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Hi Christopher, We had the same problem with film crashing on your data when run under linux on my desktop - it goes over the 2GB process limit just before saving the results. This is because of the large matrix size in your data, as there's so much padding. We got it to work fine though by killing the unneeded background data first, with for example: avwroi indata cutdatat 30 64 25 85 0 34 (or you could try tuning your kernel to allow larger processes). Cheers, Steve. On Wed, 15 Dec 2004, Christopher Bailey wrote: > Dear list, > > I have a problems running FSL on Fedora Core 2 and Debian (sarge) boxes. > In both cases I'm trying to run the precompiled RH9 binaries > (compilation from source causes problems for flame and mcflirt, will > post details later). > > I have a simple 16-minute dataset (block design) and 4 EVs. Everything > runs smoothly through prestats (including MELODIC), and seems to pass > through stats too. However, the first stage of post-stats, contrast_mgr, > causes a segfault : > > In FSL 3.2b: > 84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed > Saving results... > > /usr/local/fsl/bin/contrast_mgr -f design.fts stats design.con > ** ERROR: nifti_image_read(stats/sigmasquareds): can't open header file > ** ERROR: nifti_image_open(stats/sigmasquareds): bad header info > Error: failed to open file stats/sigmasquareds > Error:: FslGetDim: Null pointer passed for FSLIO > > In FSL 3.1: > 84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed > Saving results... > Unthresholding Series... Completed > Saving image... Completed > Thresholding Series... Completed > Unthresholding Series... > /usr/local/fsl/bin/contrast_mgr -f design.fts stats design.con > AvwOpen: Error while opening header!: No such file or directory > > > The file stats/sigmasquareds doesn't exist and I can't figure out why. I > don't think it's a memory issue, as has been discussed recently, since > the nii.gz is only 65 MB. At some stage of the analysis I get two > massive core dumps > -rw------- 1 cjb petadm 316022784 Dec 2 15:50 core.25436 > -rw------- 1 cjb petadm 794587136 Dec 2 15:54 core.27381 > > I've placed the .feat directory (minus the core dumps) tar.gzipped on > > www.pet.au.dk/~cjb/FSL > > (btw, it's SE data...) If anyone has time to check it out, I'd be > grateful! > > Best, > > Chris > -- > Christopher Bailey <[log in to unmask]> > PET Centre and > Center for Functionally Integrative Neuroscience > Aarhus University Hospital, Denmark > http://www.cfin.au.dk/ > -- Stephen M. Smith DPhil Associate Director, FMRIB and Analysis Research Coordinator Oxford University Centre for Functional MRI of the Brain John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve