tbss_4_prestats

#!/bin/sh

#   tbss_4_prestats - post-registration processing
#
#   Stephen Smith, FMRIB Image Analysis Group
#
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#   Imaging of the Brain), Department of Clinical Neurology, Oxford
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FSL_SUB=/usr/share/fsl/overlay/fsl_sub
MEMSIZE=128g
export LC_ALL=C

Usage() {
    cat <<EOF

Usage: tbss_4_prestats <threshold>

The normal recommendation for <threshold> is 0.2

EOF
    exit 1
}

[ "$1" = "" ] && Usage

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

thresh=$1

cd stats

echo "creating skeleton mask using threshold $thresh"
echo $thresh > thresh.txt
${FSLDIR}/bin/fslmaths mean_FA_skeleton -thr $thresh -bin mean_FA_skeleton_mask

echo "creating skeleton distancemap (for use in projection search)"
${FSLDIR}/bin/fslmaths mean_FA_mask -mul -1 -add 1 -add mean_FA_skeleton_mask mean_FA_skeleton_mask_dst
${FSLDIR}/bin/distancemap -i mean_FA_skeleton_mask_dst -o mean_FA_skeleton_mask_dst

echo "projecting all FA data onto skeleton"
echo "${FSLDIR}/bin/tbss_skeleton -i mean_FA -p $thresh mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA all_FA_skeletonised" > .command
$FSL_SUB -T 1440 -l logs -R ${MEMSIZE} -N prestats_skeleton -t .command -B

echo ""
echo "now run stats - for example:"
echo "randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 500 --T2 -V"
echo "(after generating design.mat and design.con)"