#! /bin/tcsh -f

#
# renormalize_subject
#
# CVS Revision Info:
#    $Author: nicks $
#    $Date: 2007/01/06 00:01:15 $
#    $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
#

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
