#!/bin/bash

set -e
set -u

subj=$1

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

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

## old coreg
#$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"

# coregister t1w to bold ..
$FSLDIR/bin/flirt -dof 6 \
    -in "${t1dir}/brain_nobias" \
    -ref "${bolddir}/brain" \
    -omat "${t1dir}/in_bold3Tp2/xfm_6dof.mat" \
    -out "${t1dir}/in_bold3Tp2/brain"

# .. and inverse transformation matrix ..
$FSLDIR/bin/convert_xfm \
    -omat "${bolddir}/in_t1w/xfm_6dof.mat" \
    -inverse "${t1dir}/in_bold3Tp2/xfm_6dof.mat"

# .. and applyXfm to coregister bold to t1w. 
$FSLDIR/bin/flirt \
    -in "${bolddir}/brain" \
    -ref "${t1dir}/brain_nobias" \
    -applyxfm \
    -init "${bolddir}/in_t1w/xfm_6dof.mat" \
    -out "${bolddir}/in_t1w/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"