#! /bin/tcsh -f

#
# fix_subject_corrected-rh
#
#
#
# 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 DIAG 0x04048

pushd $SUBJECTS_DIR/$1/
touch NOTES
echo " " >> NOTES
echo $0 $* >> NOTES
whoami >> NOTES
date >> NOTES
hostname >> NOTES
popd



pushd $SUBJECTS_DIR/$1/scripts
mris_sphere -inflate -w 0 -q ../surf/rh.inflated ../surf/rh.qsphere
mris_fix_topology -suffix _corrected $1 rh
mris_smooth ../surf/rh.orig_corrected ../surf/rh.smoothwm_corrected
mris_inflate ../surf/rh.smoothwm_corrected ../surf/rh.inflated_corrected
mris_curvature -a 10 -w ../surf/rh.smoothwm
cp ../surf/rh.smoothwm.H ../surf/rh.curv
mris_curvature -a 10 -w ../surf/rh.smoothwm_corrected
cp ../surf/rh.smoothwm_corrected.H ../surf/rh.curv_corrected
mris_make_surfaces -w 0 -suffix _corrected  $1 rh
popd