tbss_preproc_edited

#!/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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########
#This script fixes the problem of black holes in FA files. 
#Run this file instead of the original tbss_preproc
#Compared to the original script, this script saves 2 extra files per image to keep track of the different steps in the preprocessing.
########

export LC_ALL=C

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

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

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

mkdir -p FA
mkdir -p origdata

for f in `$FSLDIR/bin/imglob $@` ; do

    echo processing $f

    # erode a little and zero end slices
    X=`${FSLDIR}/bin/fslval $f dim1`; X=`echo "$X 2 - p" | dc -`
    Y=`${FSLDIR}/bin/fslval $f dim2`; Y=`echo "$Y 2 - p" | dc -`
    Z=`${FSLDIR}/bin/fslval $f dim3`; Z=`echo "$Z 2 - p" | dc -`

############## save intermediate files
    $FSLDIR/bin/fslmaths $f -min 1 -ero -roi 1 $X 1 $Y 1 $Z 0 1 FA/${f}_FA_4mask

    # create mask (for use in FLIRT & FNIRT)
    $FSLDIR/bin/fslmaths FA/${f}_FA_4mask -bin FA/${f}_FA_4mask_bin

    #extra dilation and erosion (smoothing) to avoid holes in mask
    $FSLDIR/bin/fslmaths FA/${f}_FA_4mask_bin -dilM -dilM -dilM -ero -ero FA/${f}_FA_mask_bin

    $FSLDIR/bin/fslmaths $f -mul FA/${f}_FA_mask_bin FA/${f}_FA 

    $FSLDIR/bin/fslmaths FA/${f}_FA_mask_bin -dilD -dilD -sub 1 -abs -add FA/${f}_FA_mask_bin FA/${f}_FA_mask -odt char

#################
    $FSLDIR/bin/immv $f origdata
	
done

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