slicedir

#!/bin/sh -f # 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 # 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. if [ "$1" = "" ] ; then echo "Usage: slicesdir [-o] [-p ] [-e ] [-S] " echo "-o : filelist is pairs (

) of images" echo "-p : use as red-outline image on top of all images in " echo "-e : use the specified threshold for edges (if >0 use this proportion of max-min, if <0, use the absolute value)" echo "-S : output every second axial slice rather than just 9 ortho slices" exit 1 fi /bin/rm -rf slicesdir mkdir slicesdir echo 'slicedir' > slicesdir/index.html Width=1000 Compare=0 if [ "$1" = "-o" ] ; then Width=2000 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 slicesdir/grota.png -x 0.5 slicesdir/grotb.png -x 0.6 slicesdir/grotc.png -y 0.4 slicesdir/grotd.png -y 0.5 slicesdir/grote.png -y 0.6 slicesdir/grotf.png -z 0.4 slicesdir/grotg.png -z 0.5 slicesdir/groth.png -z 0.6 slicesdir/groti.png" convertopts="slicesdir/grota.png + slicesdir/grotb.png + slicesdir/grotc.png + slicesdir/grotd.png + slicesdir/grote.png + slicesdir/grotf.png + slicesdir/grotg.png + slicesdir/groth.png + slicesdir/groti.png" if [ "$1" = "-S" ] ; then sliceropts="-S 2 1600 slicesdir/grota.png" convertopts="slicesdir/grota.png" shift fi 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 $convertopts slicesdir/${Q}.png /bin/rm -f slicesdir/grot?.png echo '

' ${Q}'
' >> slicesdir/index.html shift i=`echo "$i 1 + p" | dc -` if [ $Compare = 1 ] ; then shift i=`echo "$i 1 + p" | dc -` fi done echo '' >> slicesdir/index.html echo '' echo 'Finished. To view, point your web browser at' echo file:`pwd`/slicesdir/index.html