#! /bin/tcsh -ef

#
# ms_refine_subject
#
# CVS Revision Info:
#    $Author: nicks $
#    $Date: 2007/01/06 00:01:14 $
#    $Revision: 1.2 $
#
# Copyright (C) 2002-2007,
# The General Hospital Corporation (Boston, MA).
# All rights reserved.
#
# Distribution, usage and copying of this software is covered under the
# terms found in the License Agreement file named 'COPYING' found in the
# FreeSurfer source code root directory, and duplicated here:
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense
#
# General inquiries: freesurfer@nmr.mgh.harvard.edu
# Bug reports: analysis-bugs@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



