Hi Donna, That is correct that we want the source parcellation mapped on the subjects surfaces. I believe we are wanting it in MNINonlinear stereotaxic space.
Should I be using the fs_LR standard mesh then? With the mri_label2vol command I should be only producing a single output volume. I now input the annotation file into this command, bypassing the need for labels (the computer I am using also has trouble loading in all of the labels). I have a pre-existing script that was written in my lab to create random parcellations and I am attempting to adapt that. So I do the above and I will get a label volume for each hemisphere. Then these two label volumes are combined into a single image. Subcortical parcellations are then added to make a whole brain parcellation image which we then use to make connectomes. Sorry if anything is unclear or not elaborated on enough, I am very new to all of this. Regards, Stuart On 27 May 2015 at 07:01, Donna Dierker <[email protected]> wrote: > Hi Stuart, > > I have fewer answers than questions, but it seems like at the end of this, > you want your source (fsaverage) parcellation mapped onto the HCP subjects' > surfaces, and then projected from surface to volume (subject's orig/magnet > space or MNINonlinear stereotaxic space?). > > The HCP pipeline uses the Freesurfer ?h.sphere.reg to get surface data > onto fs_LR mesh: > > lh: freesurfer_native_mesh -> fsaverage.left -> fs_LR (32k or 164k) mesh > rh: freesurfer_native_mesh -> fsaverage.right -> fs_LR (32k or 164k) mesh > > Note that fsaverage left and right hem meshes are not in register with one > another (across hemispheres -- vertex i on the left is probably nowhere > near vertex i on the right hem). In the fs_LR standard mesh, left and > right hems are in register with one another. > > It sounds like you have an annotation on the fsaverage mesh. It seems in > principle possible to get your annotation, which is a single, atlas-like > parcellation that will be used across HCP subjects, onto the fs_LR mesh, > and then you could use the subjects' fs_LR white, midthickness, or pial > surface to project the annotation/label to volume somehow, but I don't know > how those freesurfer commands work or what they need. You can mris_convert > from GIFTI to Freesurfer format, if needed. > > It might help to zoom out a bit more, though: What do you plan to do with > the resulting individual label volumes? > > Donna > > > On May 24, 2015, at 8:45 PM, Stuart Oldham <[email protected]> > wrote: > > > Hi all, > > > > I am trying to create a random parcellation for the HCP data. I have > created the parcellations first using the fsaverage subject and am trying > to map these onto the HCP subjects. > > > > First I have map the annotation from the source (fsaverage) to the > subject using mri_surf2surf (for each hemisphere individually). Usually > this just uses a sphere.reg file but the HCP data doesn't have the file in > this format. Is the {subject}.{hemisphere}.sphere.reg.native.surf.gii > (located under MNINonLinear/Native) the file I should be using here? > > > > Next I turn the annotations into labels using mri_annotation2label. > Which surface file do I need to specify it to run (is it the same as above)? > > > > Then I run mri_label2vols. Again which surface file should I be > inputting? Should it now be the > {subject}.{hemisphere}.white.native.surf.gii? Also is there a way with this > command I can specify it to find a thickness file (i.e. > {subject}.{hemisphere}.thickness.native.surf.gii) as by default it is > looking for an lh or rh .thickness file. > > > > Thanks in advance! > > > > _______________________________________________ > > 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
