wb_command -cifti-create-dense-scalar can make a file for this purpose, take the same ROI as you gave the tractography, and import it as a label volume with a name of "CEREBRAL_WHITE_MATTER_LEFT" or _RIGHT. I forget the details of how voxel seeds get specified to the tractography, you may have to be careful about how they are ordered when you run the tractography (there is no simple way to make a cifti file with a different voxel order of the same ROI).
The "template" part is just how the file gets used (like "roi" in "roi volume"), and use that as the structure label volume. The "template" part is not a special format, it is just saying how the file gets used, it is like "ROI" in "ROI volume" - same format, different purpose. In this case, all it needs is to know which voxel each index in the tractography output corresponds to, and it is written to take that information from a cifti mapping. Tim On Thu, May 31, 2018 at 4:51 AM, Colin Reveley <[email protected]> wrote: > Hi - a while back I had a lot of success using workbench in a study of > tractography and anatomy. I seeded tractography from the midthickness > cortical surface of mostmortem macaque data. Then I used > > wb_command-convert-matrix4-to-workbench-sparse > > and > > wb_command -convert-matrix4-to-matrix2 > > to get a matrix of gray matter vertices to white matter voxels, and > also to get trajTEMP.wbsparse files from gray matter ROI to display > visually in workbench. > > This is straigtforward using surfaces as seeds. Now I want to > expand this analysis to entities within the white matter, i.e. fiber > budles. > > I want to seed from a set of voxels, and then make a > trajTEMP.wbsparse. That would be the start, in general I want to > implement, expand and enrich the ideas here > https://elifesciences.org/articles/35237. > > convert-matrix4-to-workbench-sparse will take voxels as seeds. What I > need is a matrix of seed voxels by brain voxels instead of vertices by > voxels. > > But to make this I need a cifti template. There is no way to generate > one using wb_command that I can see. > > I think I need to make this using the matlab code on github, and the > cifti specification. But I am finding it very challenging to do this. > > Is there any kind of tutorial, or gentle documentation on this? > > best wishes > > Colin > > Colin Reveley > Neuroecology and Anatomy lab > Wellcome Centre for Integrative Neuroimaging > Centre for Functional MRI of the Brain (FMRIB) > Nuffield Department of Clinical Neurosciences > John Radcliffe Hospital > University of Oxford > John Radcliffe Hospital > University of Oxford > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
