#! /bin/tcsh -ef

#
# segment_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
#
#



if (-e $SUBJECTS_DIR/$1/scripts == 0)  mkdir $SUBJECTS_DIR/$1/scripts ; endif

if (-e $SUBJECTS_DIR/$1/scripts/brain.dat == 0)  \
	if (-e $SUBJECTS_DIR/scripts/brain.dat) \
			cp $SUBJECTS_DIR/scripts/brain.dat $SUBJECTS_DIR/$1/scripts ; \
	endif
endif

pushd $SUBJECTS_DIR/$1/scripts

foreach d (../tmp ../mri/T1 ../mri/wm ../mri/filled ../mri/brain ../surf ../mri/transforms ../mri/aseg ../mri/fsamples)
    if (-e $d == 0)  mkdir $d ; endif
end




# this is just needed for diagnostic purposes
setenv DIAG 0x04048

talairach $1

# intensity normalize the data
mri_normalize ../mri/orig ../mri/T1
cp ../mri/T1/COR-.info ../mri/brain
cp ../mri/T1/COR-.info ../mri/wm

# strip the skull
#mri_strip_skull $1 1
mri_watershed $SUBJECTS_DIR/$1/mri/T1 $SUBJECTS_DIR/$1/mri/brain

# label white matter
mri_segment $SUBJECTS_DIR/$1/mri/brain $SUBJECTS_DIR/$1/mri/wm
register_subject $1
label_subject $1
inflate_subject_sc $1