tbss_non_FA

#!/bin/sh

#   tbss_non_FA - project non-FA data onto the skeleton
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 2006-2008 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
#   http://www.fmrib.ox.ac.uk/fsl
#   fsl@fmrib.ox.ac.uk
#   
#   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:
#   innovation@isis.ox.ac.uk quoting reference DE/9564.
export LC_ALL=C

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)"