#! /bin/tcsh -ef

#
# inflate_subject_sc
#
#
#
# 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 0x04040

# -P allows the specification of a point in the brainstem at which
# to cut horizontally. This must be a slice in which the brainstem
# is not connected to cortex or cerebellum, etc...

# mri_fill -P 0.4 -25.9 -17.2  ../mri/wm ../mri/filled
cd  $SUBJECTS_DIR/$1/scripts
mri_fill -segmentation ../mri/aseg ../mri/wm ../mri/filled
inflate_subject-lh $1
inflate_subject-rh $1