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Hi - not sure about that - possibly a bug in slicer - actually I had seen slicer crash a couple of times myself last week, but then couldn't reproduce it. If you want to send the data to Matthew he can have a look, Cheers, Steve. On 10 Jun 2009, at 04:51, Jonathan Ipser wrote: > Hello Steve, > > Thank you for responding so rapidly to my query. After looking at the > structural images I was using, it turns out that they were not in > the same > orientation as the standard image (though the functional data was > correctly > orientated). After using fslswapdim to reorient the structural image > so that > the labeling in fslview matched that for the standard image (using the > command "fslswapdim input RL PA IS output"), the functional images > are no > longer inverted with respect to the standard space following > registration. I > have uploaded the structural image before and after reorientation to > http://projects.pry.uct.ac.za/uploads/fMRI, for your interest. > > Unfortunately, when I use the reorientated structural image, I now > receive a > segmentation error when the slicer utility attempts to create the > functional > to structural overlay generated in the report (see error message > below). As > far as I can tell I have eliminated all the obvious explanations for > this > error (the example_func2highres and highres images are there, and > there > seems to be enough memory). > > Do you perhaps know why I might be getting this error. As everything > else > seems to be fine, with all the other images beside the functional to > structural image generated on the registration html page, is this > perhaps > something that I shouldn't worry about? > > Any advice would be much appreciated. > > Best, > Jonathan > > -----------------Error message: > sh: line 1: 7345 Segmentation fault /usr/local/fsl/bin/slicer > example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x > 0.55 > slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 > slg.png -y > 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 > sll.png > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------