vol2surf

#!/bin/bash


function usage
{
    echo "Batch convert volumes in MNI152 to freesurfer surfaces."
    echo "Output surface filenames are based on input volumes"
    echo ""
    echo "Use: "
    echo "   vol2surf <options> -v <volume(s)>"
    echo "   vol2surf <options> -V <volume list file>"
    echo ""
    echo "OPTIONS:"
    echo "   -m        Input volume(s) are in MNI305 space (default MNI152)"
    echo "   -p <val>  Proj-frac min (- is white matter, 0 is white/gray boundary)"
    echo "   -P <val>  Proj-frac max "
    echo "   -M        Use Maximum value along normal (not avg)." 
    echo "   -f <val>  Surface FWHM smoothing (default 4)"
    echo "   -n        Nearest neighbor interpolation (default trilinear)"
    echo "   -D        Output file directory is input file directory"
    echo "   -c        Mask to cortex"
    echo "   -h        Help menu"
    echo ""
    echo "Note: if specifying multiple items for an argument, use quotes."
    echo "      ex. vol2surf -v \"file1.nii.gz file2.nii.gz\" "
    
}

PROJFRAC=0.7
FWHM=4
NATIVEDIR=0
CORTEX=""
REG=" --reg $FREESURFER_HOME/average/mni152.register.dat "
PROJFRACMIN="0"
PROJFRACMAX="1"
INTERP="trilin"
NORMVAL="avg"

while getopts "v:V:p:f: h D c m n M " o ; do
    case $o in
         v ) VOLUMES=$OPTARG;;
	 V ) VOLFILE=$OPTARG;;
	 p ) PROJFRACMIN=$OPTARG;;
	 P ) PROJFRACMAX=$OPTARG;;
	 f ) FWHM=$OPTARG;;
	 D ) NATIVEDIR=1;;
	 n ) INTERP="nearest";;
	 c ) CORTEX="--cortex";;
	 m ) REG="--regheader fsaverage ";;
	 M ) NORMVAL="max";;
	 h ) usage;
	     exit 0;;
    esac
done

if [ $# -eq 0 ]; then
   usage; exit 0;
fi

if [ ${#VOLFILE} -ne 0 ]; then
    if [ -r $VOLFILE ]; then
	VOLUMES=$(cat $VOLFILE | xargs)
    else
	echo "Error: cannot read $VOLFILE"; exit 0;
    fi
fi

if [ ${#VOLUMES} -ne 0 ]; then
    for x in $VOLUMES; do
	if [ ! -r $x ]; then
    	    echo "Error: cannot read $x"; exit 0;
	fi 
    done
else
    echo "Error: no volumes found."; exit 0;
fi

for h in lh rh; do
    for x in $VOLUMES; do
    	if [ $NATIVEDIR -eq 1 ]; then
	    loc=$(dirname $x)
	else
	    loc=$(pwd)
	fi
	echo "mri_vol2surf --mov ${x} $REG --hemi ${h} --interp $INTERP --trgsubject fsaverage --out $loc/${h}.$(basename ${x%%.nii.gz}).mgh --projfrac-$NORMVAL $PROJFRACMIN $PROJFRACMAX .1 --surf-fwhm $FWHM $CORTEX"
        mri_vol2surf --mov ${x} $REG --hemi ${h} --interp $INTERP --trgsubject fsaverage --out $loc/${h}.$(basename ${x%%.nii.gz}).mgh --projfrac-$NORMVAL $PROJFRACMIN $PROJFRACMAX .1 --surf-fwhm $FWHM $CORTEX
    done
done