#!/bin/bash

# ren-dcmcnv.sh

# Version 1.2.1
# 09-Oct-2017 K.Nemoto

# Usage: ren-dcncnv.sh [-d]
# -d: option not to delete temporary files generated by dcm2nii

# DICOM to NIFTI converter with rename functions
# This script converts DICOM files into NIFTI mormat using dcm2nii.
# Not only converting DICOM images, it renmaes nifti files
# based on header information.
#
# All you need to prepare is make directories with subjects ID
#  e.g. If you prepare a directory "subj01", the following files
#       will be the following;
# Volume files: V_subj01.nii
# fMRI files: F_subj01.nii
# DTI files: D_subj01.nii
#
# Prerequisites: You need to install dcm2nii (included in MRIcron) 
# and FSL beforehand and set paths to these.

# Acknowledgement: This work was funded by ImPACT Program of Council 
# for Science, Technology and Innovation (Cabinet Office, Government 
# of Japan).

# Debug option
getopts "d" debug
if [ $debug == "d" ]; then
    echo "debug option is enabled."
    echo " "
else
    echo "debug option is disabled. (Default)"
    echo " "
fi

#Generate a log
cnvdate=$(date +%Y%m%d-%H%M%S)
touch ${cnvdate}_dcmcnv.log
log=${cnvdate}_dcmcnv.log
exec &> >(tee -a "$log")

#Check dcm2nii path
echo "Check if the path for dcm2nii is set."
dcm2nii_path=$(which dcm2nii)
if [ "$dcm2nii_path" = "" ]; then
    echo "Error: Please set path for dcm2nii!"
    exit 1
else
    echo "Path for dcm2nii is $dcm2nii_path"
    echo " "
fi

#Check FSL path
echo "Check if the path for FSL is set."
fsl_path=$(which fsl)
if [ "$fsl_path" = "" ]; then
    echo "Error: Please set path for FSL!"
    exit 1
else
    echo "Path for FSL is $fsl_path"
    echo " "
fi

#Set parent directory
modir=$(pwd)

#Prepare 'DICOM' directory
if [ ! -e $modir/DICOM ]; then
    mkdir -p $modir/DICOM
fi

#Prepare 'nifti' directory
if [ ! -e $modir/nifti ]; then
    mkdir -p $modir/nifti
fi

#Move all directories except for DICOM and nifti to DICOM directory
find . -maxdepth 1 \( -name DICOM -o -name nifti \) -prune -o \
    -type d -print | grep / | sed -e 's@./@@' -e 's/ /\n/' | \
while read line; do mv $line DICOM; done

#cd to DICOM directory
cd $modir/DICOM

for dir in $(ls -F | grep / | sed 's@/@@')
do
    echo "Begin conversion of $dir"
    echo "$(date +%F_%T)"
  
    #dcm2nii
    echo "dcm2nii for $dir"
    dcm2nii -g n -r n -x n $dir
    echo " "
  
    #cd to $dir
    cd $dir

    #(for some scanners only)
    #Delete WIPDKI
    wipdki=$(find . -maxdepth 1 -name '*WIPDKI*')
    if [ ! -z "$wipdki" ]; then
        echo "remove WIPDKI sequence"
        echo " "
        rm *WIPDKI*
    fi

    #Acquire dimension of images
    for f in *.nii
    do
    	dim1=$(fslinfo $f | grep ^dim1 | awk '{ print $2 }')
    	dim2=$(fslinfo $f | grep ^dim2 | awk '{ print $2 }')
    	dim3=$(fslinfo $f | grep ^dim3 | awk '{ print $2 }')
    	dim4=$(fslinfo $f | grep ^dim4 | awk '{ print $2 }')
    	te=$(fslhd $f | grep ^descrip |\
    	  awk '{ print $2 }' | awk -F';' '{ print $1 }'|\
    	  sed 's/TE=//' | sed 's/\.[0-9]*$//')
    	pe=$(fslhd $f | grep ^descrip |\
    	  awk '{ print $2 }' | awk -F';' '{ print $3 }'|\
    	  sed 's/phaseDir=//')
	echo "========== Rename the file based on header info =========="
    	echo "Dimensions of $f is $dim1, $dim2, $dim3, and $dim4"
    	echo "TE=${te}; phaseDir=$pe"
    
        #Decide if a nifti file is 3DT1, fMRI, or DTI.
        #Rules are as follows;
        #3DT1: dim2>=240, dim3>100, and TE<6
        #fMRI: dim4>=130 and 20<TE<40
        #DTI: dim4>=8 and 50<TE<140
        
        #3D-T1
    	if [ $dim2 -ge 240 ] && [ $dim3 -gt 100 ] && [ $te -lt 6 ]; then
           echo "$f seems 3D-T1 file."
	   resv=$(find . -maxdepth 1 -name 'V*.nii')
           if [ -z "$resv" ]; then
		echo "$f will be renamed as V_${dir}.nii"
		echo " " 
                cp $f V_${dir}.nii
           else
		echo "$f will be renamed as V_${dir}A.nii"
		echo " "
    		cp $f V_${dir}A.nii
                echo "Warning: Two volume files exist!"
		echo " "
    	   fi
    
        #fMRI
    	elif [ $dim4 -ge 130 ] && [ $te -gt 20 ] && [ $te -lt 40 ]; then
           echo "$f seems fMRI file."
	   resf=$(find . -maxdepth 1 -name 'F*.nii')
           if [ -z "$resf" ]; then
		echo "$f will be renamed as F_${dir}.nii"
		echo " "
                cp $f F_${dir}.nii
           else
		echo "$f will be renamed as F_${dir}A.nii"
		echo " "
                cp $f F_${dir}A.nii
                echo "Warning: Two fMRI files exist!"
           fi
    		
        #DTI
    	elif [ $dim4 -gt 7 ] && [ $te -gt 50 ] && [ $te -lt 140 ]; then
           echo "$f seems DTI file."
           if [[ $pe = "+" ]]; then
                echo "Phase encoding of the DTI file is AP."
	        resd=$(find . -maxdepth 1 -name 'D*.nii')
                if [ -z "$resd" ]; then
		    echo "$f will be renamed as D_AP_${dir}.nii"
		    echo " "
                    cp $f D_AP_${dir}.nii 
                    dti_ap=$(imglob $f)
                    cp ${dti_ap}.bval D_AP_${dir}.bval
                    cp ${dti_ap}.bvec D_AP_${dir}.bvec
                else
                    echo "$f will be renamed as D_AP_${dir}A.nii"
		    echo " "
                    cp $f D_AP_${dir}A.nii 
                    dti_ap=$(imglob $f)
                    cp ${dti_ap}.bval D_AP_${dir}A.bval
                    cp ${dti_ap}.bvec D_AP_${dir}A.bvec
                    echo "Warning: Two DTI files exist!"
		    echo " "
		fi
           else
                echo "Phase encoding of the DTI file is PA."
	        resd=$(find . -maxdepth 1 -name 'D*.nii')
                if [ -z "$resd" ]; then
		    echo "$f will be renamed as D_PA_${dir}.nii"
		    echo " "
                    cp $f D_PA_${dir}.nii 
                    dti_pa=$(imglob $f)
                    cp ${dti_pa}.bval D_PA_${dir}.bval
                    cp ${dti_pa}.bvec D_PA_${dir}.bvec
                else
                    echo "$f will be renamed as D_PA_${dir}A.nii"
		    echo " "
                    cp $f D_PA_${dir}A.nii 
                    dti_pa=$(imglob $f)
                    cp ${dti_pa}.bval D_PA_${dir}A.bval
                    cp ${dti_pa}.bvec D_PA_${dir}A.bvec
                    echo "Warning: Two DTI files exist!"
		    echo " "
		fi
           fi
    
          #Field Map
          #elif [ $dim4 -eq 3 -a $te -ge 7 ]; then
          #     echo "$f seems fieldmap (long TE)"
          #     echo " "
          #     cp $f LFM_${dir}.nii
          #
          #elif [ $dim4 -eq 3 -a $te -lt 5 ]; then
          #	echo "$f seems fieldmap (short TE)"
          #     echo " "
          #	cp $f SFM_${dir}.nii
    
    	else
            echo "$f seems neither 3DT1, fMRI, nor DTI."
            echo " "
    	fi

    done
  
    #move Volume files to nifti directory
    if [ -e V_${dir}.nii ]; then 
        echo "move V_*.nii to $modir/nifti"
	echo " "
        mv V_*.nii $modir/nifti
    else
        echo "No volume files!"
	echo " "
    fi
    
    #move fMRI files to nifti directory
    if [ -e F_${dir}.nii ]; then 
        echo "move F_*.nii to $modir/nifti"
	echo " "
    	mv F_*.nii $modir/nifti
    else
        echo "No fMRI files!"
        echo " "
    fi
    
    #move DTI files to nifti directory
    if [ -e D_PA_${dir}.nii ] ; then 
        echo "move D_*.{nii,bval,bvec} to $modir/nifti"
	echo " "
    	mv D_*.{nii,bval,bvec} $modir/nifti
    elif [ -e D_AP_${dir}.nii ]; then
        echo "move D_AP*.{nii,bval,bvec} to $modir/nifti"
	echo " "
    	mv D_*.{nii,bval,bvec} $modir/nifti
    else
        echo "No DTI files!"
	echo " "
    fi
    
    cd $modir/DICOM
done

#If debug option is not enabled, delete remained nifti and bv{al,ec} files
if [ $debug != "d" ]; then
    echo "Delete temprary files"
    echo " "
    find $modir/DICOM -name '*.nii' -exec rm {} \;
    find $modir/DICOM -name '*.bval' -exec rm {} \;
    find $modir/DICOM -name '*.bvec' -exec rm {} \;
else
    echo "Temporary files will not be deleted"
    echo " "
fi

#Finish
echo "Finished!"

exit