	bool manufacturerVaries, modalityVaries, derivedVaries, acqNumVaries, dimensionVaries, dateTimeVaries, studyUidVaries, echoVaries, triggerVaries, phaseVaries, coilVaries, forceStackSeries, seriesUidVaries, nameVaries, nameEmpty, orientVaries;
};

TWarnings setWarnings() {
	TWarnings r;
	r.manufacturerVaries = false;
	r.modalityVaries = false;
	r.derivedVaries = false;
	r.acqNumVaries = false;
	r.dimensionVaries = false;
	r.dateTimeVaries = false;
	r.studyUidVaries = false;
	r.phaseVaries = false;
	r.echoVaries = false;
	r.triggerVaries = false;
	r.coilVaries = false;
	r.seriesUidVaries = false;
	r.forceStackSeries = false;
	r.nameVaries = false;
	r.nameEmpty = false;
	r.orientVaries = false;
	return r;
}

bool isSameSet(struct TDICOMdata d1, struct TDICOMdata d2, struct TDCMopts *opts, struct TWarnings *warnings, bool *isMultiEcho, bool *isNonParallelSlices, bool *isCoilVaries) {
	//returns true if d1 and d2 should be stacked together as a single output
	if (!d1.isValid)
		return false;
	if (!d2.isValid)
		return false;
	if ((opts->isVerbose) && (d1.seriesNum == d2.seriesNum)) {
		//one would never want to combine in these situations: only raise warning for verbose modes to help troubleshooting
		if ((d1.manufacturer != d2.manufacturer) && (!warnings->manufacturerVaries)) {
			printMessage("Volumes not stacked: manufacturer varies.\n");
			warnings->manufacturerVaries = true;
		}
		if ((d1.modality != d2.modality) && (!warnings->modalityVaries)) {
			printMessage("Volumes not stacked: modality varies.\n");
			warnings->modalityVaries = true;
		}
		if ((d1.isDerived != d2.isDerived) && (!warnings->derivedVaries)) {
			printMessage("Volumes not stacked: derived varies.\n");
			warnings->derivedVaries = true;
		}
	}
	if (d1.manufacturer != d2.manufacturer)
		return false; //do not stack data from different vendors
	if (d1.modality != d2.modality)
		return false; //do not stack MR and CT data!
	if (d1.isDerived != d2.isDerived)
		return false; //do not stack raw and derived image types
	bool isForceStackSeries = false;
	if ((opts->isForceStackDCE) && (d1.isStackableSeries) && (d2.isStackableSeries) && (d1.seriesNum != d2.seriesNum)) {
		if (!warnings->forceStackSeries)
			printMessage("Volumes stacked despite varying series number (use '-m o' to turn off merging).\n");
		warnings->forceStackSeries = true;
		isForceStackSeries = true;
	}
	if ((d1.manufacturer == kMANUFACTURER_SIEMENS) && (strcmp(d1.protocolName, d2.protocolName) == 0) && (strlen(d1.softwareVersions) > 4) && (strlen(d1.sequenceName) > 4) && (strlen(d2.sequenceName) > 4)) {
		if (strstr(d1.sequenceName, "_ep_b") && strstr(d2.sequenceName, "_ep_b") && (strstr(d1.softwareVersions, "VB13") || strstr(d1.softwareVersions, "VB12"))) {
			//Siemens B12/B13 users with a "DWI" but not "DTI" license would often create multi-series acquisitions
			if (!warnings->forceStackSeries)
				printMessage("Diffusion images stacked despite varying series number (early Siemens DTI).\n");
			warnings->forceStackSeries = true;
			isForceStackSeries = true;
		}
	}
	if (isForceStackSeries)
		;
	else if ((d1.isXA10A) && (d2.isXA10A) && (d1.seriesNum > 1000) && (d2.seriesNum > 1000)) {
		//kludge XA10A (0020,0011) increments [16001, 16002, ...] https://github.com/rordenlab/dcm2niix/issues/236
		//images from series 16001,16002 report different study times (0008,0030)!
		if ((d1.seriesNum / 1000) != (d2.seriesNum / 1000))
			return false;
	} else if (d1.seriesNum != d2.seriesNum)
		return false;
#ifdef mySegmentByAcq
	if (d1.acquNum != d2.acquNum)
		return false;
#endif
	bool isSameStudyInstanceUID = false;
	if ((strlen(d1.studyInstanceUID) > 1) && (strlen(d2.studyInstanceUID) > 1)) {
		if (strcmp(d1.studyInstanceUID, d2.studyInstanceUID) == 0)
			isSameStudyInstanceUID = true;
	}
	bool isSameTime = isSameFloatDouble(d1.dateTime, d2.dateTime);
	if ((isSameStudyInstanceUID) && (d1.isXA10A) && (d2.isXA10A))
		isSameTime = true; //kludge XA10A 0008,0030 incorrect https://github.com/rordenlab/dcm2niix/issues/236
	bool isDimensionVaries = ((d1.xyzDim[1] != d2.xyzDim[1]) || (d1.xyzDim[2] != d2.xyzDim[2]) || (d1.xyzDim[3] != d2.xyzDim[3]));
	if ((!isSameStudyInstanceUID) && (!isSameTime)) {
		if (opts->isForceStackDCE) {
			if (!warnings->studyUidVaries)
				printMessage("Slices stacked despite Study Date/Time (0008,0020;0008,0030) and Study UID (0020,000E) variation %12.12f ~= %12.12f\n", d1.dateTime, d2.dateTime);
			warnings->studyUidVaries = true;
		} else {
			if (!warnings->studyUidVaries)
				printMessage("Slices not stacked: Study Date/Time (0008,0020;0008,0030) and Study UID (0020,000E) varies %12.12f ~= %12.12f\n", d1.dateTime, d2.dateTime);
			warnings->studyUidVaries = true;
			return false;
		}
	}
	if (isDimensionVaries) {
		if (!warnings->dimensionVaries)
			printMessage("Slices not stacked: dimensions vary across slices\n");
		warnings->dimensionVaries = true;
		return false;
	}
#ifndef myIgnoreStudyTime
	if (!isSameTime) { //beware, some vendors incorrectly store Image Time (0008,0033) as Study Time (0008,0030).
		if (!warnings->dateTimeVaries)
			printMessage("Slices not stacked: Study Date/Time (0008,0020;0008,0030) varies %12.12f ~= %12.12f\n", d1.dateTime, d2.dateTime);
		warnings->dateTimeVaries = true;
		return false;
	}
#endif
	if ((opts->isForceStackSameSeries == 1) || ((opts->isForceStackSameSeries == 2) && (d1.isXRay))) {
		// "isForceStackSameSeries == 2" will automatically stack CT scans but not MR
		//if (((!(isSameFloat(d1.TE, d2.TE))) || (d1.echoNum != d2.echoNum)) && (!d1.isXRay)) {
		//	*isMultiEcho = true;
		//}
#ifdef USING_DCM2NIIXFSWRAPPER
               /* for mgh conversion set opts->isForceStackSameSeries = 1 by default, *isMultiEcho, *isNonParallelSlices, and *isCoilVaries remain unchanged.
                *
                * local variable isForceStackSeries is set to true if following condition met:
	        *  if ((opts->isForceStackDCE) && (d1.isStackableSeries) && (d2.isStackableSeries) && (d1.seriesNum != d2.seriesNum)) {
		*    if (!warnings->forceStackSeries)
		*      printMessage("Volumes stacked despite varying series number (use '-m o' to turn off merging).\n");
		*    warnings->forceStackSeries = true;
		*    isForceStackSeries = true;
                *  }
                */

	        //printf("isForceStackSameSeries = true, seriesNum %ld, %ld, seriesInstanceUidCrc %d, %d\n", d1.seriesNum, d2.seriesNum, d1.seriesUidCrc, d2.seriesUidCrc);
#endif
		return true; //we will stack these images, even if they differ in the following attributes
	}
	if ((d1.isHasImaginary != d2.isHasImaginary) || (d1.isHasPhase != d2.isHasPhase) || (d1.isHasReal != d2.isHasReal)) {
		if (!warnings->phaseVaries)
			printMessage("Slices not stacked: some are phase/real/imaginary/phase maps, others are not. Instances %d %d\n", d1.imageNum, d2.imageNum);
		warnings->phaseVaries = true;
		return false;
	}
	if (!(isSameFloat(d1.TR, d2.TR))) {
		if (d1.numberOfTR > 1)
			return false;
		if (!warnings->echoVaries)
		printMessage("Slices not stacked: TR varies (%g, %g, issue 641). Use 'merge 2D slices' option to force stacking\n", d1.TR, d2.TR);
		*isMultiEcho = true;
		warnings->echoVaries = true;
		return false;
	}
	if (!(isSameFloat(d1.flipAngle, d2.flipAngle))) {
		if (!warnings->echoVaries)
		printMessage("Slices not stacked: flip angle varies (%g, %g, issue 646).\n", d1.TR, d2.TR);
		*isMultiEcho = true;
		warnings->echoVaries = true;
		return false;
	}
	//if ((d1.TE != d2.TE) || (d1.echoNum != d2.echoNum)) {
	if ((!(isSameFloat(d1.TE, d2.TE))) || (d1.echoNum != d2.echoNum)) {
		if ((!warnings->echoVaries) && (d1.isXRay)) //for CT/XRay we check DICOM tag 0018,1152 (XRayExposure)
			printMessage("Slices not stacked: X-Ray Exposure varies (exposure %g, %g; number %d, %d). Use 'merge 2D slices' option to force stacking\n", d1.TE, d2.TE, d1.echoNum, d2.echoNum);
		if ((!warnings->echoVaries) && (!d1.isXRay)) //for MRI
			printMessage("Slices not stacked: echo varies (TE %g, %g; echo %d, %d). Use 'merge 2D slices' option to force stacking\n", d1.TE, d2.TE, d1.echoNum, d2.echoNum);
		warnings->echoVaries = true;
		*isMultiEcho = true;
		return false;
	}
	if ((d1.triggerDelayTime != d2.triggerDelayTime) && (d1.manufacturer == kMANUFACTURER_PHILIPS) && (d1.aslFlags == kASL_FLAG_NONE)) { //issue 384
		if (!warnings->triggerVaries)
			printMessage("Slices not stacked: trigger time varies\n");
		warnings->triggerVaries = true;
		return false;
	}
	if (d1.coilCrc != d2.coilCrc) {
		if (opts->isForceStackDCE) {
			if (!warnings->coilVaries)
				printMessage("Slices stacked despite coil variation '%s' vs '%s' (use '-m o' to turn off merging)\n", d1.coilName, d2.coilName);
			warnings->coilVaries = true;
			*isCoilVaries = true;
		} else {
			if (!warnings->coilVaries)
				printMessage("Slices not stacked: coil varies '%s' vs '%s'\n", d1.coilName, d2.coilName);
			warnings->coilVaries = true;
			*isCoilVaries = true;
			return false;
		}
	}
	if ((strlen(d1.protocolName) < 1) && (strlen(d2.protocolName) < 1)) {
		if (!warnings->nameEmpty)
			printWarning("Empty protocol name(s) (0018,1030)\n");
		warnings->nameEmpty = true;
	} else if ((strcmp(d1.protocolName, d2.protocolName) != 0)) {
		if (!warnings->nameVaries)
			printMessage("Slices not stacked: protocol name varies '%s' != '%s'\n", d1.protocolName, d2.protocolName);
		warnings->nameVaries = true;
		return false;
	}
	if ((*isNonParallelSlices) && (d1.CSA.mosaicSlices > 1))
		return false; //issue481
	if ((!isSameFloatGE(d1.orient[1], d2.orient[1]) || !isSameFloatGE(d1.orient[2], d2.orient[2]) || !isSameFloatGE(d1.orient[3], d2.orient[3]) ||
			!isSameFloatGE(d1.orient[4], d2.orient[4]) || !isSameFloatGE(d1.orient[5], d2.orient[5]) || !isSameFloatGE(d1.orient[6], d2.orient[6]))) {
		if ((!warnings->orientVaries) && (!d1.isNonParallelSlices) && (!d1.isLocalizer))
			printMessage("Slices not stacked: orientation varies (vNav or localizer?) [%g %g %g %g %g %g] != [%g %g %g %g %g %g]\n",
				d1.orient[1], d1.orient[2], d1.orient[3], d1.orient[4], d1.orient[5], d1.orient[6],
				d2.orient[1], d2.orient[2], d2.orient[3], d2.orient[4], d2.orient[5], d2.orient[6]);
		warnings->orientVaries = true;
		*isNonParallelSlices = true;
		return false;
	}
	if (d1.acquNum != d2.acquNum) {
		if ((!warnings->acqNumVaries) && (opts->isVerbose)) //virtually always people want to stack these
			printMessage("Slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')\n");
		warnings->acqNumVaries = true;
	}
	if ((!isForceStackSeries) && (d1.seriesUidCrc != d2.seriesUidCrc)) {
		if (!warnings->seriesUidVaries)
			printMessage("Slices not stacked: series instance UID varies (duplicates all other properties)\n");
		warnings->seriesUidVaries = true;
		return false;
	}
	return true;
} // isSameSet()

void freeNameList(struct TSearchList nameList) {
	if (nameList.numItems > 0) {
		unsigned long n = nameList.numItems;
		if (n > nameList.maxItems)
			n = nameList.maxItems; //assigned if (nameList->numItems < nameList->maxItems)
		for (unsigned long i = 0; i < n; i++)
			free(nameList.str[i]);
	}
	free(nameList.str);
}

int singleDICOM(struct TDCMopts *opts, char *fname) {
	if (isDICOMfile(fname) == 0) {
		printError("Not a DICOM image : %s\n", fname);
		return 0;
	}
	struct TDICOMdata *dcmList = (struct TDICOMdata *)malloc(sizeof(struct TDICOMdata));
	struct TDTI4D *dti4D = (struct TDTI4D *)malloc(sizeof(struct TDTI4D));
	struct TSearchList nameList;
	struct TDCMprefs prefs;
	opts2Prefs(opts, &prefs);
	nameList.maxItems = 1; // larger requires more memory, smaller more passes
	nameList.str = (char **)malloc((nameList.maxItems + 1) * sizeof(char *)); //reserve one pointer (32 or 64 bits) per potential file
	nameList.numItems = 0;
	nameList.str[nameList.numItems] = (char *)malloc(strlen(fname) + 1);
	strcpy(nameList.str[nameList.numItems], fname);
	nameList.numItems++;
	TDCMsort *dcmSort = (TDCMsort *)malloc(sizeof(TDCMsort));
	dcmList[0].converted2NII = 1;
	dcmList[0] = readDICOMx(nameList.str[0], &prefs, dti4D); //ignore compile warning - memory only freed on first of 2 passes
	//dcmList[0] = readDICOMv(nameList.str[0], opts->isVerbose, opts->compressFlag, dti4D); //ignore compile warning - memory only freed on first of 2 passes
	fillTDCMsort(dcmSort[0], 0, dcmList[0]);
	int ret = saveDcm2Nii(1, dcmSort, dcmList, &nameList, *opts, dti4D);
	freeNameList(nameList);
	free(dti4D);
	free(dcmSort);
	free(dcmList);
	return ret;
} // singleDICOM()

size_t fileBytes(const char *fname) {
	FILE *fp = fopen(fname, "rb");
	if (!fp)
		return 0;
	fseek(fp, 0, SEEK_END);
	size_t fileLen = ftell(fp);
	fclose(fp);
	return fileLen;
} //fileBytes()

int searchDirForDICOM(char *path, struct TSearchList *nameList, int maxDepth, int depth, struct TDCMopts *opts) {
	int ret = kEXIT_NOMINAL;
	tinydir_dir dir;
	tinydir_open(&dir, path);
	while (dir.has_next) {
		tinydir_file file;
		file.is_dir = 0; //avoids compiler warning: this is set by tinydir_readfile
		tinydir_readfile(&dir, &file);
		//printMessage("%s\n", file.name);
		char filename[768] = "";
		strcat(filename, path);
		strcat(filename, kFileSep);
		strcat(filename, file.name);
		if ((file.is_dir) && (depth < maxDepth) && (file.name[0] != '.')) {
			int tmp = searchDirForDICOM(filename, nameList, maxDepth, depth + 1, opts);
			if (tmp != kEXIT_NOMINAL) ret = tmp; //e.g. found ecat
		} else if (!file.is_reg) //ignore files "." and ".."
			;
		else if ((strlen(file.name) < 1) || (file.name[0] == '.'))
			; //printMessage("skipping hidden file %s\n", file.name);
		else if ((strlen(file.name) == 8) && (strcicmp(file.name, "DICOMDIR") == 0))
			; //printMessage("skipping DICOMDIR\n");
		else if ((isDICOMfile(filename) > 0) || (isExt(filename, ".par"))) {
			if (nameList->numItems < nameList->maxItems) {
				nameList->str[nameList->numItems] = (char *)malloc(strlen(filename) + 1);
				strcpy(nameList->str[nameList->numItems], filename);
			}
			nameList->numItems++;
			//printMessage("dcm %lu %s \n",nameList->numItems, filename);
#ifndef USING_R
		} else {
			if (fileBytes(filename) > 2048) {
				int tmp = convert_foreign(filename, *opts);
				if (tmp == EXIT_SUCCESS) ret = tmp; //e.g. found ecat
			}
#ifdef MY_DEBUG
			printMessage("Not a dicom:\t%s\n", filename);
#endif
#endif
		}
		tinydir_next(&dir);
	}
	tinydir_close(&dir);
	return ret;
} // searchDirForDICOM()

int removeDuplicates(int nConvert, struct TDCMsort dcmSort[]) {
	//done AFTER sorting, so duplicates will be sequential
	if (nConvert < 2)
		return nConvert;
	int nDuplicates = 0;
	for (int i = 1; i < nConvert; i++) {
		if (compareTDCMsort(&dcmSort[i], &dcmSort[i - 1]) == 0) {
			nDuplicates++;
		} else {
			dcmSort[i - nDuplicates].img = dcmSort[i].img;
			dcmSort[i - nDuplicates].indx = dcmSort[i].indx;
			for (int j = 0; j < MAX_NUMBER_OF_DIMENSIONS; ++j)
				dcmSort[i - nDuplicates].dimensionIndexValues[j] = dcmSort[i].dimensionIndexValues[j];
		}
	}
	if (nDuplicates > 0)
		printMessage("%d images have identical time, series, acquisition and instance values. DUPLICATES REMOVED.\n", nDuplicates);
	return nConvert - nDuplicates;
} // removeDuplicates()

int removeDuplicatesVerbose(int nConvert, struct TDCMsort dcmSort[], struct TSearchList *nameList) {
	//done AFTER sorting, so duplicates will be sequential
	if (nConvert < 2)
		return nConvert;
	int nDuplicates = 0;
	for (int i = 1; i < nConvert; i++) {
		if (compareTDCMsort(&dcmSort[i], &dcmSort[i - 1]) == 0) {
			printMessage("\t%s\t=\t%s\n", nameList->str[dcmSort[i - 1].indx], nameList->str[dcmSort[i].indx]);
			nDuplicates++;
		} else {
			dcmSort[i - nDuplicates].img = dcmSort[i].img;
			dcmSort[i - nDuplicates].indx = dcmSort[i].indx;
			for (int j = 0; j < MAX_NUMBER_OF_DIMENSIONS; ++j)
				dcmSort[i - nDuplicates].dimensionIndexValues[j] = dcmSort[i].dimensionIndexValues[j];
		}
	}
	if (nDuplicates > 0)
		printMessage("%d images have identical time, series, acquisition and instance values. Duplicates removed.\n", nDuplicates);
	return nConvert - nDuplicates;
} // removeDuplicatesVerbose()

int convert_parRec(char *fnm, struct TDCMopts opts) {
	//sample dataset from Ed Gronenschild <ed.gronenschild@maastrichtuniversity.nl>
	struct TSearchList nameList;
	int ret = EXIT_FAILURE;
	nameList.numItems = 1;
	nameList.maxItems = 1;
	nameList.str = (char **)malloc((nameList.maxItems + 1) * sizeof(char *)); //we reserve one pointer (32 or 64 bits) per potential file
	struct TDICOMdata *dcmList = (struct TDICOMdata *)malloc(nameList.numItems * sizeof(struct TDICOMdata));
	nameList.str[0] = (char *)malloc(strlen(fnm) + 1);
	strcpy(nameList.str[0], fnm);
	//nameList.str[0] = (char *)malloc(strlen(opts.indir)+1);
	//strcpy(nameList.str[0],opts.indir);
	struct TDTI4D *dti4D = (struct TDTI4D *)malloc(sizeof(struct TDTI4D));
	dcmList[0] = nii_readParRec(nameList.str[0], opts.isVerbose, dti4D, false);
	struct TDCMsort dcmSort[1];
	dcmSort[0].indx = 0;
	if (dcmList[0].isValid)
		ret = saveDcm2Nii(1, dcmSort, dcmList, &nameList, opts, dti4D);
	free(dti4D);
	free(dcmList); //if (nConvertTotal == 0)
	if (nameList.numItems < 1)
		printMessage("No valid PAR/REC files were found\n");
	freeNameList(nameList);
	return ret;
} // convert_parRec()

int copyFile(char *src_path, char *dst_path) {
#define BUFFSIZE 32768
	unsigned char buffer[BUFFSIZE];
	FILE *fin = fopen(src_path, "rb");
	if (fin == NULL) {
		printError("Check file permissions: Unable to open input %s\n", src_path);
		return EXIT_SUCCESS;
	}
	if (is_fileexists(dst_path)) {
		if (true) {
			printWarning("Naming conflict (duplicates?): '%s' '%s'\n", src_path, dst_path);
			return EXIT_SUCCESS;
		} else {
			printError("File naming conflict. Existing file %s\n", dst_path);
			return EXIT_FAILURE;
		}
	}
	FILE *fou = fopen(dst_path, "wb");
	if (fou == NULL) {
		printError("Check file permission. Unable to open output %s\n", dst_path);
		return EXIT_FAILURE;
	}
	size_t bytes;
	while ((bytes = fread(buffer, 1, BUFFSIZE, fin)) != 0) {
		if (fwrite(buffer, 1, bytes, fou) != bytes) {
			printError("Unable to write %zu bytes to output %s\n", bytes, dst_path);
			return EXIT_FAILURE;
		}
	}
	fclose(fin);
	fclose(fou);
	return EXIT_SUCCESS;
}

#ifdef USING_R

// This implementation differs enough from the mainline one to be separated
int searchDirRenameDICOM(char *path, int maxDepth, int depth, struct TDCMopts *opts) {
	// The tinydir_open_sorted function reads the whole directory at once,
	// which is necessary in this context since we may be creating new
	// files in the same directory, which we don't want to further examine
	tinydir_dir dir;
	int count = 0;
	if (tinydir_open_sorted(&dir, path) != 0)
		return -1;
	for (size_t i = 0; i < dir.n_files; i++) {
		// If this directory entry is a subdirectory, search it recursively
		tinydir_file &file = dir._files[i];
		const std::string sourcePath = std::string(path) + kFileSep + file.name;
		char *sourcePathPtr = const_cast<char *>(sourcePath.c_str());
		if ((file.is_dir) && (depth < maxDepth) && (file.name[0] != '.')) {
			const int subdirectoryCount = searchDirRenameDICOM(sourcePathPtr, maxDepth, depth + 1, opts);
			if (subdirectoryCount < 0) {
				tinydir_close(&dir);
				return -1;
			}
			count += subdirectoryCount;
		} else if (file.is_reg && strlen(file.name) > 0 && file.name[0] != '.' && strcicmp(file.name, "DICOMDIR") != 0 && isDICOMfile(sourcePathPtr)) {
			TDICOMdata dcm = readDICOM(sourcePathPtr);
			if (dcm.imageNum > 0) {
				if ((opts->isIgnoreDerivedAnd2D) && ((dcm.isLocalizer) || (strcmp(dcm.sequenceName, "_tfl2d1") == 0) || (strcmp(dcm.sequenceName, "_fl3d1_ns") == 0) || (strcmp(dcm.sequenceName, "_fl2d1") == 0))) {
					printMessage("Ignoring localizer %s\n", sourcePathPtr);
					opts->ignoredPaths.push_back(sourcePath);
				} else if ((opts->isIgnoreDerivedAnd2D && dcm.isDerived)) {
					printMessage("Ignoring derived %s\n", sourcePathPtr);
					opts->ignoredPaths.push_back(sourcePath);
				} else {
					// Create an initial file name
					char outname[PATH_MAX] = {""};
					if (dcm.echoNum > 1)
						dcm.isMultiEcho = true;
					nii_createFilename(dcm, outname, *opts);
					// If the file name part of the target path has no extension, add ".dcm"
					std::string targetPath(outname);
					std::string targetStem, targetExtension;
					const size_t periodLoc = targetPath.find_last_of('.');
					if (periodLoc == targetPath.length() - 1) {
						targetStem = targetPath.substr(0, targetPath.length() - 1);
						targetExtension = ".dcm";
					} else if (periodLoc == std::string::npos || periodLoc < targetPath.find_last_of("\\/")) {
						targetStem = targetPath;
						targetExtension = ".dcm";
					} else {
						targetStem = targetPath.substr(0, periodLoc);
						targetExtension = targetPath.substr(periodLoc);
					}
					// Deduplicate the target path to avoid overwriting existing files
					targetPath = targetStem + targetExtension;
					GetRNGstate();
					while (is_fileexists(targetPath.c_str())) {
						std::ostringstream suffix;
						unsigned suffixValue = static_cast<unsigned>(round(R::unif_rand() * (R_pow_di(2.0, 24) - 1.0)));
						suffix << std::hex << std::setfill('0') << std::setw(6) << suffixValue;
						targetPath = targetStem + "_" + suffix.str() + targetExtension;
					}
					PutRNGstate();
					// Copy the file, unless the source and target paths are the same
					if (targetPath.compare(sourcePath) == 0) {
						if (opts->isVerbose > 1)
							printMessage("Skipping %s, which would be copied onto itself\n", sourcePathPtr);
					} else if (copyFile(sourcePathPtr, const_cast<char *>(targetPath.c_str())) == EXIT_SUCCESS) {
						opts->sourcePaths.push_back(sourcePath);
						opts->targetPaths.push_back(targetPath);
						count++;
						if (opts->isVerbose > 0)
							printMessage("Copying %s -> %s\n", sourcePathPtr, targetPath.c_str());
					} else {
						printWarning("Unable to copy to path %s\n", targetPath.c_str());
					}
				}
			}
		}
	}
	return count;
}

#else

int searchDirRenameDICOM(char *path, int maxDepth, int depth, struct TDCMopts *opts) {
	int retAll = 0;
	tinydir_dir dir;
	if (tinydir_open_sorted(&dir, path) != 0) {
		if (opts->isVerbose > 0)
			printMessage("Unable to open %s\n", path);
		return -1;
	}
	if (dir.n_files < 1) {
		if (opts->isVerbose > 0)
			printMessage("No files in %s\n", path);
		return 0;
	}
	if (opts->isVerbose > 0)
		printMessage("Found %zu items in %s\n", dir.n_files, path); //%lu -> %zu
	for (size_t i = 0; i < dir.n_files; i++) {
		// If this directory entry is a subdirectory, search it recursively
		tinydir_file &file = dir._files[i];
		char filename[768] = "";
		strcat(filename, path);
		strcat(filename, kFileSep);
		strcat(filename, file.name);
		if ((file.is_dir) && (depth < maxDepth) && (file.name[0] != '.')) {
			int retSub = searchDirRenameDICOM(filename, maxDepth, depth + 1, opts);
			if (retSub < 0)
				return retSub;
			retAll += retSub;
		} else if (!file.is_reg) //ignore files "." and ".."
			;
		else if ((strlen(file.name) < 1) || (file.name[0] == '.'))
			; //printMessage("skipping hidden file %s\n", file.name);
		else if ((strlen(file.name) == 8) && (strcicmp(file.name, "DICOMDIR") == 0))
			; //printMessage("skipping DICOMDIR\n");
		else if (isDICOMfile(filename) > 0) {
			//printMessage("dcm %s \n", filename);
			struct TDICOMdata dcm = readDICOM(filename); //ignore compile warning - memory only freed on first of 2 passes
			//~ if ((dcm.isValid) &&((dcm.totalSlicesIn4DOrder != NULL) ||(dcm.patientPositionNumPhilips > 1) || (dcm.CSA.numDti > 1))) { //4D dataset: dti4D arrays require huge amounts of RAM - write this immediately
			if (dcm.imageNum > 0) { //use imageNum instead of isValid to convert non-images (kWaveformSq will have instance number but is not a valid image)
				if ((opts->isIgnoreDerivedAnd2D) && ((dcm.isLocalizer) || (strcmp(dcm.sequenceName, "_tfl2d1") == 0) || (strcmp(dcm.sequenceName, "_fl3d1_ns") == 0) || (strcmp(dcm.sequenceName, "_fl2d1") == 0))) {
					printMessage("Ignoring localizer %s\n", filename);
				} else if ((opts->isIgnoreDerivedAnd2D && dcm.isDerived)) {
					printMessage("Ignoring derived %s\n", filename);
				} else {
					char outname[PATH_MAX] = {""};
					if (dcm.echoNum > 1)
						dcm.isMultiEcho = true; //last resort: Siemens gives different echoes the same image number: avoid overwriting, e.g "-f %r.dcm" should generate "1.dcm", "1_e2.dcm" for multi-echo volumes
					nii_createFilename(dcm, outname, *opts);
					//if (isDcmExt) strcat (outname,".dcm");
					int ret = copyFile(filename, outname);
					if (ret != EXIT_SUCCESS) {
						printError("Unable to rename all DICOM images.\n");
						return -1;
					}
					retAll += 1;
					if (opts->isVerbose > 0)
						printMessage("Renaming %s -> %s\n", filename, outname);
				}
			}
		}
		tinydir_next(&dir);
	}
	tinydir_close(&dir);
	return retAll;
} // searchDirForDICOM()

#endif // USING_R

//Timing
#define myTimer

//"BubbleSort" method uses nested "for i = 0..nDCM; for j = i+1..nDCM"
// the alternative is to quick-sort based on seriesUID and only test for matches in buckets where seriesUID matches
// the advantage of the bubble sort method is that it has been used extensively
// the quick sort method should be faster when handling thousands of files.
// difference very small for typical datasets (~0.1s for 3200 DICOMs)
//#define myBubbleSort
#ifndef myBubbleSort
struct TCRCsort {
	uint64_t indx;
	uint32_t crc;
};

void fillTCRCsort(struct TCRCsort &tcrcref, const uint64_t indx, const uint32_t crc) {
	tcrcref.indx = indx;
	tcrcref.crc = crc;
}

int compareTCRCsort(void const *item1, void const *item2) {
	//for quicksort http://blog.ablepear.com/2011/11/objective-c-tuesdays-sorting-arrays.html
	struct TCRCsort const *dcm1 = (const struct TCRCsort *)item1;
	struct TCRCsort const *dcm2 = (const struct TCRCsort *)item2;
	if (dcm1->crc < dcm2->crc)
		return -1;
	else if (dcm1->crc > dcm2->crc)
		return 1;
	return 0; //tie
}
#endif

#ifdef myTimer
int reportProgress(int progressPct, float frac) {
	int newProgressPct = round(100.0 * frac);
	const int kMinPct = 5; //e.g. if 10 then report 0.1, 0.2, 0.3...
	newProgressPct = (newProgressPct / kMinPct) * kMinPct; //if MinPct is 5 and we are 87 percent done report 85%
	if (newProgressPct == progressPct)
		return progressPct;
	if (newProgressPct != progressPct) //only report for change
		printProgress((float)newProgressPct / 100.0);
	return newProgressPct;
}
#endif

int nii_loadDirCore(char *indir, struct TDCMopts *opts) {
#ifdef USING_DCM2NIIXFSWRAPPER
	memset(&mrifsStruct, 0, sizeof(mrifsStruct));
#endif

	struct TSearchList nameList;
	int nConvertTotal = 0;
#if defined(_WIN64) || defined(_WIN32) || defined(USING_R)
	nameList.maxItems = 24000; // larger requires more memory, smaller more passes
#else //UNIX, not R
	nameList.maxItems = 96000; // larger requires more memory, smaller more passes
#endif
	//progress variables
	const float kStage1Frac = 0.05; //e.g. finding files requires ~05pct
	const float kStage2Frac = 0.45; //e.g. reading headers and converting 4D files requires ~45pct
	const float kStage3Frac = 0.50; //e.g. converting 2D/3D files to 3D/4D files requires ~50pct
	int progressPct = 0;			//proportion correct, 0..100
	if (opts->isProgress)
		progressPct = reportProgress(-1, 0.0); //report 0%
#ifdef myTimer
	clock_t start = clock();
#endif
	if ((is_fileNotDir(opts->indir)) && isExt(opts->indir, ".txt")) {
		nameList.str = (char **)malloc((nameList.maxItems + 1) * sizeof(char *)); //reserve one pointer (32 or 64 bits) per potential file
		nameList.numItems = 0;
		FILE *fp = fopen(opts->indir, "r"); //textDICOM
		if (fp == NULL)
			return EXIT_FAILURE;
		char dcmname[2048];
		while (fgets(dcmname, sizeof(dcmname), fp)) {
			int sz = (int)strlen(dcmname);
			if (sz > 0 && dcmname[sz - 1] == '\n')
				dcmname[sz - 1] = 0; //Unix LF
			if (sz > 1 && dcmname[sz - 2] == '\r')
				dcmname[sz - 2] = 0; //Windows CR/LF
			if ((!is_fileexists(dcmname)) || (!is_fileNotDir(dcmname))) { //<-this will accept meta data
				fclose(fp);
				printError("Problem with file '%s'\n", dcmname);
				return EXIT_FAILURE;
			}
			if (nameList.numItems < nameList.maxItems) {
				nameList.str[nameList.numItems] = (char *)malloc(strlen(dcmname) + 1);
				strcpy(nameList.str[nameList.numItems], dcmname);
			}
			nameList.numItems++;
		}
		fclose(fp);
		if (nameList.numItems >= nameList.maxItems) {
			printError("Too many file names in '%s'\n", opts->indir);
			return EXIT_FAILURE;
		}
		if (nameList.numItems < 1)
			return kEXIT_NO_VALID_FILES_FOUND;
		printMessage("Found %lu files in '%s'\n", nameList.numItems, opts->indir);
	} else {
		//1: find filenames of dicom files: up to two passes if we found more files than we allocated memory
		for (int i = 0; i < 2; i++) {
			nameList.str = (char **)malloc((nameList.maxItems + 1) * sizeof(char *)); //reserve one pointer (32 or 64 bits) per potential file
			nameList.numItems = 0;
			int ret = searchDirForDICOM(indir, &nameList, opts->dirSearchDepth, 0, opts);
			if (ret == EXIT_SUCCESS) //e.g. converted ECAT
				nConvertTotal++;
			if (nameList.numItems <= nameList.maxItems)
				break;
			freeNameList(nameList);
			nameList.maxItems = nameList.numItems + 1;
			//printMessage("Second pass required, found %ld images\n", nameList.numItems);
		}
		if (nameList.numItems < 1) {
			if ((opts->dirSearchDepth > 0) && (nConvertTotal < 1))
				printError("Unable to find any DICOM images in %s (or subfolders %d deep)\n", indir, opts->dirSearchDepth);
			else //keep silent for dirSearchDepth = 0 - presumably searching multiple folders
			{
			};
			free(nameList.str); //ignore compile warning - memory only freed on first of 2 passes
			if (nConvertTotal > 0) return EXIT_SUCCESS; //e.g. converted ECAT
			return kEXIT_NO_VALID_FILES_FOUND;
		}
	}
	size_t nDcm = nameList.numItems;
	printMessage("Found %lu DICOM file(s)\n", nameList.numItems); //includes images and other non-image DICOMs
	if (opts->onlySearchDirForDICOM == 2) {
		printMessage("List of DICOM file(s):\n");
		for (int i = 0; i < nameList.numItems; i++)
			printMessage("%s\n", nameList.str[i]);
		printMessage("End of list (%lu in total)\n", nameList.numItems);
	}
#ifdef myTimer
	if (opts->isProgress > 1)
		printMessage("Stage 1 (Count number of DICOMs) required %f seconds.\n", ((float)(clock() - start)) / CLOCKS_PER_SEC);
	start = clock();
#endif
	if (opts->isProgress)
		progressPct = reportProgress(progressPct, kStage1Frac); //proportion correct, 0..100															// struct TDICOMdata dcmList [nameList.numItems]; //<- this exhausts the stack for large arrays
	struct TDICOMdata *dcmList = (struct TDICOMdata *)malloc(nameList.numItems * sizeof(struct TDICOMdata));
	struct TDTI4D *dti4D = (struct TDTI4D *)malloc(sizeof(struct TDTI4D));
	struct TDCMprefs prefs;
	opts2Prefs(opts, &prefs);
	bool compressionWarning = false;
	bool convertError = false;
	bool isDcmExt = isExt(opts->filename, ".dcm"); // "%r.dcm" with multi-echo should generate "1.dcm", "1e2.dcm"
	if (isDcmExt)
		opts->filename[strlen(opts->filename) - 4] = 0; // "%s_%r.dcm" -> "%s_%r"
			//consider OpenMP
			// g++-9 -I. main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -o dcm2niix -DmyDisableOpenJPEG -fopenmp
	for (int i = 0; i < (int)nDcm; i++) {
		if ((isExt(nameList.str[i], ".par")) && (isDICOMfile(nameList.str[i]) < 1)) {
			//strcpy(opts->indir, nameList.str[i]); //set to original file name, not path
			dcmList[i].converted2NII = 1;
			int ret = convert_parRec(nameList.str[i], *opts);
			if (ret == EXIT_SUCCESS)
				nConvertTotal++;
			else
				convertError = true;
			continue;
		}
		dcmList[i] = readDICOMx(nameList.str[i], &prefs, dti4D); //ignore compile warning - memory only freed on first of 2 passes
		//dcmList[i] = readDICOMv(nameList.str[i], opts->isVerbose, opts->compressFlag, dti4D); //ignore compile warning - memory only freed on first of 2 passes
		if (opts->isIgnoreSeriesInstanceUID)
			dcmList[i].seriesUidCrc = dcmList[i].seriesNum;
		//if (!dcmList[i].isValid) printf(">>>>Not a valid DICOM %s\n", nameList.str[i]);
		if ((dcmList[i].isValid) && ((dti4D->sliceOrder[0] >= 0) || (dcmList[i].CSA.numDti > 1))) { //4D dataset: dti4D arrays require huge amounts of RAM - write this immediately
			struct TDCMsort dcmSort[1];
			fillTDCMsort(dcmSort[0], i, dcmList[i]);
			dcmList[i].converted2NII = 1;
			int ret = saveDcm2Nii(1, dcmSort, dcmList, &nameList, *opts, dti4D);
			if (ret == EXIT_SUCCESS)
				nConvertTotal++;
			else
				convertError = true;
		}
		if ((dcmList[i].compressionScheme != kCompressNone) && (!compressionWarning) && (opts->compressFlag != kCompressNone)) {
			compressionWarning = true; //generate once per conversion rather than once per image
			printMessage("Image Decompression is new: please validate conversions\n");
		}
		if (opts->isProgress)
			progressPct = reportProgress(progressPct, kStage1Frac + (kStage2Frac * (float)i / (float)nDcm)); //proportion correct, 0..100
	}
#ifdef myTimer
	if (opts->isProgress > 1)
		printMessage("Stage 2 (Read DICOM headers, Convert 4D) required %f seconds.\n", ((float)(clock() - start)) / CLOCKS_PER_SEC);
	start = clock();
#endif
	if ((opts->isRenameNotConvert) || (opts->onlySearchDirForDICOM != 0)) {
		free(dcmList);
		free(dti4D);
		return EXIT_SUCCESS;
	}
#ifdef USING_R
	if (opts->isScanOnly) {
		TWarnings warnings = setWarnings();
		// Create the first series from the first DICOM file
		TDicomSeries firstSeries;
		char firstSeriesName[2048] = "";
		nii_createFilename(dcmList[0], firstSeriesName, *opts);
		firstSeries.name = firstSeriesName;
		firstSeries.representativeData = dcmList[0];
		firstSeries.files.push_back(nameList.str[0]);
		opts->series.push_back(firstSeries);
		// Iterate over the remaining files
		for (size_t i = 1; i < nDcm; i++) {
			bool matched = false;
			// If the file matches an existing series, add it to the corresponding file list
			for (size_t j = 0; j < opts->series.size(); j++) {
				bool isMultiEcho = false, isNonParallelSlices = false, isCoilVaries = false;
				if (isSameSet(opts->series[j].representativeData, dcmList[i], opts, &warnings, &isMultiEcho, &isNonParallelSlices, &isCoilVaries)) {
					opts->series[j].files.push_back(nameList.str[i]);
					matched = true;
					break;
				}
			}
			// If not, create a new series object
			if (!matched) {
				TDicomSeries nextSeries;
				char nextSeriesName[2048] = "";
				nii_createFilename(dcmList[i], nextSeriesName, *opts);
				nextSeries.name = nextSeriesName;
				nextSeries.representativeData = dcmList[i];
				nextSeries.files.push_back(nameList.str[i]);
				opts->series.push_back(nextSeries);
			}
		}
		// To avoid a spurious warning below
		nConvertTotal = nDcm;
	} else {
#endif
#ifdef myBubbleSort
		//3: stack DICOMs with the same Series
		struct TWarnings warnings = setWarnings();
		for (int i = 0; i < (int)nDcm; i++) {
			if ((dcmList[i].converted2NII == 0) && (dcmList[i].isValid)) {
				int nConvert = 0;
				bool isMultiEcho = false;
				bool isNonParallelSlices = false;
				bool isCoilVaries = false;
				for (int j = i; j < (int)nDcm; j++)
					if (isSameSet(dcmList[i], dcmList[j], opts, &warnings, &isMultiEcho, &isNonParallelSlices, &isCoilVaries))
						nConvert++;
				if (nConvert < 1)
					nConvert = 1; //prevents compiler warning for next line: never executed since j=i always causes nConvert ++
				TDCMsort *dcmSort = (TDCMsort *)malloc(nConvert * sizeof(TDCMsort));
				nConvert = 0;
				for (int j = i; j < (int)nDcm; j++) {
					isMultiEcho = false;
					isCoilVaries = false;
					isNonParallelSlices = false;
					if (isSameSet(dcmList[i], dcmList[j], opts, &warnings, &isMultiEcho, &isNonParallelSlices, &isCoilVaries)) {
						dcmList[j].converted2NII = 1; //do not reprocess repeats
						fillTDCMsort(dcmSort[nConvert], j, dcmList[j]);
						nConvert++;
					} else {
						if (isNonParallelSlices) {
							dcmList[i].isNonParallelSlices = true;
							dcmList[j].isNonParallelSlices = true;
						}
						if (isMultiEcho) {
							dcmList[i].isMultiEcho = true;
							dcmList[j].isMultiEcho = true;
						}
						if (isCoilVaries) {
							dcmList[i].isCoilVaries = true;
							dcmList[j].isCoilVaries = true;
						}
					} //unable to stack images: mark files that may need file name dis-ambiguation
				}
				qsort(dcmSort, nConvert, sizeof(struct TDCMsort), compareTDCMsort); //sort based on series and image numbers....
				//dcmList[dcmSort[0].indx].isMultiEcho = isMultiEcho;
				if (opts->isVerbose)
					nConvert = removeDuplicatesVerbose(nConvert, dcmSort, &nameList);
				else
					//nConvert = removeDuplicatesVerbose(nConvert, dcmSort, &nameList);
					nConvert = removeDuplicates(nConvert, dcmSort);
				int ret = saveDcm2Nii(nConvert, dcmSort, dcmList, &nameList, *opts, dti4D);
				if (ret == EXIT_SUCCESS)
					nConvertTotal += nConvert;
				else
					convertError = true;
				free(dcmSort);
			} //convert all images of this series
		}
#else //avoid bubble sort - do not check all images for match, only those with identical series instance UID
	//3: stack DICOMs with the same Series
	struct TWarnings warnings = setWarnings();
	//sort by series instance UID ... avoids bubble-sort penalty
	TCRCsort *crcSort = (TCRCsort *)malloc(nDcm * sizeof(TCRCsort));
	for (int i = 0; i < (int)nDcm; i++)
		fillTCRCsort(crcSort[i], i, dcmList[i].seriesUidCrc);
	qsort(crcSort, nDcm, sizeof(struct TCRCsort), compareTCRCsort); //sort based on series and image numbers....
	int *convertIdxs = (int *)malloc(sizeof(int) * (nDcm));
	for (int i = 0; i < (int)nDcm; i++) {
		int ii = crcSort[i].indx;
		if (dcmList[ii].converted2NII)
			continue;
		if (!dcmList[ii].isValid)
			continue;

#ifdef USING_DCM2NIIXFSWRAPPER
		if (opts->numSeries > 0) {
			double seriesNum = (double) dcmList[ii].seriesUidCrc;
			if (!isSameDouble(opts->seriesNumber[0], seriesNum))
				continue;   // we convert one series at a time, skip the ones that we are not interested in
		}
#endif

		int nConvert = 0;
		bool isMultiEcho = false;
		bool isNonParallelSlices = false;
		bool isCoilVaries = false;
		int jMax = i;
		for (int j = i; j < (int)nDcm; j++) {
			int ji = crcSort[j].indx;
			if (dcmList[ii].seriesUidCrc != dcmList[ji].seriesUidCrc)
				break; //seriesUID no longer matches no need to examine any subsequent images
			jMax = j;
			if (isSameSet(dcmList[ii], dcmList[ji], opts, &warnings, &isMultiEcho, &isNonParallelSlices, &isCoilVaries)) {
				dcmList[ji].converted2NII = 1; //do not reprocess repeats
				convertIdxs[nConvert] = ji;
				nConvert++;
			}
		} //for all images with same seriesUID as first one

		// MGH set Opts.isForceStackSameSeries = 1 by default, isMultiEcho, isNonParallelSlices, isCoilVaries remain false for MGH default run after isSameSet
		if ((isNonParallelSlices) && (dcmList[ii].CSA.mosaicSlices > 1) && (nConvert > 0)) { //issue481: if ANY volumes are non-parallel, save ALL as 3D
			printWarning("Saving mosaics with non-parallel slices as 3D (issue 481)\n");
			for (int j = i; j < (int)nDcm; j++) {
				int ji = crcSort[j].indx;
				if (dcmList[ii].seriesUidCrc != dcmList[ji].seriesUidCrc)
					break;
				dcmList[ji].converted2NII = 1;
				dcmList[ji].isNonParallelSlices = true;
				if (isMultiEcho)
					dcmList[ji].isMultiEcho = true;
				if (isCoilVaries)
					dcmList[ji].isCoilVaries = true;
				struct TDCMsort dcmSort[1];
				fillTDCMsort(dcmSort[0], ji, dcmList[ji]);
				int ret = saveDcm2Nii(1, dcmSort, dcmList, &nameList, *opts, dti4D);
				if (ret == EXIT_SUCCESS)
					nConvertTotal++;
				else
					convertError = true;
			}
			continue;
		} //issue481
		//issue 381: ensure all images are informed if there are variations in echo, parallel slices, coil name:
		if (isMultiEcho)
			for (int j = i; j <= jMax; j++) {
				int ji = crcSort[j].indx;
				dcmList[ji].isMultiEcho = true;
			}
		if (isNonParallelSlices)
			for (int j = i; j <= jMax; j++) {
				int ji = crcSort[j].indx;
				dcmList[ji].isNonParallelSlices = true;
			}
		if (isCoilVaries)
			for (int j = i; j <= jMax; j++) {
				int ji = crcSort[j].indx;
				dcmList[ji].isCoilVaries = true;
			}
		TDCMsort *dcmSort = (TDCMsort *)malloc(nConvert * sizeof(TDCMsort));
		for (int j = 0; j < nConvert; j++)
			fillTDCMsort(dcmSort[j], convertIdxs[j], dcmList[convertIdxs[j]]);
		qsort(dcmSort, nConvert, sizeof(struct TDCMsort), compareTDCMsort); //sort based on series and image numbers....
		if (opts->isVerbose)
			nConvert = removeDuplicatesVerbose(nConvert, dcmSort, &nameList);
		else
			nConvert = removeDuplicates(nConvert, dcmSort);
		int ret = saveDcm2Nii(nConvert, dcmSort, dcmList, &nameList, *opts, dti4D);
		if (ret == EXIT_SUCCESS)
			nConvertTotal += nConvert;
		else
			convertError = true;
		free(dcmSort);
		if (opts->isProgress)
			progressPct = reportProgress(progressPct, kStage1Frac + kStage2Frac + (kStage3Frac * (float)nConvertTotal / (float)nDcm)); //proportion correct, 0..100
	}
	free(convertIdxs);
	free(crcSort);
#endif
#ifdef USING_R
	}
#endif
#ifdef myTimer
	if (opts->isProgress > 1)
		printMessage("Stage 3 (Convert 2D and 3D images) required %f seconds.\n", ((float)(clock() - start)) / CLOCKS_PER_SEC);
#endif
	if (opts->isProgress)
		progressPct = reportProgress(progressPct, 1); //proportion correct, 0..100
	free(dcmList);
	free(dti4D);
	freeNameList(nameList);
	if (convertError) {
		if (nConvertTotal == 0)
			return EXIT_FAILURE; //nothing converted
		printError("Converted %d of %zu files\n", nConvertTotal, nDcm);
		//printError("Converted %d of %lu files\n", nConvertTotal, nDcm);
		return kEXIT_SOME_OK_SOME_BAD; //partial failure
	}
	if (nConvertTotal == 0) {
		printMessage("No valid DICOM images were found\n"); //we may have found valid DICOM files but they are not DICOM images
		return kEXIT_NO_VALID_FILES_FOUND;
	}
	return EXIT_SUCCESS;
} //nii_loadDirCore()

int nii_loadDirOneDirAtATime(char *path, struct TDCMopts *opts, int maxDepth, int depth) {
	//return kEXIT_NO_VALID_FILES_FOUND if no files in ANY sub folders
	//return EXIT_FAILURE if ANY failure
	//return EXIT_SUCCESS if no failures and at least one image converted
	int ret = nii_loadDirCore(path, opts);
	if (ret == EXIT_FAILURE)
		return ret;
	tinydir_dir dir;
	tinydir_open(&dir, path);
	while (dir.has_next) {
		tinydir_file file;
		file.is_dir = 0; //avoids compiler warning: this is set by tinydir_readfile
		tinydir_readfile(&dir, &file);
		char filename[768] = "";
		strcat(filename, path);
		strcat(filename, kFileSep);
		strcat(filename, file.name);
		if ((file.is_dir) && (depth < maxDepth) && (file.name[0] != '.')) {
			int retSub = nii_loadDirOneDirAtATime(filename, opts, maxDepth, depth + 1);
			if (retSub == EXIT_FAILURE)
				return retSub;
			if (retSub == EXIT_SUCCESS)
				ret = retSub;
		}
		tinydir_next(&dir);
	}
	tinydir_close(&dir);
	return ret;
}

int nii_loadDir(struct TDCMopts *opts) {
	//Identifies all the DICOM files in a folder and its subfolders
	if (strlen(opts->indir) < 1) {
		printMessage("No input\n");
		return EXIT_FAILURE;
	}
	char indir[512];
	strcpy(indir, opts->indir);
	bool isFile = is_fileNotDir(indir);
	if (isFile) //if user passes ~/dicom/mr1.dcm we will look at all files in ~/dicom
		dropFilenameFromPath(opts->indir);
	dropTrailingFileSep(opts->indir);
	if (!is_dir(opts->indir, true)) {
		printError("Input folder invalid: %s\n", opts->indir);
		return kEXIT_INPUT_FOLDER_INVALID;
	}
#ifdef USING_R
	// Full file paths are only used by R/divest when reorganising DICOM files
	if (opts->isRenameNotConvert) {
#endif
		if (strlen(opts->outdir) < 1) {
			strcpy(opts->outdir, opts->indir);
		} else
			dropTrailingFileSep(opts->outdir);
		if (!is_dir(opts->outdir, true)) {
#ifdef myUseInDirIfOutDirUnavailable
			printWarning("Output folder invalid %s will try %s\n", opts->outdir, opts->indir);
			strcpy(opts->outdir, opts->indir);
#else
		printError("Output folder invalid: %s\n", opts->outdir);
		return kEXIT_OUTPUT_FOLDER_INVALID;
#endif
		}
		//check file permissions
		if ((opts->isCreateBIDS != false) || (opts->isOnlyBIDS != true)) { //output files expected: either BIDS or images
			int w = access(opts->outdir, W_OK);
			if (w != 0) {
#ifdef USE_CWD_IF_OUTDIR_NO_WRITE
				char outdir[512];
				strcpy(outdir, opts->outdir);
				strcpy(opts->outdir, opts->indir);
				w = access(opts->outdir, W_OK);
				if (w != 0) {
					printError("Unable to write to output folder: %s\n", outdir);
					return kEXIT_OUTPUT_FOLDER_READ_ONLY;
				} else
					printWarning("Writing to working directory, unable to write to output folder: %s\n", outdir);
#else
			printError("Unable to write to output folder: %s\n", opts->outdir);
			return kEXIT_OUTPUT_FOLDER_READ_ONLY;
#endif
			}
		}
#ifdef USING_R
	}
#endif
	getFileNameX(opts->indirParent, opts->indir, 512);
#ifndef USING_R
	if (isFile && ((isExt(indir, ".v"))))
		return convert_foreign(indir, *opts);
#endif
	if (isFile && ((isExt(indir, ".par")) || (isExt(indir, ".rec")))) {
		char pname[512], rname[512];
		strcpy(pname, indir);
		strcpy(rname, indir);
		changeExt(pname, "PAR");
		changeExt(rname, "REC");
#ifndef _MSC_VER //Linux is case sensitive, #include <unistd.h>
		if (access(rname, F_OK) != 0)
			changeExt(rname, "rec");
		if (access(pname, F_OK) != 0)
			changeExt(pname, "par");
#endif
		if (is_fileNotDir(rname) && is_fileNotDir(pname)) {
			//strcpy(opts->indir, pname); //set to original file name, not path
			return convert_parRec(pname, *opts);
		};
	}
	if (isFile && (opts->isOnlySingleFile) && isExt(indir, ".txt")) {
		strcpy(opts->indir, indir);
		return nii_loadDirCore(opts->indir, opts);
	}
	if (opts->isRenameNotConvert) {
		int nConvert = searchDirRenameDICOM(opts->indir, opts->dirSearchDepth, 0, opts);
		if (nConvert < 0)
			return kEXIT_RENAME_ERROR;
#ifdef USING_R
		printMessage("Renamed %d DICOMs\n", nConvert);
#else
		printMessage("Converted %d DICOMs\n", nConvert);
#endif
		return EXIT_SUCCESS;
	}
	if ((isFile) && (opts->isOnlySingleFile))
		return singleDICOM(opts, indir);
	if (opts->isOneDirAtATime) {
		int maxDepth = opts->dirSearchDepth;
		opts->dirSearchDepth = 0;
		strcpy(indir, opts->indir);
		return nii_loadDirOneDirAtATime(indir, opts, maxDepth, 0);
	} else
		return nii_loadDirCore(opts->indir, opts);
} // nii_loadDir()

#if defined(_WIN64) || defined(_WIN32) || defined(USING_R)
#else //UNIX, not R

int findpathof(char *pth, const char *exe) {
	//Find executable by searching the PATH environment variable.
	// http://www.linuxquestions.org/questions/programming-9/get-full-path-of-a-command-in-c-117965/
	char *searchpath;
	char *beg, *end;
	int stop, found;
	size_t len;
	if (strchr(exe, '/') != NULL) {
		if (realpath(exe, pth) == NULL)
			return 0;
		return is_exe(pth);
	}
	searchpath = getenv("PATH");
	if (searchpath == NULL)
		return 0;
	if (strlen(searchpath) <= 0)
		return 0;
	beg = searchpath;
	stop = 0;
	found = 0;
	do {
		end = strchr(beg, ':');
		if (end == NULL) {
			len = strlen(beg);
			if (len == 0)
				return 0;
			//gcc 8.1 warning: specified bound depends on the length of the source argument
			//https://developers.redhat.com/blog/2018/05/24/detecting-string-truncation-with-gcc-8/
			//strncpy(pth, beg, len);
			strcpy(pth, beg);
			stop = 1;
		} else {
			strncpy(pth, beg, end - beg);
			pth[end - beg] = '\0';
			len = end - beg;
		}
		//gcc8.1 warning: specified bound depends on the length of the source argument
		//if (pth[len - 1] != '/') strncat(pth, "/", 1);
		if (pth[len - 1] != '/')
			strcat(pth, "/");
		strncat(pth, exe, PATH_MAX - len);
		found = is_exe(pth);
		if (!stop)
			beg = end + 1;
	} while (!stop && !found);
	if (!found)
		strcpy(pth, "");
	return found;
}
#endif

#ifndef USING_R
void readFindPigz(struct TDCMopts *opts, const char *argv[]) {
#if defined(_WIN64) || defined(_WIN32)
	strcpy(opts->pigzname, "pigz.exe");
	if (is_exe(opts->pigzname)) 
		return;
	if (!is_exe(opts->pigzname)) {
		char exepth[PATH_MAX];
		strcpy(exepth, argv[0]);
		dropFilenameFromPath(exepth); //, opts.pigzname);
		char appendChar[2] = {"a"};
		appendChar[0] = kPathSeparator;
		strcat(exepth, appendChar);
		strcat(exepth, opts->pigzname);
		strcpy(opts->pigzname, exepth);
	}
	if (is_exe(opts->pigzname)) 
		return;
	HMODULE hModule = GetModuleHandle(NULL);
	if (hModule != NULL) {
		// https://stackoverflow.com/questions/1528298/get-path-of-executable
		char exepth[PATH_MAX];
		GetModuleFileName(hModule, exepth, (sizeof(exepth)));
		dropFilenameFromPath(exepth); //, opts.pigzname);
		char appendChar[2] = {"a"};
		appendChar[0] = kPathSeparator;
		strcat(exepth, appendChar);
		strcpy(opts->pigzname, "pigz.exe");
		strcat(exepth, opts->pigzname);
		strcpy(opts->pigzname, exepth);
	}
	if (is_exe(opts->pigzname)) 
		return;
#ifdef myDisableZLib
		printMessage("Compression requires %s in the same folder as the executable\n", opts->pigzname);
#else //myUseZLib
		if (opts->isVerbose > 0)
			printMessage("Compression will be faster with %s in the same folder as the executable\n", opts->pigzname);
#endif
	strcpy(opts->pigzname, "");
	return;
#else //if windows else linux
	char str[PATH_MAX];
	//possible pigz names
	const char *names[] = {
		"pigz",
		"pigz_mricron",
		"pigz_afni",
	};
#define n_nam (sizeof(names) / sizeof(const char *))
	for (int n = 0; n < (int)n_nam; n++) {
		if (findpathof(str, names[n])) {
			strcpy(opts->pigzname, str);
			//printMessage("Found pigz: %s\n", str);
			return;
		}
	}
	//possible pigz paths
	const char *pths[] = {
		"/usr/local/bin/",
		"/usr/bin/",
	};
#define n_pth (sizeof(pths) / sizeof(const char *))
	char exepth[PATH_MAX];
	strcpy(exepth, argv[0]);
	dropFilenameFromPath(exepth); //, opts.pigzname);
	char appendChar[2] = {"a"};
	appendChar[0] = kPathSeparator;
	if (exepth[strlen(exepth) - 1] != kPathSeparator)
		strcat(exepth, appendChar);
	//see if pigz in any path
	for (int n = 0; n < (int)n_nam; n++) {
		//printf ("%d: %s\n", i, names[n]);
		for (int p = 0; p < (int)n_pth; p++) {
			strcpy(str, pths[p]);
			strcat(str, names[n]);
			if (is_exe(str))
				goto pigzFound;
		} //p
		//check exepth
		strcpy(str, exepth);
		strcat(str, names[n]);
		if (is_exe(str))
			goto pigzFound;
	} //n
	//Failure:
#if defined(__APPLE__)
#ifdef myDisableZLib
	printMessage("Compression requires 'pigz' to be installed http://macappstore.org/pigz/\n");
#else //myUseZLib
	if (opts->isVerbose > 0)
		printMessage("Compression will be faster with 'pigz' installed http://macappstore.org/pigz/\n");
#endif
#else //if APPLE else ...
#ifdef myDisableZLib
	printMessage("Compression requires 'pigz' to be installed\n");
#else //myUseZLib
	if (opts->isVerbose > 0)
		printMessage("Compression will be faster with 'pigz' installed\n");
#endif
#endif
	return;
pigzFound: //Success
	strcpy(opts->pigzname, str);
//printMessage("Found pigz: %s\n", str);
#endif
} //readFindPigz()
#endif

void setDefaultOpts(struct TDCMopts *opts, const char *argv[]) { //either "setDefaultOpts(opts,NULL)" or "setDefaultOpts(opts,argv)" where argv[0] is path to search
	strcpy(opts->pigzname, "");
#ifndef USING_R
	if (argv != NULL)
		readFindPigz(opts, argv);
#endif
#ifdef myEnableJasper
	opts->compressFlag = kCompressYes; //JASPER for JPEG2000
#else
#ifdef myDisableOpenJPEG
	opts->compressFlag = kCompressNone; //no decompressor
#else
	opts->compressFlag = kCompressYes; //OPENJPEG for JPEG2000
#endif
#endif
	//printMessage("%d %s\n",opts->compressFlag, opts->compressname);
	strcpy(opts->outdir, "");
	strcpy(opts->indir, "");
	strcpy(opts->pigzname, "");
	strcpy(opts->optsname, "");
	strcpy(opts->indirParent, "");
	strcpy(opts->imageComments, "");
	strcpy(opts->bidsSubject, "");
	strcpy(opts->bidsSession, "");
	opts->isOnlySingleFile = false; //convert all files in a directory, not just a single file
	opts->isOneDirAtATime = false;
	opts->isRenameNotConvert = false;
	opts->isGuessBidsFilename = true;
	opts->isForceStackSameSeries = 2; //automatic: stack CTs, do not stack MRI
	opts->isForceStackDCE = true;
	opts->isIgnoreSeriesInstanceUID = false;
	opts->isIgnoreDerivedAnd2D = false;
	opts->isForceOnsetTimes = true;
	opts->isPhilipsFloatNotDisplayScaling = true;
	opts->isCrop = false;
	opts->isRotate3DAcq = true;
	opts->isGz = false;
	opts->isSaveNativeEndian = true;
	opts->isAddNamePostFixes = true; //e.g. "_e2" added for second echo
	opts->isTestx0021x105E = false; //GE test slice times stored in 0021,105E
	opts->diffCyclingModeGE = -1;
	opts->isIgnoreTriggerTimes = false;
	opts->saveFormat = kSaveFormatNIfTI;
	opts->isPipedGz = false; //e.g. pipe data directly to pigz instead of saving uncompressed to disk
	opts->isSave3D = false;
	opts->dirSearchDepth = 5;
	opts->onlySearchDirForDICOM = 0;
	opts->isProgress = 0;
	opts->nameConflictBehavior = kNAME_CONFLICT_ADD_SUFFIX;
#ifdef myDisableZLib
	opts->gzLevel = 6;
#else
	opts->gzLevel = MZ_DEFAULT_LEVEL;	//-1;
#endif
	//opts->isMaximize16BitRange = kMaximize16BitRange_False; //e.g. if INT16 image has range 0..500 scale to be 0..50000 with hdr.scl_slope = hdr.scl_slope * 0.01
	opts->isMaximize16BitRange = kMaximize16BitRange_Raw; //future version will use this option as default: preserve UINT16 even if it can be losslessly converted to INT16
	opts->isFlipY = true; //false: images in raw DICOM orientation, true: image rows flipped to cartesian coordinates
	opts->isRGBplanar = false; //false for NIfTI (RGBRGB...), true for Analyze (RRR..RGGG..GBBB..B)
	opts->isCreateBIDS = true;
	opts->isOnlyBIDS = false;
	opts->isSortDTIbyBVal = false;
#ifdef myNoAnonymizeBIDS
	opts->isAnonymizeBIDS = false;
#else
	opts->isAnonymizeBIDS = true;
#endif
	opts->isCreateText = false;
#ifdef myDebug
	opts->isVerbose = true;
#else
	opts->isVerbose = false;
#endif
	opts->isTiltCorrect = true;
	opts->numSeries = 0;
	memset(opts->seriesNumber, 0, sizeof(opts->seriesNumber));
	strcpy(opts->filename, "%f_%p_%t_%s");
	opts->isDumpNotConvert = false;
} // setDefaultOpts()

#if defined(_WIN64) || defined(_WIN32)
//windows has unusual file permissions for many users - lets save preferences to the registry
void saveIniFile(struct TDCMopts opts) {
	HKEY hKey;
	if (RegOpenKeyExA(HKEY_CURRENT_USER, "Software\\dcm2nii", 0, KEY_SET_VALUE, &hKey) != ERROR_SUCCESS) {
		RegCloseKey(hKey);
		return;
	}
	printMessage("Saving defaults to registry\n");
	DWORD dwValue = opts.isGz;
	RegSetValueExA(hKey, "isGZ", 0, REG_DWORD, reinterpret_cast<BYTE *>(&dwValue), sizeof(dwValue));
	dwValue = opts.isMaximize16BitRange;
	RegSetValueExA(hKey, "isMaximize16BitRange", 0, REG_DWORD, reinterpret_cast<BYTE *>(&dwValue), sizeof(dwValue));
	RegSetValueExA(hKey, "filename", 0, REG_SZ, (LPBYTE)opts.filename, strlen(opts.filename) + 1);
	RegCloseKey(hKey);
} //saveIniFile()

void readIniFile(struct TDCMopts *opts, const char *argv[]) {
	setDefaultOpts(opts, argv);
	HKEY hKey;
	DWORD vSize = 0;
	DWORD dwDataType = 0;
	DWORD dwValue = 0;
	//RegOpenKeyEx(RegOpenKeyEx, key, 0, accessRights, keyHandle);
	//if(RegOpenKeyEx(HKEY_CURRENT_USER,(WCHAR)"Software\\dcm2nii", 0, KEY_QUERY_VALUE,&hKey) != ERROR_SUCCESS) {
	if (RegOpenKeyExA(HKEY_CURRENT_USER, "Software\\dcm2nii", 0, KEY_QUERY_VALUE, &hKey) != ERROR_SUCCESS) {
		RegCloseKey(hKey);
		return;
	}
	vSize = sizeof(dwValue);
	//if(RegQueryValueExA(hKey,"isGZ", 0, (LPDWORD )&dwDataType, (&dwValue), &vSize) == ERROR_SUCCESS)
	if (RegQueryValueExA(hKey, "isGZ", 0, (LPDWORD)&dwDataType, reinterpret_cast<BYTE *>(&dwValue), &vSize) == ERROR_SUCCESS)
		opts->isGz = dwValue;
	if (RegQueryValueExA(hKey, "isMaximize16BitRange", 0, (LPDWORD)&dwDataType, reinterpret_cast<BYTE *>(&dwValue), &vSize) == ERROR_SUCCESS)
		opts->isMaximize16BitRange = dwValue;
	vSize = 512;
	char buffer[512];
	if (RegQueryValueExA(hKey, "filename", 0, NULL, (LPBYTE)buffer, &vSize) == ERROR_SUCCESS)
		strcpy(opts->filename, buffer);
	RegCloseKey(hKey);
} //readIniFile()

#else
//for Unix we will save preferences in a hidden text file in the home directory
#define STATUSFILENAME "/.dcm2nii.ini"

void readIniFile(struct TDCMopts *opts, const char *argv[]) {
	setDefaultOpts(opts, argv);
	snprintf(opts->optsname, kOptsStr, "%s%s", getenv("HOME"), STATUSFILENAME);
	FILE *fp = fopen(opts->optsname, "r");
	if (fp == NULL)
		return;
	char Setting[255], Value[255];
	//while ( fscanf(fp, "%[^=]=%s\n", Setting, Value) == 2 ) {
	//while ( fscanf(fp, "%[^=]=%s\n", Setting, Value) == 2 ) {
	while (fscanf(fp, "%[^=]=%[^\n]\n", Setting, Value) == 2) {
		//printMessage(">%s<->'%s'\n",Setting,Value);
		if (strcmp(Setting, "isGZ") == 0)
			opts->isGz = atoi(Value);
		if (strcmp(Setting, "isMaximize16BitRange") == 0)
			opts->isMaximize16BitRange = atoi(Value);
		else if (strcmp(Setting, "isBIDS") == 0)
			opts->isCreateBIDS = atoi(Value);
		else if (strcmp(Setting, "filename") == 0)
			strcpy(opts->filename, Value);
	}
	fclose(fp);
} // readIniFile()

void saveIniFile(struct TDCMopts opts) {
	FILE *fp = fopen(opts.optsname, "w");
	//printMessage("%s\n",localfilename);
	if (fp == NULL)
		return;
	printMessage("Saving defaults file %s\n", opts.optsname);
	fprintf(fp, "isGZ=%d\n", opts.isGz);
	fprintf(fp, "isMaximize16BitRange=%d\n", opts.isMaximize16BitRange);
	fprintf(fp, "isBIDS=%d\n", opts.isCreateBIDS);
	fprintf(fp, "filename=%s\n", opts.filename);
	fclose(fp);
} //saveIniFile()

#endif


#ifdef USING_DCM2NIIXFSWRAPPER
// this function outputs information in imageList.dat for dcmunpack
// the following fields from struct TDICOMdata are printed:
//   patientName  seriesNum  studyDate  studyTime  TE  TR  flipAngle  xyzMM[1]\xyzMM[2]  phaseEncodingRC  pixelBandwidth  dicom-file  imageType
void dcmListDump(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata dcmList[], struct TSearchList *nameList, struct TDCMopts opts) {
    for (int i = 0; i < nConvert; i++) {
      int indx = dcmSort[i].indx;
      mrifsStruct.dicomlst[i] = new char[strlen(nameList->str[indx])+1];
      memset(mrifsStruct.dicomlst[i], 0, strlen(nameList->str[indx])+1);
      memcpy(mrifsStruct.dicomlst[i], nameList->str[indx], strlen(nameList->str[indx]));
      
      printMessage("%s %ld %s %s %f %f %f %f\\%f %c %f %s %s\n",
                   dcmList[indx].patientName, dcmList[indx].seriesNum, dcmList[indx].studyDate, dcmList[indx].studyTime,
                   dcmList[indx].TE, dcmList[indx].TR, dcmList[indx].flipAngle, dcmList[indx].xyzMM[1], dcmList[indx].xyzMM[2], 
                   dcmList[indx].phaseEncodingRC, dcmList[indx].pixelBandwidth, nameList->str[indx], dcmList[indx].imageType);
    }
}
#endif