Workbench doesn't have that kind of visualization - it can be displayed as a matrix, or interactively selecting a "seed" parcel and coloring the other parcels. The FSLNets stuff has something related to what you want, but is based on networks, and doesn't really spatially organize them:
https://db.humanconnectome.org/megatrawl/3T_HCP820_MSMAll_d50_ts2/megatrawl_1/netjs/index.html The cortical coordinates are stored in .surf.gii files, and can be turned into metric files with wb_command -surface-coordinates-to-metric . It doesn't have a way to put voxel coordinates into voxel data, unfortunately, but it may be simple to do in matlab or python. From these, you can make a cifti file containing coordinates in each grayordinate, and then you can use wb_command -cifti-parcellate on it to get the center of gravity of each parcel. You do have to select what surface you take coordinates from, which runs into our usual advice that functionally-aligned cortical data has substantial coordinate uncertainty - folding patterns are different across subjects, and functional areas move around somewhat with respect to folds (moreso in some regions than others). However, since it sounds like you only need a rough estimate of distances for display purposes, you probably don't need to worry about this much. You can use the MSMAll aligned group average surfaces to match the functional alignment used by the MMP labels - midthickness will give you the average anatomical coordinates, while inflated or very_inflated will "unfold" the surface a bit more (group averaging already smooths many folds out somewhat), which may help avoid having some areas obscure the view of other areas. Tim On Thu, Sep 13, 2018 at 8:17 PM, Leonardo Tozzi <lto...@stanford.edu> wrote: > To Whom it may concern, > > > > I have created a pconn.nii file based on connectivity measures obtained > based on a parcellation that I put together (dlabel.nii), which contains > cortical and subcortical areas (Glasser + Gordon subcortical). > > This question might be trivial, but I would like to know if it is possible > to visualize this matrix as a graph in workbench, i.e. if I can visualize > lines “connecting” my parcels based on the values of the pconn file. If > this is not possible, I would ask for any tips on how I could get the > coordinates of my parcels in a space that at least resembles the brain, so > that I can then connect them in another software. From the information I > found in the mailing list, there seem to be ways to extract the > greyordinate coordinates based on the dlabel.nii file and a corresponding > .gii file. However, I was wondering if someone could outline the procedure > for me or have any tips on achieving what I am trying to do in an optimal > way. > > Thank you very much. > > Yours sincerely, > > > > > > Leonardo Tozzi, MD, PhD > > Williams PanLab | Postdoctoral Fellow > > Stanford University | 401 Quarry Rd > <https://maps.google.com/?q=401+Quarry+Rd&entry=gmail&source=g> > > lto...@stanford.edu | (650) 5615738 > > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
