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slicesdir.brainageR
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slicesdir.brainageR
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#!/bin/sh -f
## edited version of slicesdir for use in brainageR software
## changes made so that output directory takes a unique name
# slicesdir - call slicer on all input images and produce web page output
#
# Stephen Smith, FMRIB Image Analysis Group
#
# Copyright (C) 1999-2007 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.
usage() {
cat <<EOF
slicesdir.brainageR software version 1.0 09 Aug 2018
Command usage:
slicesdir.brainageR [-n output directory name] [-o] [-p <image>] [-e <thr>] [-S] <filelist>
-n : necessary argument - the name to be given to the output directory
-o : filelist is pairs ( <underlying> <red-outline> ) of images
-p <image> : use <image> as red-outline image on top of all images in <filelist>
-e <thr> : use the specified threshold for edges (if >0 use this proportion of max-min, if <0, use the absolute value)
-S : output every second axial slice rather than just 9 ortho slices
For example:
slicesdir.brainageR -n subject01_T1 T1.nii
EOF
exit 1
}
Width=1500
Compare=0
if [ "$1" != "-n" ] ; then
usage
exit 1
fi
if [ ! -f "$3" ] ; then
usage
exit 1
fi
if [ "$1" = "-n" ] ; then
file_name=`basename $2`
if [[ "$OSTYPE" == "darwin"* ]]; then
full_path=`greadlink -f $2 | sed -e "s@${file_name}@@"`
else
full_path=`readlink -f $2 | sed -e "s@${file_name}@@"`
fi
dir_name=${full_path}/slicesdir_${file_name}
mkdir $dir_name
shift 2
fi
if [ "$1" = "-o" ] ; then
Width=3000
Compare=1
shift
fi
if [ "$1" = "-p" ] ; then
pairimage=$2
shift 2
fi
edgeopts="";
if [ "$1" = "-e" ] ; then
edgeopts="-e $2";
shift 2
fi
sliceropts="$edgeopts -x 0.4 ${dir_name}/grota.png -x 0.5 ${dir_name}/grotb.png -x 0.6 ${dir_name}/grotc.png -y 0.4 ${dir_name}/grotd.png -y 0.5 ${dir_name}/grote.png -y 0.6 ${dir_name}/grotf.png -z 0.4 ${dir_name}/grotg.png -z 0.5 ${dir_name}/groth.png -z 0.6 ${dir_name}/groti.png"
convertopts="${dir_name}/grota.png + ${dir_name}/grotb.png + ${dir_name}/grotc.png + ${dir_name}/grotd.png + ${dir_name}/grote.png + ${dir_name}/grotf.png + ${dir_name}/grotg.png + ${dir_name}/groth.png + ${dir_name}/groti.png"
if [ "$1" = "-S" ] ; then
sliceropts="-S 2 1600 ${dir_name}/grota.png"
convertopts="${dir_name}/grota.png"
shift
fi
echo '<HTML><TITLE>slicedir</TITLE><BODY BGCOLOR="#458dd1">' > ${dir_name}/index.html
number=`echo $* | wc -w`
i=0
while [ $i -lt $number ] ; do
A=`${FSLDIR}/bin/remove_ext $1`
echo $A
if [ $Compare = 0 ] ; then
${FSLDIR}/bin/slicer $A $pairimage -s 1 $sliceropts
Q=`echo $A | sed "s/\//_/g"`
else
B=`${FSLDIR}/bin/remove_ext $2`
${FSLDIR}/bin/slicer $A $B -s 1 $sliceropts
Q=`echo $A | sed "s/\//_/g"`_to_`echo $B | sed "s/\//_/g"`
fi
${FSLDIR}/bin/pngappend $convertopts ${dir_name}/${Q}.png
/bin/rm -f ${dir_name}/grot?.png
echo '<a href="'${Q}'.png"><img src="'${Q}'.png" WIDTH='$Width' >' ${Q}'</a><br>' >> ${dir_name}/index.html
shift
i=`echo "$i 1 + p" | dc -`
if [ $Compare = 1 ] ; then
shift
i=`echo "$i 1 + p" | dc -`
fi
done
echo '</BODY></HTML>' >> ${dir_name}/index.html
echo ''
echo 'Finished. To view, point your web browser at'
echo file:${dir_name}/index.html