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If you make sure your nodif_brain_mask is binary, everythin runs ok. e.g. fslmaths nodif_brain_mask -thr 0.5 -bin nodif_brain_mask You might also want to check your bvecs/bvals files and get rid of the rather strange appearance of decimal points at the end of integers. I don't know if they will be read correctly. T On 24 Sep 2007, at 23:01, Roman Loonis wrote: > Hey Tim, > > I just uploaded the files (session 377404) for Tim Behrens. Thank > you so much for your help in looking at my files. > > Roman > > > On 9/22/07, Tim Behrens <[log in to unmask]> wrote: > Can you upload your data to the upload site: > http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi > > and we will have a look on Monday. > > T > On 21 Sep 2007, at 21:33, Roman Loonis wrote: > > > I would like to use Bedpostx to process nifti files I have already > > pre- > > processed with home software. The nifti files can be read without a > > problem on FSL view and do not pose any problem with DTIFit. The > > DTIFit > > results can be viewed with FSLview. Using the bedpostx_datacheck, > the > > provided files pass the test. When I run, bedpostx I do not get any > > error > > messages. However, the program runs in about a minute and a half > > (computer > > is a pentium 3.4 GHz processor) and does not produce the expected > > files. It > > produces .bedpostx file with three folders (diff_slices, xfms, > > logs) and > > bvals, bvecs, commands.txt, and nodif_brain_mask(.img, .hdr) files. > > The > > program also produces in my original directory, a series of > > data_slice_00*.nii.gz as well as > > nodif_brain_mask_slice_00*.nii.gz. And > > thats all. If I attempt the Probtrackx, I get the following error: > > child > > killed:segmentation violation. > > > > I obtained the log files (and I have attached them) and there > > appears to > > be an error for each of the slices. What does it mean? What should > > I do? > > > > > > > > > > > > An exception has been thrown > > Logic error:- detected by Newmat: index error: requested indices = > > 1, 2683 > > > > MatrixType = Rect # Rows = 86; # Cols = 2682 > > > > > > > > Done > > > > > > Log directory is: /root/Desktop/Veronika.bedpostX/diff_slices/ > > data_slice_0000 > > > > > > ** ERROR (nifti_image_read): failed to find header file for '/root/ > > Desktop/Veronika/nodif' > > ** ERROR: nifti_image_open(/root/Desktop/Veronika/nodif): bad > > header info > > Error: failed to open file /root/Desktop/Veronika/nodif > > Cannot open volume /root/Desktop/Veronika/nodif for reading! > > > > >