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Hello, Thank you for your response and suggestion. Just doing a quick check: fslsize nodif_brain_mask.nii.gz dim1 128 dim2 128 dim3 72 dim4 1 pixdim1 1.7968750000 pixdim2 1.7968750000 pixdim3 2.0000000000 pixdim4 1.0000000000 fslsize merged_ph2samples.nii dim1 128 dim2 128 dim3 63 dim4 50 pixdim1 1.7968750000 pixdim2 1.7968750000 pixdim3 2.0000000000 pixdim4 1.0000000000 fslsize mean_f1samples.nii.gz dim1 128 dim2 128 dim3 63 dim4 1 pixdim1 1.7968750000 pixdim2 1.7968750000 pixdim3 2.0000000000 pixdim4 1.0000000000 If you look at dim3 for the first 2 files, they differ. And for the latter 2 files, hey differ in dim4 size. Could this be the issue, and what would be the cause? Is bedpostx producing something incorrectly? Or is it something with the nodif_brain_mask? D. Michael On Mon, 29 Apr 2013 14:06:31 +0100, Saad Jbabdi <[log in to unmask]> wrote: >Hi >Can you check that all nifti files in your bedpostx directory have the same image size (with fslsize). > >Cheers >Saad > > >On 29 Apr 2013, at 13:44, D. Michael <[log in to unmask]> wrote: > >> Hello, >> >> We are having issues running probtrackx. We are using FSL 5.02 through the debian package on Ubuntu 10.04. >> >> Every time attempt to run it, we get this output: >> >> rm -rf /probtrackdirectory >> mkdir -p /probtrackdirectory >> /probtrackdirectory/fdt_script.sh >> >> >> However, nothing seems to run. We checked the fdt_script.sh.e67 file and it reads this: >> >> Image Exception : #3 :: Mask of different size used in matrix() >> terminate called after throwing an instance of 'RBD_COMMON::BaseException' >> Aborted (core dumped) >> >> Not sure what exactly is going here. Anyone experience similar problems? Any help would be appreciated. >> >> Thanks, >> >> D. Michael >> > >-- >Saad Jbabdi >University of Oxford, FMRIB Centre > >JR Hospital, Headington, OX3 9DU, UK >(+44)1865-222466 (fax 717) >www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi > > > > > > > > > > > >