#! /bin/tcsh -ef

#
# label_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
#
#


set s=$1

set M3D=talairach.m3z
set LTA=talairach.lta

set label=mri_ca_label
set emreg=mri_em_register
set careg=mri_ca_register
set canorm=mri_ca_normalize
set mdir = $SUBJECTS_DIR/$s/mri

if (-e $mdir/brain.mgz == 0) then
		set BRAIN=brain
else
		set BRAIN=brain.mgz
endif

if (-e $mdir/nu.mgz == 0) then
		set NU=nu
else
		set NU=nu.mgz
endif

set echo=1

# run nu_correct if needed
if (-e $NU == 0) then
		set NU=nu.mgz
		if (-e $mdir/orig.mgz != 0) then
				set ORIG = orig.mgz
		else
				set ORIG = orig
		endif
		mri_convert $mdir/$ORIG /tmp/nu$$0.mnc
		nu_correct -stop .0001 -iterations 3 -normalize_field -clobber /tmp/nu$$0.mnc /tmp/nu$$1.mnc
		mri_convert /tmp/nu$$1.mnc $mdir/$NU
		rm /tmp/nu$$0.mnc /tmp/nu$$1.mnc
		find  /tmp  -prune -name "*.imp" -user $LOGNAME -exec rm -f {} \;
endif
$emreg  -mask $mdir/$BRAIN $mdir/$NU $GCA $mdir/transforms/$LTA
$canorm -mask $mdir/$BRAIN $mdir/$NU $GCA $mdir/transforms/$LTA $mdir/norm.mgz
$careg -cross-sequence  -mask $mdir/$BRAIN -T $mdir/transforms/$LTA $mdir/norm.mgz $GCA $mdir/transforms/$M3D
$label -cross-sequence $mdir/norm.mgz $mdir/transforms/$M3D $GCA $mdir/aseg.mgz