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generate_b0
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generate_b0
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#!/bin/sh
# POSSUM
#
# Ivana Drobnjak & Mark Jenkinson, FMRIB Analysis Group
#
# Copyright (C) 2005-2007 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 Oxford
# University Innovation ("OUI"), the technology transfer company of the
# University, to negotiate a licence. Contact details are:
# [email protected] quoting reference DE/9564.
export LC_ALL=C
Usage() {
echo "./generate_b0 <structural> <fieldmap> <TEdiff>"
echo ""
echo "Used for generating B0 inhomogeneity image for POSSUM."
echo ""
echo "<structural> is a T1 weighted image, preferably 1x1x1mm voxel size."
echo "<fieldmap> are 2 complex volumes (in the one file) acquired for two different TE's."
echo "<TEdiff> is the difference of those two TE's (default=2.5ms)."
echo "Note that structural and fieldmap need to have the same dimensions and voxel sizes."
echo "Default filename of the output is <fieldmap>_possum."
echo ""
exit 1
}
[ "$1" = "" ] && Usage
struct=`remove_ext $1`
fmap=`remove_ext $2`
TEdiff=$3
if [ "$3" = "" ]; then
TEdiff=2.5
fi
echo "b0 inhomogeneity generation ... "
gamma=2.675e+8
fslcomplex -realabs ${fmap} ${fmap}abs_possumtmp 0 1
fslcomplex -realphase ${fmap} ${fmap}phase1_possumtmp 0 0
fslcomplex -realphase ${fmap} ${fmap}phase2_possumtmp 1 1
fslmaths ${fmap}phase1_possumtmp -sub ${fmap}phase2_possumtmp ${fmap}phasediff_possumtmp -odt float
fslcomplex -complexpolar ${fmap}abs_possumtmp ${fmap}phasediff_possumtmp ${fmap}complex_possumtmp 0 0
fslcomplex -realphase ${fmap}complex_possumtmp ${fmap}phase_possumtmp 0 0
prelude -a ${fmap}abs_possumtmp -p ${fmap}phase_possumtmp -o ${fmap}uphase_possumtmp -v
fslmaths ${fmap}uphase_possumtmp -mul 1000 -div ${TEdiff} ${fmap}_b0_radps_possumtmp -odt float
fslmaths ${fmap}_b0_radps_possumtmp -div ${gamma} ${fmap}_b0_tesla_possumtmp -odt float
#register b0 (which is now in tesla) to the structural image
bet ${fmap}abs_possumtmp ${fmap}abs_brain_possumtmp -f 0.5 -g 0
flirt -in ${fmap}abs_brain_possumtmp -ref ${struct} -omat ${fmap}_regmatrix_possumtmp.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 7
flirt -in ${fmap}_b0_tesla_possumtmp -ref ${struct} -out ${fmap}_b0_possumtmp -applyxfm -init ${fmap}_regmatrix_possumtmp.mat -interp trilinear
fslmaths ${fmap}_b0_possumtmp -mul -1 ${fmap}_possum
rm ${fmap}*possumtmp*