#! /bin/tcsh -ef

#
# ms_refine_subject
#
#
# Copyright © 2021 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#

setenv subject  $1
setenv hemi $2
setenv FDIR $SUBJECTS_DIR/$subject/mri/flash/parameter_maps
echo SUBJECTS_DIR=$SUBJECTS_DIR

set dest_dir = $SUBJECTS_DIR/$subject/mri/flash/parameter_maps
pushd $dest_dir
#setenv VOL_LIST "`ls -1 vol*_orig.mgh`"
setenv VOL_LIST "`ls -1 vol*.mgh`"
popd
set echo=1
mris_ms_refine -sdir $SUBJECTS_DIR $subject $hemi vol1.lta $VOL_LIST