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tbss_preproc_edited
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tbss_preproc_edited
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#!/bin/sh
# tbss_1_preproc - preprocess FA data for TBSS
#
# Stephen Smith, FMRIB Image Analysis Group
#
# Copyright (C) 2005-2008 University of Oxford
#
# Part of FSL - FMRIB's Software Library
# http://www.fmrib.ox.ac.uk/fsl
#
# 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")
#
# The Software remains the property of the University of Oxford ("the
# University").
#
# The Software is distributed "AS IS" under this Licence solely for
# non-commercial use in the hope that it will be useful, but in order
# that the University as a charitable foundation protects its assets for
# the benefit of its educational and research purposes, the University
# makes clear that no condition is made or to be implied, nor is any
# warranty given or to be implied, as to the accuracy of the Software,
# or that it will be suitable for any particular purpose or for use
# under any specific conditions. Furthermore, the University disclaims
# all responsibility for the use which is made of the Software. It
# further disclaims any liability for the outcomes arising from using
# the Software.
#
# The Licensee agrees to indemnify the University and hold the
# University harmless from and against any and all claims, damages and
# liabilities asserted by third parties (including claims for
# negligence) which arise directly or indirectly from the use of the
# Software or the sale of any products based on the Software.
#
# No part of the Software may be reproduced, modified, transmitted or
# transferred in any form or by any means, electronic or mechanical,
# without the express permission of the University. The permission of
# the University is not required if the said reproduction, modification,
# transmission or transference is done without financial return, the
# conditions of this Licence are imposed upon the receiver of the
# product, and all original and amended source code is included in any
# transmitted product. You may be held legally responsible for any
# copyright infringement that is caused or encouraged by your failure to
# abide by these terms and conditions.
#
# You are not permitted under this Licence to use this Software
# commercially. Use for which any financial return is received shall be
# defined as commercial use, and includes (1) integration of all or part
# of the source code or the Software into a product for sale or license
# by or on behalf of Licensee to third parties or (2) use of the
# Software or any derivative of it for research with the final aim of
# developing software products for sale or license to a third party or
# (3) use of the Software or any derivative of it for research with the
# final aim of developing non-software products for sale or license to a
# third party, or (4) use of the Software to provide any service to an
# external organisation for which payment is received. If you are
# interested in using the Software commercially, please contact Isis
# Innovation Limited ("Isis"), the technology transfer company of the
# University, to negotiate a licence. Contact details are:
# [email protected] quoting reference DE/9564.
########
#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