tbss_1_preproc

#!/bin/sh

#   tbss_1_preproc - preprocess FA data for TBSS
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 2005-2008 University of Oxford
#
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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
export LC_ALL=C

Usage() {
    echo ""
    echo "Usage: tbss_1_preproc <image1> <image2> ..."
    echo ""
    exit 1
}

[ x"$1" = "x" ] || [ "$1" = "-h" ] && Usage

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

mkdir -p FA
mkdir -p origdata

rm -f .commands
for f in `$FSLDIR/bin/imglob $@` ; do

    cmd="echo processing $f"
    cmd=$cmd";f=$f"

    # erode a little and zero end slices
    cmd="$cmd;"'X=`${FSLDIR}/bin/fslval $f dim1`;X=`echo "$X 2 - p" | dc -`'
    cmd="$cmd;"'Y=`${FSLDIR}/bin/fslval $f dim2`;Y=`echo "$Y 2 - p" | dc -`'
    cmd="$cmd;"'Z=`${FSLDIR}/bin/fslval $f dim3`;Z=`echo "$Z 2 - p" | dc -`'
    cmd="$cmd;"'$FSLDIR/bin/fslmaths $f -min 1 -ero -roi 1 $X 1 $Y 1 $Z 0 1 FA/${f}_FA'

    # create mask (for use in FLIRT & FNIRT)
    cmd="$cmd;"'$FSLDIR/bin/fslmaths FA/${f}_FA -bin FA/${f}_FA_mask'
    cmd="$cmd;"'$FSLDIR/bin/fslmaths FA/${f}_FA_mask -dilD -dilD -sub 1 -abs -add FA/${f}_FA_mask FA/${f}_FA_mask -odt char'
    cmd="$cmd;"'$FSLDIR/bin/immv $f origdata'

    echo $cmd >> .commands
done

# submit everything in .commands with chunksize $chunksize and wait for completion
chunksize=4  # tweak me
$FSL_SUB -l tbss_logs -T 1 -N tbss_1_preproc -t .commands -c $chunksize -B
rm -f .commands

echo "Now running \"slicesdir\" to generate report of all input images"
cd FA
$FSLDIR/bin/slicesdir `$FSLDIR/bin/imglob *_FA.*` > grot 2>&1
cat grot | tail -n 2
/bin/rm grot