NEOS_watershed_shrink.sh

#!/bin/sh
#
#	Create BEM surfaces using the watershed algoritm included with
#       FreeSurfer
#
#       Copyright 2006
#
#       Matti Hamalainen
#       Athinoula A. Martinos Center for Biomedical Imaging
#       Massachusetts General Hospital
#       Charlestown, MA, USA
#
#       $Header: /space/orsay/8/users/msh/CVS/CVS-MSH/MNE/mne_scripts/mne_watershed_bem,v 1.7 2008/10/23 21:41:45 msh Exp $
#       $log$
#		
# OH, April '20
# FM, copied from FPVS repo https://github.com/olafhauk/FPVS_sweep/

# Olaf:
shrink_by=2 # shrink by mm, used at bottom

cleanup()
{
	echo "Temporary files removed."
}
usage()
{
	echo "usage: $0 [options]"
	echo 
	echo "     --overwrite             (to write over existing files)"
	echo "     --subject subject       (defaults to SUBJECT environment variable)"
	echo "     --volume  name          (defaults to T1)"
	echo "     --atlas                 specify the --atlas option for mri_watershed"
	echo
	echo "Minimal invocation:"
	echo
	echo "$0                      (SUBJECT environment variable set)"
	echo "$0 --subject subject    (define subject on the command line)"
	echo 
}
#
if [ ! "$FREESURFER_HOME" ] ; then 
    echo "The FreeSurfer environment needs to be set up for this script"
    exit 1
fi
#
if [ ! "$SUBJECTS_DIR" ]
then
	echo "The environment variable SUBJECTS_DIR should be set"
	exit 1
fi
if [ ! "$MNE_ROOT" ]
then
    echo "MNE_ROOT environment variable is not set"
    exit 1
fi
force=false
atlas=
volume=T1
#
#	Parse the options
#
while [ $# -gt 0 ]
do
	case "$1" in  
	--subject) 
		shift
		if [ $# -eq 0 ]
		then
			echo "--subject: argument required."
			exit 1
		else
			export SUBJECT=$1
		fi
		;;
	--volume) 
		shift
		if [ $# -eq 0 ]
		then
			echo "--volume: argument required."
			exit 1
		else
			export volume=$1
		fi
		;;
	--overwrite)
		force=true
		;;
	--atlas)
		atlas=-atlas
		;;
	--help)
		usage
		exit 1
		;;
	esac

	shift
done
#
#	Check everything is alright
#
if [ ! "$SUBJECT" ]
then
	usage
	exit 1
fi
#
subject_dir=$SUBJECTS_DIR/$SUBJECT
mri_dir=$subject_dir/mri
T1_dir=$mri_dir/$volume
T1_mgz=$mri_dir/$volume.mgz
bem_dir=$subject_dir/bem
ws_dir=$subject_dir/bem/watershed3
#
if [ ! -d $subject_dir ]
then 
	echo "Could not find the MRI data directory $subject_dir"
	exit 1
fi
if [ ! -d $bem_dir ]
then 
    mkdir -p $bem_dir
    if [ $? -ne 0 ]
    then
	echo "Could not create the model directory $bem_dir"
	exit 1
    fi
fi
if [ ! -d $T1_dir -a ! -f $T1_mgz ]
then 
    echo "Could not find the MRI data"
    exit 1
fi
if [ -d $ws_dir ]
then
	if [ $force = "false" ]
	then
		echo "$ws_dir already exists. Use the --overwrite option to recreate it"
		exit 1
	else
		rm -rf $ws_dir
		if [ $? -ne 0 ]
		then 
			echo "Could not remove $ws_dir"
			exit 1
		fi
	fi
fi
#
#	Report
#
echo 
echo "Running mri_watershed for BEM segmentation with the following parameters"
echo
echo "SUBJECTS_DIR = $SUBJECTS_DIR"
echo "Subject      = $SUBJECT"
echo "Result dir   = $ws_dir"
echo
mkdir -p $ws_dir/ws
if [ $? -ne 0 ]
then 
    echo "Could not create the destination directories"
    exit 1
fi
cleanup
if [ -f $T1_mgz ]
then
    mri_watershed $atlas -useSRAS -shk_br_surf $shrink_by int_h -surf $ws_dir/$SUBJECT $T1_mgz $ws_dir/ws
else
    mri_watershed $atlas -useSRAS -shk_br_surf $shrink_by int_h -surf $ws_dir/$SUBJECT $T1_dir $ws_dir/ws
fi    
if [ $? -ne 0 ]
then
    exit 1
fi
#
cd $bem_dir
rm -f $SUBJECT-head.fif
mne_surf2bem --surf $ws_dir/"$SUBJECT"_outer_skin_surface --id 4 --fif $SUBJECT-head.fif
echo "Created $bem_dir/$SUBJECT-head.fif"
echo
echo "Complete."
echo
exit 0