visual-areas/code/reg2std4feat

#!/bin/bash
#
# Usage: reg2std4feat <tntdir> <inspace> <stdspace> <feat_dir> [<feat_dir> ...]
#
# Example: reg2std4feat src/tnt/ bold3Tp2 grpbold3Tp2 sub-/run*_testme.feat
#
# This script makes the assumption that there is no highres space, but
# alignment was performed from BOLD directly to a group template (most
# likely computed from BOLD as well)
#

set -e
set -u

tntdir="$1"
shift
inspace="$1"
shift
stdspace="$1"
shift

for featdir in $@; do
	subj="$(echo $featdir| sed -e 's,.*\(sub-.*\)/.*,\1,g')"
	tntsubdir="${tntdir}/${subj}"
	# sane defaults
	tmpl2std_mat="$FSLDIR/etc/flirtsch/ident.mat"
	tmpl2std_warp=""
	# cleanup existing standard space registration
	[ -d "$featdir/reg_standard" ] && rm -rf "$featdir/reg_standard" || true
	# place reg info in existing featdir in a way that featregapply would
	# swallow it
	regdir="$featdir/reg"
	mkdir -p "$regdir"
	# remove any possibly existing standard space setup
	rm -rf "$regdir"/*standard*
	if [ "$inspace" != "$stdspace" ]; then
		xfmdir="$tntsubdir/$inspace/in_$stdspace"
		# check that we have the xfm info
		[ $(imtest "$xfmdir/head") -eq 1 ] && : || echo "cannot find transformation"
		if [ -e "$xfmdir/xfm_12dof.mat" ]; then
			tmpl2std_mat="$xfmdir/xfm_12dof.mat"
		fi
		if [ $(imtest "$xfmdir/subj2tmpl_warp") -eq 1 ]; then
			tmpl2std_warp="$xfmdir/subj2tmpl_warp"
		fi
		imcp "$xfmdir/head" "$regdir/standard"
	else
		# we stay in the 
		imcp "$tntsubdir/$inspace/brain" "$regdir/standard"
	fi
	if [ -e "$regdir/example_func2highres.mat" ]; then
		convert_xfm -omat "$regdir/example_func2standard.mat" \
			-concat "$tmpl2std_mat" \
			"$regdir/example_func2highres.mat"
	else
		cp "$tmpl2std_mat" "$regdir/example_func2highres.mat"
		cp "$tmpl2std_mat" "$regdir/example_func2standard.mat"
	fi
	if [ -n "$tmpl2std_warp" ]; then
		imcp "$tmpl2std_warp" "$regdir/highres2standard_warp"
	fi
done