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old_betall
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old_betall
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#!/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
# 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.
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*