#! /bin/tcsh -ef

#
# register_subject_mixed
#
#
#
# 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/mixed.gca
setenv LTA talairach.lta
setenv GCA $CMA/average/mixed_a1_ma.gca

setenv s $1

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

mri_em_register -fsamples $sdir/fsamples -norm $sdir/norm $sdir/orig $GCA $sdir/transforms/$LTA