aseg2srf

#!/bin/bash

# Print usage if no argument is given
if [ -z "$1" ]; then
cat <<EOU
Generate surfaces for the subcortical structures
segmented with FreeSurfer.

Usage:
sub2srf -s <list of subjects> [-l <list of labels>] [-d]

Options:
-s <list>         Specify a list of subjects between quotes,
                    e.g. -s "john bill mary mark" or a text file
                    containing one subject per line.
-l <list>         Specify a list of labels between quotes,
                    e.g. "10 11 14 52 253", or a text file
                    containing one label per line, or ignore
                    this option to convert all labels.
-o <output_dir>   Output directory
-d                Debug mode. Leave all temporary files.

Requirements:
FreeSurfer must have been configured and the variables
FREESURFER_HOME and SUBJECTS_DIR must have been correctly set.

_____________________________________
Anderson M. Winkler
Institute of Living / Yale University
Jul/2009
http://brainder.org
EOU
exit
fi

# List of labels to be converted if no list is specified
LABLIST="4 5 7 8 10 11 12 13 14 15 16 17 18 26 28 43 44 46 47 49 50 51 52 53 54 58 60 251 252 253 254 255"

# Check and accept arguments
SBJLIST=""
ASEG="aseg.mgz"
OUTDIR="aseg2srf"
DEBUG=N
while getopts 'a:s:l:o:d' OPTION
do
  case ${OPTION} in
    a) ASEG=${OPTARG} ;;
    s) SBJLIST=$( [[ -f ${OPTARG} ]] && cat ${OPTARG} || echo "${OPTARG}" ) ;;
    l) LABLIST=$( [[ -f ${OPTARG} ]] && cat ${OPTARG} || echo "${OPTARG}" ) ;;
    o) OUTDIR=${OPTARG} ;;
    d) DEBUG=Y ;;
  esac
done


# Prepare a random string to save temporary files
#if hash md5 2> /dev/null ; then
#  RND0=$(head -n 1 /dev/random | md5)
#elif hash md5sum 2> /dev/null ; then
#  RND0=$(head -n 1 /dev/random | md5sum)
#fi
#RNDSTR=${RND0:0:12}
RNDSTR=${RANDOM:0:12}

# Define a function for Ctrl+C as soon as the RNDSTR is defined
trap bashtrap INT
bashtrap()
{
  break ; break
  [[ "${s}" != "" ]] && rm -rf ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR} # try to delete temp files
  exit 1
}

# For each subject
for s in ${SBJLIST} ; do

  # Create directories for temp files and results
  mkdir -p ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}
  mkdir -p ${SUBJECTS_DIR}/${s}/${OUTDIR}

  # For each label
  for lab in ${LABLIST} ; do

    # Label string
    lab0=$(printf %05d ${lab})

    # Extract label, because it seems that mri_pretess cannot handle labels > 255.
    python $UTILDIR/extract_label.py ${SUBJECTS_DIR}/${s}/mri/${ASEG} ${lab} \
            ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.mgz

    # Pre-tessellate
    echo "==> Pre-tessellating: ${s}, ${lab0}"
    ${FREESURFER_HOME}/bin/mri_pretess \
           ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.mgz 1 \
           ${SUBJECTS_DIR}/${s}/mri/norm.mgz  \
           ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz

    # Tessellate
    echo "==> Tessellating: ${s}, ${lab0}"
    ${FREESURFER_HOME}/bin/mri_tessellate -n \
           ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz 1 \
           ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth

    # Smooth
    echo "==> Smoothing: ${s}, ${lab0}"
    ${FREESURFER_HOME}/bin/mris_smooth -nw \
           ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth \
           ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}

    # Convert to ASCII
    echo "==> Converting to ASCII: ${s}, ${lab0}"
    ${FREESURFER_HOME}/bin/mris_convert \
           ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0} \
           ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc
    mv ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc \
       ${SUBJECTS_DIR}/${s}/${OUTDIR}/aseg_${lab0}.srf
  done

  # Get rid of temp files
  if [ "${DEBUG}" == "Y" ] ; then
    echo "==> Temporary files for ${s} saved at:"
    echo "${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}"
  else
    echo "==> Removing temporary files for ${s}"
    rm -rf ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}
  fi
  echo "==> Done: ${s}"
done
exit 0