#! /bin/tcsh -ef

#
# talairach_mgh
#
#
#
# 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 GCA ${FREESURFER_HOME}/average/young_new_b.gca
setenv GCA ${FREESURFER_HOME}/average/talairach_young_new_b.gca
setenv LTA talairach.xfm

setenv s $1

set sdir = $SUBJECTS_DIR/$s/mri
foreach d (fsamples norm transforms)
	mkdir -p $sdir/$d ;\
end

setenv bin ${FREESURFER_HOME}/bin/mri_em_register.old
#$bin -mask $sdir/brain -fsamples $sdir/fsamples -norm $sdir/norm $sdir/orig $GCA $sdir/transforms/$LTA
$bin -mask $sdir/brain $sdir/orig $GCA $sdir/transforms/$LTA