#!/bin/bash

if [ -z "$1" ]; then
cat <<EOU
Capture some screenshots of surfaces produced by
FreeSurfer in standard orientations.

Usage: takeshots [options]

The options are:
-s <subjid> : Specify one subject ID.
-l <listid> : Specify a file list with the subject IDs, one per line.
-m <mesh>   : Specify a surface file (pial, white, inflated, sphere, etc.).
-p <parc>   : Specify a parcellation to load (aparc, aparc.a2009s, aparc.a2005s).
-c          : Run also for curv.
-u          : Run also for sulc.
-t          : Run also for thickness.
-y          : Run also for myelin maps (requires ?h.myelin.mgz exist)
-g          : Run also for gwc (requires ?h.gwc to exist)
-v          : Run also for volumes (aseg + overlaid surfaces).

_____________________________________
Anderson M. Winkler
Yale University / Institute of Living
Jan/2010
http://brainder.org
EOU
exit 1
fi

DOASEG="N"
DOSURF="N"
DOCURV="N"
DOSULC="N"
DOTHCK="N"
DOMYEL="N"
DOGWCO="N"

# Check and accept the arguments
while getopts 's:l:m:p:cutygv' OPTION
do
  case ${OPTION} in
    s) SUBJ_LIST="${SUBJ_LIST} ${OPTARG}" ;;
    l) SUBJ_LIST="${SUBJ_LIST} $(cat ${OPTARG})" ;;
    m) DOSURF="Y" ; MESH_LIST="${MESH_LIST} ${OPTARG}" ;;
    p) DOSURF="Y" ; PARC_LIST="${PARC_LIST} ${OPTARG}" ;;
    c) DOSURF="Y" ; DOCURV="Y" ;;
    u) DOSURF="Y" ; DOSULC="Y" ;;
    t) DOSURF="Y" ; DOTHCK="Y" ;;
    y) DOSURF="Y" ; DOMYEL="Y" ;;
    g) DOSURF="Y" ; DOGWCO="Y" ;;
    v) DOASEG="Y" ;; 
  esac
done

if [[ ${DOSURF} == "Y" ]] ; then
for s in ${SUBJ_LIST} ; do
mkdir -p ${SUBJECTS_DIR}/${s}/shots
  export SUBJECT_NAME=${s}
  for h in lh rh ; do
    for m in ${MESH_LIST} ; do
      export SURF=${m}
      for p in ${PARC_LIST} ; do
        export WHAT=${p}
        tksurfer ${s} ${h} ${m} -tcl  $(dirname $0)/shots_tksurfer.tcl
      done
      if [[ ${DOCURV} == "Y" ]] ; then
        export WHAT=curv
        tksurfer ${s} ${h} ${m} -curv -tcl  $(dirname $0)/shots_tksurfer.tcl
      fi
      if [[ ${DOSULC} == "Y" ]] ; then
        export WHAT=sulc
        tksurfer ${s} ${h} ${m} -sulc -tcl  $(dirname $0)/shots_tksurfer.tcl
      fi
      if [[ ${DOTHCK} == "Y" ]] ; then
        export WHAT=thickness
        tksurfer ${s} ${h} ${m} -overlay ${SUBJECTS_DIR}/${s}/surf/${h}.thickness -fminmax 0 4.5 -tcl  $(dirname $0)/shots_tksurfer.tcl
      fi
      if [[ ${DOMYEL} == "Y" ]] ; then
        export WHAT=myelin
        tksurfer ${s} ${h} ${m} -overlay ${SUBJECTS_DIR}/${s}/surf/${h}.myelin.mgz -fminmax 0.5 1.5 -tcl  $(dirname $0)/shots_tksurfer.tcl
      fi
      if [[ ${DOGWCO} == "Y" ]] ; then
        export WHAT=gwc
        # you can replace ?h.gwc for ?h.w-g.pct.mgz if these were created by FS. The two have a .88 correlation
        tksurfer ${s} ${h} ${m} -overlay ${SUBJECTS_DIR}/${s}/surf/${h}.gwc -fminmax 0 100 -tcl  $(dirname $0)/shots_tksurfer.tcl
      fi
    done
  done
done
fi

if [[ ${DOASEG} == "Y" ]] ; then
for s in ${SUBJ_LIST} ; do
  export SUBJECT_NAME=${s}
  tkmedit ${s} brainmask.mgz -tcl $(dirname $0)/shots_tkmedit.tcl
done
fi