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 <sjo...@student.monash.edu> 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
> 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
