The main current limitation with the probabilistic trajectory feature (which tracks exactly which fiber is chosen by the tractography algorithm out of the 1-3 modeled fibers in each voxel) is that it only works with single threaded probtrackx2, and not with the GPU accelerated version.
Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Thursday, April 11, 2019 at 1:41 PM To: DE CASTRO Vanessa <vanessa.decas...@cnrs.fr<mailto:vanessa.decas...@cnrs.fr>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] connectome for monkeys // fiber trajectories Connectome workbench is agnostic to species, though there are some defaults (identification symbol size) which default to a size suited to the human brain. We frequently use it with primate data. Workbench can display probabilistic trajectories generated with fsl's bedpostx/probtrackx tools (for the specific type of output that saves the fiber orientations used per-seed and per-voxel, matrix4 I think), but I don't think we have made a tutorial for it (and it still has some rough edges, as it hasn't been a priority for us). The wb_command -convert-matrix4-to-workbench-sparse and -convert-fiber-orientations (or -estimate-fiber-binghams for starting with just the direction samples, but is less accurate) commands are the starting points - once you have converted the files to workbench formats with the expected extensions (currently .trajTEMP.wbsparse and .fiberTEMP.nii), loaded them into wb_view, enabled them in features or layers (I don't recall exactly how), clicking on a seed point will display the trajectories to/from it. There is also wb_command -probtrackx-dot-convert, which allows converting the other probtrackx matrix types to cifti files (can show how much each voxel/vertex is used for a seed, but can't be displayed the way the trajectory files can). Tim On Thu, Apr 11, 2019 at 9:23 AM DE CASTRO Vanessa <vanessa.decas...@cnrs.fr<mailto:vanessa.decas...@cnrs.fr>> wrote: Hi! I've started to work with the human connectome workbench, and I was wondering if is ready to use with monkeys as well, like Caret. And I also read in the tutorial that you are already working in a new feature: probabilistic fiber trajectories... how soon it will come?? :D Thank you very much for everything. Sinceresly yours, -- Vanessa DeCastro, PhD Centre de Recherche Cerveau et Cognition - UMR 5549 - CNRS Pavillon Baudot CHU Purpan 31052 Toulouse Cedex 03, France _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
