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Hi, When running probtrackx using classification targets in standard (MNI) space, is it possible to get the results in diffusion space? In previous runs, I’ve chosen the ‘seed space is not diffusion’ option and supplied the ‘standard2diff’ linear transformation matrix, and have gotten results in standard space (the original space of the ROIs). However, I would like to visually verify the results by examining the fdt paths for each subject in fslview. This would require the probtrackx results to be in diffusion space. If this is not an option, given masks in standard space, how can I be confident that the registrations from standard to diffusion space worked adequately for every subject? A second issue relates to the following. When registering ROIs from standard to diffusion space, there are interpolation effects that make the ROIs not binary any longer and adjacent ROIs can overlap. I assume that these effects are ignored by protrackx, so if one wanted to make sure that there was no overlap across regions, it would always be better to transform the ROIs to individual space and then do some editing before running the tractography. Could someone please give their experience on this? Thank you for your help. Katie Gambale Catherine Gambale, B.S. Post-Baccalaureate IRTA Genes, Cognition, and Psychosis Program Clinical Brain Disorders Branch, NIMH 10 Center Dr., Bldg. 10, Room 3C205 Bethesda, MD 20852 Phone: (301)-496-9672 Email: [log in to unmask]