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Satra--- can you send the command line? So a couple of possibilities outside of the random/weird library changes... and assuming you ran the same parameters--- (i.e. # of threads and same burn in, as well as sampling from both the f1 and f2 population). The module uses a random seed to start off the Markov Chain module--- which can be set explicitly or more commonly left blank and is set by whatever random number generator they use---- the markv model generally converges after running 5000 or so simulations per voxel... i.e. if you run 10,000 -P,--nsamples Number of samples - default=5000 vs 5,000--- your output image will roughly have "twice" the intensity as running with 5000...... but the numbers (I don't think) are guaranteed to be exactly accurate... --rseed Random seed See if specifying a specific rseed and running it back to back produces the same results... Just a guess. On Tue, Jan 29, 2013 at 10:29 AM, Satrajit Ghosh <[log in to unmask]> wrote: > hi folks, > > this is primarily to see if anybody has observed this before and might > have some clues for us. > > program: probtrackx2 > version: 5.0.2-2 from neurodebian > > these were the changes we found related to fsl. > Install: fsl-subthalamic-nucleus-atlas:**amd64 (5.0.2-2, automatic) > Upgrade: fsl-atlases:amd64 (5.0.0-2, 5.0.2-2) > > (we are trying to see if there are any hardware or other software changes). > > we ran probtrackx2 on the same rois two weeks back and again in the last > few days. > > Main changes: > > 1) Waytotal values changed. The new values are reproducible under the seed > - target mode, but slightly different from previous values. > > 2) The voxel values in the fdt_paths images decreased by 2 - 3 orders of > magnitude, at least inside my target ROIs. > > 3) It looks like that previously, the tracts went into the target > stopmask, but currently, they tend to stop (albeit not completely) at the > target stopmask. > > would the atlas changes have affected this? if not any other thoughts > would be much appreciated. > > cheers, > > satra > > -- David A Gutman, M.D. Ph.D. Assistant Professor of Biomedical Informatics Senior Research Scientist, Center for Comprehensive Informatics Emory University School of Medicine