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Hi Longchuan, 1) When you are using path distribution mode, each voxel contains the number of samples that pass through it between seed and target. Sometimes, the samples sent out from multiple seed voxels will pass through a particular voxel in the brain, leading to numbers of samples greater than the total sent out from each seed voxel. This happens in particular when you have your seed near the cortical termination of a pathway and you are looking at the probabilities in voxels of the deep white matter of the pathway. Samples from multiple seed voxels will converge in the deep white matter leading to higher probabilities. 2) When you are using seed classification mode, you will get results called seeds_to_<some target>, which have values in the same region as your seed. For each voxel in the seed, the seeds_to_target file contains the number of samples that reached the target. These are particularly useful for doing the kind of hard segmentation we talked about yesterday at lunch. I think you should give some more details about exactly what question you are trying to ask of the data. Also, so long as you include the --xfm argument (or seed space is not diffusion) and provide a transformation matrix, it is okay to use seed masks that are on the T1. Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Longchuan Li Sent: Wednesday, April 30, 2008 11:59 AM To: [log in to unmask] Subject: [FSL] How to interpret the numbers in the probtrackx results Hi, Dr. Behrens I have some questions regarding to interpreting the meanings of numbers in the tratography results. 1) when I seeded a mask, i.e., on cortical-spinal tract, and ran probtrackx, I got a fdt_path.nii.gz file which shows how the tracts are projected in brain. The number of samples I set was 2000. But some values on the fdt_path.nii.gz are are over 10,000. What is the best way to interpret these numbers? 2) When I drew a cortical target mask and ran probtrackx again, I got a file named "seeds_to_cortical mask.nii.gz" with different numbers there. How was those numbers obtained and how should I interpret this numbers? From your paper (Behrens et al. MRM, 2003), it seems that the way to quantify this uncertainty is counting the number of probabilistic streamlines which pass through a voxel B from seed voxel A and then dividing by the total number of probabilistic streamlines. But I do have problems associating this counting method to the results I have here. P.S: my seek mask is on the T1 image, which may also involve some interpretation issue. Hope this information will help your diagnosis. Your help is greatly appreciated Longchuan