#!/bin/sh # first_flirt - initial standard space registration before running the main part of FIRST # # Brian Patenaude, Courtney Bishop and Mark Jenkinson, FMRIB Image Analysis Group # # Copyright (C) 2006-2010 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: first_flirt [options]" echo "" echo "-b : input is already brain extracted" echo "-d : debug (don't delete intermediate files)" echo "-inweight : use a weighting mask on the first registration" echo "-strucweight : use a specific structure weighting mask (in standard space) for an (optional) third-stage registration step" echo "-cort : use a weighting mask of the whole brain on the first registration (for specific models)" echo "-cost : specify the costfunction to be used by all FLIRT calls" echo "" echo "e.g.: first_flirt subject10rawT1 subject10rawT1_to_std_sub" echo "" exit 1 } [ "$2" = "" ] && Usage [ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage A=`${FSLDIR}/bin/remove_ext $1` B=`${FSLDIR}/bin/remove_ext $2` shift 2 refim=MNI152_T1_1mm debug=0 doCortAlignment=0 inweightCom="" strucweight="" costCom="" while [ _$1 != _ ] ; do if [ $1 = -d ] ; then debug=1 shift elif [ $1 = -b ] ; then refim=MNI152_T1_1mm_brain shift elif [ $1 = "-cort" ] ; then doCortAlignment=1 shift elif [ $1 = -cost ] ; then costCom="${1} ${2}" shift 2 elif [ $1 = -inweight ] ; then inweightCom="${1} ${2}" shift 2 elif [ $1 = -strucweight ] ; then strucweight="${2}" shift 2 fi done echo "initial registration $doCortAlignment" ${FSLDIR}/bin/flirt -in $A -out ${B}_tmp_stage1 -ref ${FSLDIR}/data/standard/${refim} -omat ${B}_tmp_stage1.mat $inweightCom $costCom echo "Stage 2: use subcortical mask" #do subcortical alignment ${FSLDIR}/bin/flirt -in ${B}_tmp_stage1 -out ${B}_tmp_stage2 -ref ${FSLDIR}/data/standard/${refim} -omat ${B}_tmp_stage2.mat -nosearch -refweight ${FSLDIR}/data/standard/MNI152lin_T1_1mm_subbr_mask $costCom ${FSLDIR}/bin/convert_xfm -omat ${B}.mat -concat ${B}_tmp_stage2.mat ${B}_tmp_stage1.mat #generate registered images ${FSLDIR}/bin/flirt -in ${A} -out ${B} -ref ${FSLDIR}/data/standard/${refim} -applyxfm -init ${B}.mat if [ $doCortAlignment -eq 1 ] ; then #do hemisphere/cerebellum alignment echo "Alternate Stage 2: Use brain mask" ${FSLDIR}/bin/flirt -in ${B}_tmp_stage1 -out ${B}_tmp_cort_stage2 -ref ${FSLDIR}/data/standard/${refim} -omat ${B}_tmp_cort_stage2.mat -nosearch -refweight ${FSLDIR}/data/standard/MNI152_T1_1mm_first_brain_mask.nii.gz $costCom ${FSLDIR}/bin/convert_xfm -omat ${B}_cort.mat -concat ${B}_tmp_cort_stage2.mat ${B}_tmp_stage1.mat ${FSLDIR}/bin/flirt -in ${A} -out ${B}_cort -ref ${FSLDIR}/data/standard/${refim} -applyxfm -init ${B}_cort.mat fi if [ X$strucweight != X ] ; then ${FSLDIR}/bin/flirt -in ${A} -ref ${FSLDIR}/data/standard/${refim} -init ${B}.mat -out ${B} -omat ${B}_tmp_stage3.mat -refweight ${strucweight} -nosearch $costCom cp ${B}_tmp_stage3.mat ${B}.mat fi if [ $debug = 0 ] ; then /bin/rm ${B}_tmp_stage* fi exit 0