#!/bin/sh # slices - call slicer with default cuts and display # # Stephen Smith,Mark Jenkinson and Matthew Webster, 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 # 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 "" echo "Usage: slices [input2] [-s scale] [-i ] [-o ]" echo "" exit 1 } [ "$1" = "" ] && Usage if [ _$FSLDIR = _ ] ; then FSLDIR=/usr/local/fsl export FSLDIR fi # NEED PARSING IN ORDER TO HAVE A -o OPTION outputname="" # if statement checks if -o option was given if [ `echo "$@" | grep -- -o | wc -w` -gt 0 ] ; then # extract the name if the -o option is present outputname=`echo "$@" | sed 's/.*-o *\([^ ]*\).*/\1/'`; fi f=/tmp/`${FSLDIR}/bin/remove_ext $1 | sed "s/\//_/g"` touch $f > /dev/null 2>&1 if [ ! -w $f ] ; then f=`${FSLDIR}/bin/tmpnam $f` fi # deal with complex images separately if [ X`${FSLDIR}/bin/fslval $1 datatype` = X32 ] ; then nm1=${f}_abs nm2=${f}_ph nm0=`${FSLDIR}/bin/remove_ext $1`; if [ X$1 != X ] ; then shift ; fi ${FSLDIR}/bin/fslcomplex -realpolar $nm0 $nm1 $nm2 ${FSLDIR}/bin/slices $nm1 $@ ${FSLDIR}/bin/slices $nm2 $@ ${FSLDIR}/bin/imrm $nm1 $nm2 exit 0 fi # deal with 2D and 3D images separately if [ X`${FSLDIR}/bin/fslval $1 dim3` = X1 ] ; then # 2D case slicenum=-0 im1=`${FSLDIR}/bin/remove_ext $1`; if [ X$2 != X ] ; then shift ; im2=`${FSLDIR}/bin/remove_ext $1`; fi if [ X$1 != X ] ; then shift ; fi if [ X$im2 != X ] ; then if [ `$FSLDIR/bin/imtest $im2` -eq 1 ] ; then # make a stacked version for getting edges ${FSLDIR}/bin/fslmerge -z ${f}b $im1 $im1 $im1 ${FSLDIR}/bin/fslmerge -z ${f}c $im2 $im2 $im2 im1=${f}b im2=${f}c slicenum=-1 fi fi # NEED PARSING IN ORDER TO HAVE A -o OPTION opts="$@" # remove the "-o " from the command line list opts=`echo $opts | sed 's/-o *[^ ]*//'`; if ${FSLDIR}/bin/slicer $im1 $im2 $opts -z $slicenum ${f}a.png ; then retval=0; # do nothing else exit -1; fi ${FSLDIR}/bin/pngappend ${f}a.png ${f}.gif else # 3D case # NEED PARSING IN ORDER TO HAVE A -o OPTION opts="$@" # remove the "-o " from the command line list opts=`echo $opts | sed 's/-o *[^ ]*//'`; if ${FSLDIR}/bin/slicer $opts -x 0.4 ${f}a.png -x 0.5 ${f}b.png -x 0.6 ${f}c.png -y 0.4 ${f}d.png -y 0.5 ${f}e.png -y 0.6 ${f}f.png -z 0.4 ${f}g.png -z 0.5 ${f}h.png -z 0.6 ${f}i.png ; then retval=0; # do nothing else exit -1; fi ${FSLDIR}/bin/pngappend ${f}a.png + ${f}b.png + ${f}c.png - ${f}d.png + ${f}e.png + ${f}f.png - ${f}g.png + ${f}h.png + ${f}i.png ${f}.gif fi # if using the -o option then just copy the file, otherwise display it if [ X$outputname != X ] ; then cp ${f}.gif $outputname else if [ X`uname | grep CYGWIN`X != XX ] ; then /cygdrive/c/Program\ Files/Internet\ Explorer/IEXPLORE.EXE C:/cygwin${f} & elif [ X`uname | grep -i darwin`X != XX ] ; then g=`${FSLDIR}/bin/tmpnam $f`.gif ; cp $f $g ; open ${f}.gif ; else $FSLWISH ${FSLDIR}/tcl/display.tcl $f.gif & fi fi \rm -f ${f}a.png ${f}b.png ${f}c.png ${f}d.png ${f}e.png ${f}f.png ${f}g.png ${f}h.png ${f}i.png ( sleep 20 ; \rm -f ${f}.gif ) &