#!/bin/bash

set -e
set -u

subj=$1

b7dir="${subj}/bold7Tp1"
b3dir="${subj}/bold3Tp2"

mkdir -p "${b3dir}/in_bold7Tp1"
mkdir -p "${b7dir}/in_bold3Tp2"


$FSLDIR/bin/flirt -dof 6 \
	-forcescaling -paddingsize 10 -minsampling 1 -bins 256 \
	-in ${b7dir}/brain \
	-ref ${b3dir}/brain \
	-omat "${b7dir}/in_bold3Tp2/xfm_6dof.mat" \
	-out "${b7dir}/in_bold3Tp2/brain"

$FSLDIR/bin/convert_xfm \
	-omat "${b3dir}/in_bold7Tp1/xfm_6dof.mat" \
	-inverse "${b7dir}/in_bold3Tp2/xfm_6dof.mat"

$FSLDIR/bin/flirt \
	-in "${b3dir}/brain" \
	-ref "${b7dir}/brain" \
	-applyxfm \
	-init "${b3dir}/in_bold7Tp1/xfm_6dof.mat" \
	-out "${b3dir}/in_bold7Tp1/brain"