old_betall

#!/bin/sh

#   betall - get brain, skull and scalp surfaces
#
#   Mikael Pechaud, Stephen Smith and Mark Jenkinson
#   FMRIB Image Analysis Group
#
#   Copyright (C) 1999-2004 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
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#   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
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#   without the express permission of the University. The permission of
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#   
#   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
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#   (3) use of the Software or any derivative of it for research with the
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#   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.


Usage() {
    echo "Usage: betall <t1_fileroot> <t2_fileroot>"
    exit
}

[ "$2" = "" ] && Usage
[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
[ `${FSLDIR}/bin/imtest $2` = 0 ] && Usage
A1=`${FSLDIR}/bin/remove_ext $1`
A2=`${FSLDIR}/bin/remove_ext $2`

# register T2 to T1
${FSLDIR}/bin/flirt -ref ${A1} -in ${A2} -out ${A2}_to_${A1} -interp sinc

# register T1 to standard space
${FSLDIR}/bin/flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm -in ${A1} -omat ${A1}_to_tal.mat

# run brain extraction and save brain mesh
${FSLDIR}/bin/bet2 ${A1} ${A1}_brain -e

# find other surfaces
${FSLDIR}/bin/betsurf -o -m -s ${A1} ${A2}_to_${A1} ${A1}_brain_mesh.off ${A1}_to_tal.mat ${A1}_brain

# clean up
#/bin/rm ${A2}_to_${A1}.hdr* ${A2}_to_${A1}.img*