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Hi Stephen, The platform is Red Hat Linux 9 (x86). The output data look plausible, except for the fact that superimposing them onto an FA map generated by dtifit sometimes shows bright areas in CSF, as I mentioned. Is it valid to overlay these two images, and if not, what should I be putting "under" the probtrack results in fslview? Thanks, Jon On 6 Nov 2004, at 10:04, Stephen Smith wrote: > Hi Jon. > > Don't worry about the -ve pixdims - that's something we'll tidy up in > a future release but they should always not make a difference anyway. > > The analysis could well be that quick if your data is lower > resolution/field-of-view than we used for the example timings in the > manual. > > The error message on completion looks odd, particularly as the bedpost > script is only 293 lines long. What platform are you using? It does > look > as if it probably did finish fine - I assume that the output data > looked > ok. > > Cheers. > > > > On Wed, 3 Nov 2004, Jon Clayden wrote: > >> Hi, >> >> I have a couple of questions that are bothering me and don't seem to >> be >> answered by the FAQ. >> >> First, I've noticed that running avwhd on some of the Analyze files >> generated by various stages of the FDT pipeline produces a seemingly >> arbitrary mixture of positive and negative "pixdim1" values. (See, for >> example, the bedpost_datacheck output below.) Is this expected; and if >> so, what is happening? When I overlay output from probtrack with an FA >> map from the same data the tractography results look rather unlikely >> in >> parts, occasionally straying into CSF, so I wondered if one of the >> images might be back-to-front with respect to the other. >> >> Secondly, when I run bedpost it processes the data for about 12 hours, >> which seems suspiciously short considering the spec of the box it's >> running on (Red Hat 9 derivative, 2GHz or so, 512Mb RAM), and then >> finishes with output like the following: >> >> [...] >> 40 slices processed >> 41 slices processed >> 41 slices processed >> 42 slices processed >> 43 slices processed >> 44 slices processed >> 45 slices processed >> Merging outputs into 4D files >> DONE >> /disk/home/cornell/s0343526/fsl/bin/bedpost: line 294: syntax error: >> unexpected end of file >> >> Should it be finishing at this point, or is something really wrong? >> >> Thanks, >> Jon >> >> >> bedpost_datacheck output: >> >> ./data >> dim1 128 >> dim2 128 >> dim3 48 >> dim4 52 >> datatype 4 >> pixdim1 -1.7187500000 >> pixdim2 1.7187500000 >> pixdim3 2.7999999523 >> pixdim4 1.0000000000 >> cal_max 0.0000 >> cal_min 0.0000 >> glmax 0 >> glmin 0 >> origin1 0 >> origin2 0 >> origin3 0 >> file_type ANALYZE-7.5 >> >> ./nodif >> dim1 128 >> dim2 128 >> dim3 48 >> dim4 1 >> datatype 4 >> pixdim1 1.7187500000 >> pixdim2 1.7187500000 >> pixdim3 2.7999999523 >> pixdim4 1.0000000000 >> cal_max 1385.0000 >> cal_min 0.0000 >> glmax 0 >> glmin 0 >> origin1 0 >> origin2 0 >> origin3 0 >> file_type ANALYZE-7.5 >> >> ./nodif_brain_mask >> dim1 128 >> dim2 128 >> dim3 48 >> dim4 1 >> datatype 4 >> pixdim1 -1.7187500000 >> pixdim2 1.7187500000 >> pixdim3 2.7999999523 >> pixdim4 1.0000000000 >> cal_max 1.0000 >> cal_min 0.0000 >> glmax 0 >> glmin 0 >> origin1 0 >> origin2 0 >> origin3 0 >> file_type ANALYZE-7.5 >> >> num lines in ./bvals >> 1 >> num words in ./bvals >> 52 >> num lines in ./bvecs >> 3 >> num words in ./bvecs >> 156 >> > > 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