#! /bin/tcsh -f

#
# renormalize_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
#
#

pushd $SUBJECTS_DIR/$1/scripts
mri_normalize -f ../tmp/control.dat ../mri/orig ../mri/T1
#mri_strip_skull $1 1
mri_watershed $SUBJECTS_DIR/$1/mri/T1 $SUBJECTS_DIR/$1/mri/brain
mri_segment ../mri/brain ../mri/wm
inflate_subject $1