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Strange - this must be a platform-dependent bug, as it works fine on my mactop, and gives good results too. What platform are you using? However, anyway: the attached script eddy_correct (which will be part of FDT, the diffusion toolkit, when it's released later this summer) uses FLIRT instead of mcflirt to realign diffusion data, the point being that when you have eddy currents you need affine alignment not rigid body, which is more of an issue with diff data...you might want to try that instead, though on this data it seems to give similar results. Cheers. On Wed, 7 Jul 2004, Russ Poldrack wrote: > hi - I'm running into an odd segmentation fault when using mcflirt to > realign a series of diffusion-weighted images (from a DTI sequence). I > have four runs that I'm trying to realign, and I found that upon > merging them into a single file I got the following output from mcflirt > (using default options expect for -report): > > > poldrack::dlpfc:=>mcflirt -in DTI_d1.img -report > > No output name specified. Processed data will be saved as > > DTI_d1_mcf.(hdr/img) > > > > McFLIRT v 2.0 - fMRI affine motion correction tool > > > > Reading time series... > > first iteration - 8mm scaling, set tolerance > > Rescaling reference volume [2] to 8 mm pixels > > Registering volumes ... [3][1][0] > > second iteration - drop to 4mm scaling > > Rescaling reference volume [2] to 4 mm pixels > > Registering volumes ... [3][1]Segmentation fault > > The crash appears to occur when image #3 (of the four runs) is in the > reference spot (i.e. it happens if I merge them as 1 2 3 4 or 1 3 4, > but not as 4 3 2 1). oddly, however, I still get the crash if I use > -meanvol. Any ideas? I've put the offending dataset here: > > http://poldracklab.psych.ucla.edu/fsl_data/ > > cheers > rp > > --- > Russell A. Poldrack, Ph.D. > Assistant Professor of Psychology, UCLA > Franz Hall, Box 951563 > Los Angeles, CA 90095-1563 > email: [log in to unmask] > phone: 310.794.1224 > fax: 310.206.5895 > web: http://www.poldracklab.org/ > 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