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Dear Saad, I've checked the two things but no luck. So I uploaded the file. The ID # is 324683. Thank you very much. Regards, -Hu ________________________________ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Saad Jbabdi Sent: Friday, February 09, 2007 9:37 AM To: [log in to unmask] Subject: Re: [FSL] ProbTrack - no connectivity generated Hi, I can't see what's happening here. Could you try : * check whether the voxel 88,52,11 is inside the brain mask > avwstats results88_52_11 -r -R (to check whether the output values are all zeros). If these two don't help, then could you upload your tar-gzipped bedpost directory in www.fmrib.ox.ac.uk/cgi-bin/upload.cgi and send us the ID, we'll have a look. Thanks, Saad On 9 Feb 2007, at 14:16, Cheng, Hu wrote: Hi, Matt, I don't see probtrack.log, but there is a file called fdt.log. The content is as following: set tool probtrack set probtrack(bedpost_dir) /usr/local/data/DTI/subj3.bedpost set probtrack(xfm) set probtrack(mode) simple set probtrack(exclude_yn) 0 set probtrack(usereference_yn) 0 set probtrack(verbose_yn) 0 set probtrack(loopcheck_yn) 1 set probtrack(modeuler_yn) 0 set probtrack(curvature) 0.2 set probtrack(nsteps) 2000 set probtrack(steplength) 0.5 set probtrack(nparticles) 5000 set probtrack(x) 88 set probtrack(y) 52 set probtrack(z) 11 set probtrack(units) vox set probtrack(output) results Thanks. Regards, -Hu ________________________________ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Matt Sent: Thursday, February 08, 2007 2:18 PM To: [log in to unmask] Subject: Re: [FSL] ProbTrack - no connectivity generated Hu, Can you post the contents of probtrack.log? It will be in the folder where you saved your results. Peace, Matt. ________________________________ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Cheng, Hu Sent: Thursday, February 08, 2007 2:03 PM To: [log in to unmask] Subject: [FSL] ProbTrack - no connectivity generated Dear FSL user, We tried to get a fiber out of the DTI images. The DTIFit and BEDPOST ran well and the results looked reasonable. There was no error message after we performed the ProbTrack, however, the resulted image was 0 everywhere. We couldn't see any non-zero values even at the seed voxel. We changed the seed location, but this remained the same. Does anyone know what the problem is? Thanks. Hu Cheng, Ph.D. MRI Physicist, Imaging Research Facility Department of Psychological and Brain Sciences Indiana University Bloomington, IN 47405 Tel. 812-856-2518 Fax. 812-855-4691 ------------------------------------------------------------------------ --- Saad Jbabdi, Postdoctoral Research Assistant, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222545 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~saad ------------------------------------------------------------------------ ---