#!/bin/bash

set -e
set -u

subj=$1

t1dir="${subj}/t1w"
bolddir="${subj}/bold3Tp2"

mkdir -p "${bolddir}/in_t1w"
mkdir -p "${t1dir}/in_bold3Tp2"


#$FSLDIR/bin/flirt -dof 6 \
#	-in ${bolddir}/brain \
#	-ref ${t1dir}/brain_nobias \
#	-omat "${bolddir}/in_t1w/xfm_6dof.mat" \
#	-out "${bolddir}/in_t1w/brain"
#
#$FSLDIR/bin/convert_xfm \
#	-omat "${t1dir}/in_bold3Tp2/xfm_6dof.mat" \
#	-inverse "${bolddir}/in_t1w/xfm_6dof.mat"
#
#$FSLDIR/bin/flirt \
#	-in "${t1dir}/brain_nobias" \
#	-ref "${bolddir}/brain" \
#	-applyxfm \
#	-init "${t1dir}/in_bold3Tp2/xfm_6dof.mat" \
#	-out "${t1dir}/in_bold3Tp2/brain"

#
# occiptal focus
#

$FSLDIR/bin/fslmaths \
	/usr/share/data/mni-structural-atlas/MNI/MNI-maxprob-thr0-2mm.nii.gz \
	-thr 5 -uthr 5 -bin -dilF -dilF \
	${t1dir}/in_mni152/dil_occ_mask.nii.gz

$FSLDIR/bin/flirt \
	-in ${t1dir}/in_mni152/dil_occ_mask.nii.gz \
	-ref "${t1dir}/brain" \
	-applyxfm \
	-init "${t1dir}/in_mni152/tmpl2subj.mat" \
	-out "${t1dir}/dil_occ_mask"

$FSLDIR/bin/flirt \
	-in "${t1dir}/dil_occ_mask" \
	-ref "${bolddir}/brain" \
	-applyxfm \
	-init "${t1dir}/in_bold3Tp2/xfm_6dof.mat" \
	-out "${bolddir}/dil_occ_mask"

$FSLDIR/bin/flirt -dof 6 \
	-in ${bolddir}/brain \
	-ref ${t1dir}/brain_nobias \
	-refweight ${t1dir}/dil_occ_mask \
	-inweight ${bolddir}/dil_occ_mask \
	-init "${bolddir}/in_t1w/xfm_6dof.mat" \
	-searchrx -20 20 \
	-searchry -20 20 \
	-searchrz -20 20 \
	-omat "${bolddir}/in_t1w/xfm_6dof_occ.mat" \
	-out "${bolddir}/in_t1w/brain_occ"

$FSLDIR/bin/convert_xfm \
	-omat "${t1dir}/in_bold3Tp2/xfm_6dof_occ.mat" \
	-inverse "${bolddir}/in_t1w/xfm_6dof_occ.mat"

$FSLDIR/bin/flirt \
	-in "${t1dir}/brain_nobias" \
	-ref "${bolddir}/brain" \
	-applyxfm \
	-init "${t1dir}/in_bold3Tp2/xfm_6dof_occ.mat" \
	-out "${t1dir}/in_bold3Tp2/brain_occ"