#!/bin/sh

#   filmbabescript
#
#   Mark Woolrich, FMRIB Image Analysis Group
#
#   Copyright (C) 2002-2004 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
#   http://www.fmrib.ox.ac.uk/fsl
#   fsl@fmrib.ox.ac.uk
#   
#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
#   Imaging of the Brain), Department of Clinical Neurology, Oxford
#   University, Oxford, UK
#   
#   
#   LICENCE
#   
#   FMRIB Software Library, Release 5.0 (c) 2012, The University of
#   Oxford (the "Software")
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export LC_NUMERIC=C

# $1 is feat directory
#
# e.g.featdir=/home/fs3/steve/data/fmri_test/heatpain+vis_1352/epi3.4_SDfixed_junkscut_FLOBS.feat

if [ $# -ne 2 ] ; then
	echo "Usage: filmbabescript featdir flobsdir"
	exit 1
fi	

if [ $1 = "--help" ] ; then
	echo "Usage: filmbabescript featdir flobsdir"
	exit
fi	

cd $1
featdir=`pwd`

flobsdir=$2

echo "$FSLDIR/bin/filmbabe --df=filtered_func_data --mask=mask --dm=design.mat --frf=design.frf --ld=filmbabe --ni=5 --ntar=3 --fd=$flobsdir"

$FSLDIR/bin/filmbabe --df=filtered_func_data --mask=mask --dm=design.mat --frf=design.frf --ld=filmbabe --ni=5 --ntar=3 --fd=$flobsdir

echo "$FSLDIR/bin/contrast_mgr -f design.fts filmbabe design.con"
$FSLDIR/bin/contrast_mgr -f design.fts filmbabe design.con

cd filmbabe

files=`$FSLDIR/bin/imglob zfstat*.*`
files=`$FSLDIR/bin/remove_ext $files`

echo "<HTML> <TITLE>Filmbabe results for $featdir </TITLE>" > report.html
echo "<BODY BACKGROUND=\"file:$FSLDIR/doc/images/fsl-bg.jpg\">" >> report.html
echo "<hr><CENTER><H1>Filmbabe results for <br> $featdir </H1><hr><p>" >> report.html
echo "<A HREF=$flobsdir/report.html> Optimal basis set report </A><p>" >> report.html

for filename in $files ; do
    fname=$filename
    echo "$FSLDIR/bin/mm --mask=mask --sdf=$fname --logdir=mm_$fname --ni=30 --zfstatmode"
    $FSLDIR/bin/mm --mask=mask --sdf=$fname --logdir=mm_$fname --ni=30 --zfstatmode;     
    echo "<A HREF=mm_$fname/MM.html> $fname mixture model fit results </A><p>"  >> report.html
done

echo "<img BORDER=0 SRC=\"gamAhist.png\">" >> report.html
echo "</CENTER><p>Analysis carried out by filmbabe, based on:<br>" >> report.html
echo "M.W. Woolrich, T.E.J. Behrens, and S.M. Smith. Constrained linear basis sets for HRF modelling using Variational Bayes. NeuroImage, 21:4(1748-1761) 2004." >> report.html

echo "<HR><FONT SIZE=1>This page produced automatically by filmbabescript - a part of <A HREF="http://www.fmrib.ox.ac.uk/fsl">FSL</A>.</FONT>" >>  report.html

echo "</BODY></HTML>" >> report.html

echo "View results at $featdir/filmbabe/report.html"