#!/bin/sh # filmbabescript # # Mark Woolrich, FMRIB Image Analysis Group # # Copyright (C) 2002-2004 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. export LC_NUMERIC=C # $1 is feat directory # # e.g.featdir=/home/fs3/steve/data/fmri_test/heatpain+vis_1352/epi3.4_SDfixed_junkscut_FLOBS.feat if [ $# -ne 2 ] ; then echo "Usage: filmbabescript featdir flobsdir" exit 1 fi if [ $1 = "--help" ] ; then echo "Usage: filmbabescript featdir flobsdir" exit fi cd $1 featdir=`pwd` flobsdir=$2 echo "$FSLDIR/bin/filmbabe --df=filtered_func_data --mask=mask --dm=design.mat --frf=design.frf --ld=filmbabe --ni=5 --ntar=3 --fd=$flobsdir" $FSLDIR/bin/filmbabe --df=filtered_func_data --mask=mask --dm=design.mat --frf=design.frf --ld=filmbabe --ni=5 --ntar=3 --fd=$flobsdir echo "$FSLDIR/bin/contrast_mgr -f design.fts filmbabe design.con" $FSLDIR/bin/contrast_mgr -f design.fts filmbabe design.con cd filmbabe files=`$FSLDIR/bin/imglob zfstat*.*` files=`$FSLDIR/bin/remove_ext $files` echo " Filmbabe results for $featdir " > report.html echo "" >> report.html echo "

Filmbabe results for
$featdir


" >> report.html echo " Optimal basis set report

" >> report.html for filename in $files ; do fname=$filename echo "$FSLDIR/bin/mm --mask=mask --sdf=$fname --logdir=mm_$fname --ni=30 --zfstatmode" $FSLDIR/bin/mm --mask=mask --sdf=$fname --logdir=mm_$fname --ni=30 --zfstatmode; echo " $fname mixture model fit results

" >> report.html done echo "" >> report.html echo "

Analysis carried out by filmbabe, based on:
" >> report.html echo "M.W. Woolrich, T.E.J. Behrens, and S.M. Smith. Constrained linear basis sets for HRF modelling using Variational Bayes. NeuroImage, 21:4(1748-1761) 2004." >> report.html echo "


This page produced automatically by filmbabescript - a part of FSL." >> report.html echo "" >> report.html echo "View results at $featdir/filmbabe/report.html"