#!/bin/sh

#   tbss_non_FA - project non-FA data onto the skeleton
#
#   Stephen Smith, FMRIB Image Analysis Group
#
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#   Imaging of the Brain), Department of Clinical Neurology, Oxford
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if [ _$1 = _ ] ; then
    echo "Usage: tbss_non_FA <alternative-image-rootname>"
    echo "e.g.: tbss_non_FA L2"
    exit 1
else
    ALTIM=$1
fi

echo [`date`] [`hostname`] [`uname -a`] [`pwd`] [$0 $@] >> .tbsslog

best=`cat FA/best.msf`
echo "using pre-chosen registration target: $best"

echo "upsampling alternative images into standard space"
# re-create temporary analyze version of MNI152 for use by IRTK
cd FA
postaffine=""
if [ -f target_to_MNI152.mat ] ; then
    postaffine="--postmat=target_to_MNI152.mat"
fi
for f in `$FSLDIR/bin/imglob *_FA.*` ; do
    f=` echo $f | sed 's/_FA$//g'`
    echo $f
    $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w ${f}_FA_to_${best}_warp $postaffine
done

echo "merging all upsampled $ALTIM images into single 4D image"
${FSLDIR}/bin/fslmerge -t ../stats/all_$ALTIM `$FSLDIR/bin/imglob *_to_target_${ALTIM}.*`
cd ../stats
$FSLDIR/bin/fslmaths all_$ALTIM -mas mean_FA_mask all_$ALTIM

echo "projecting all_$ALTIM onto mean FA skeleton"
thresh=`cat thresh.txt`
${FSLDIR}/bin/tbss_skeleton -i mean_FA -p $thresh mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA all_${ALTIM}_skeletonised -a all_$ALTIM

echo "now run stats - for example:"
echo "randomise -i all_${ALTIM}_skeletonised -o tbss_$ALTIM -m mean_FA_skeleton_mask -d design.mat -t design.con -n 500 --T2 -V"
echo "(after generating design.mat and design.con)"