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I think the issue is that you are starting tractography from the center of a pathway that goes in two directions. Samples that go in the direction of LV1 will never turn around and visit RV1 and vice-versa (and that is what you are asking for if you put both LV1 and RV1 as waypoints, that particular streamlines will reach both masks, rather than just one or the other). What question are you trying to ask with this data? Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Markus Gschwind Sent: Sunday, March 22, 2009 5:13 PM To: [log in to unmask] Subject: [FSL] probtrackx with two waypointmasks Dear FSLers, I have the following problem: I am trying to probtrackx from the corpus callosum to two homologue regions in both hemispheres (for example an 10mm sphere ROI in left and right V1). The corpus callosum mask is binary and drawn on the median sagittal slice (the data are acquired under 30 diffusion directions). I am using a seed mask (CC) and two waypoint masks (LV1 and RV1). I am getting 0 waytotals. However: a) When I am probtrackxing each ROI alone (with only 1 waypointmask), I am getting 1800 resp. 3200 waytotals for the resulting tracts to LV1 resp. RV1. b) By looking at the two resulting fdt_paths in fslview I see that the touch c) By intersecting (fslmaths -mul ) the two resulting fdt_paths I get 590 voxels of intersecting volume. d) When I am probtrackxing from CC without waypointmask I get an intersection of the resulting fdt_path with leftV1 of 58 voxels and with rightV1 of 68 voxels. My question is: Given all this evidence of connectivity of CC to LV1 and RV1, why do get waytotals=0 in the 2-waypoints probtrackx? What could I do different in to help? Any help is greatly appreciated! Thank you! Markus -- Dr. med. Markus Gschwind, M.D. Laboratory for Neurology and Imaging of Cognition Dept of Neurosciences University Medical Center (CMU) 1 Michel-Servet - 1211 GENEVA - CH Tel 0041 (0) 22 379 5324 Fax 0041 (0) 22 379 5402 email: [log in to unmask] http://labnic.unige.ch