standard mesh 141 of HCP parcellation

AFNI Message Board
1

Hi afni group,

Thanks for include the HCP atlas in afni/suma!!

I’m trying to extract the HCP parcellations from individual surface space, with the instruction of link here: https://openwetware.org/wiki/Beauchamp:CorticalSurfaceHCP

But I don’t see how to get std.141.?h.HCP.annot.niml.dset from *h.HCPMMP1.annot. Maybe I missed something.

Anyway, I was doing functional connectivity in surface world, and I have extracted individual anatomical seed regions from sub*/freesurfer/SUMA/std.141.?h.aparc.a2009s.annot.niml.dset.
Now the HCP atlas is available, but freesurfer doesn’t do the segmentation with HCP atlas, so I guess I could not extract the parcellations of HCP in native surface space, right?
If so, will you recommend using the mask from std.141.?h.HCP.annot.niml.dset in common space( if I could get one) as the seeds for each individual?

Also, I tried load the HCP surfs for each area shared in afni here https://afni.nimh.nih.gov/pub/dist/atlases/MNI_HCP/MNI_Glasser_HCP_2019_v1.0/surfs, with spec file of std.141.MNI152_2009_lh.spec, seems like it’s not in std.141 mesh?

Thanks!
Mengxing

2

I have added the following surface annotations for HCP and Freesurfer aparc 2009 segmentations to the MNI_HCP download, available separately.

MNI_Glasser_HCP_2019_v1.0/std.141.lh.aparc.a2009s.annot.niml.dset
MNI_Glasser_HCP_2019_v1.0/std.141.lh.Glasser_HCP.lbl.niml.dset
MNI_Glasser_HCP_2019_v1.0/std.141.lh.Glasser_HCP.niml.dset
MNI_Glasser_HCP_2019_v1.0/std.141.rh.aparc.a2009s.annot.niml.dset
MNI_Glasser_HCP_2019_v1.0/std.141.rh.Glasser_HCP.lbl.niml.dset
MNI_Glasser_HCP_2019_v1.0/std.141.rh.Glasser_HCP.niml.dset

You can download those files here:

https://afni.nimh.nih.gov/pub/dist/atlases/MNI_HCP/MNI_Glasser_HCP_2019_v1.0/
and as a single download here:
https://afni.nimh.nih.gov/pub/dist/atlases/MNI_HCP/MNI_Glasser_HCP_v1.0.tgz

You are right; the individual region surfaces are not on a standard mesh.

3

Thanks Daniel for uploading the data.

I am trying to parcellate my individual subject brain with HCP parcellation, so I could extract the structure from each sub in native space.
I’m following the method below, except do it in each subject instead with MNI_152_T1.
https://afni.nimh.nih.gov/pub/dist/atlases/MNI_HCP/MNI_Glasser_HCP_2019_v1.0/Atlas_notes.txt


— convert to nii 
mri_convert ?h.Glasser2016.mgz ?h.Glasser2016.nii

— use Freesurfer to move from fsaverage to sub01
mri_surf2surf —srcsubject fsaverage —trgsubject sub01 —sval atlasmgz/?h.Glasser2016.nii —tval sub01/SUMA/?h.Glasser_HCP.gii —mapmethod nnf —hemi ?h
cd sub01/SUMA

— use SUMA to resample the surface to std.141
SurfToSurf -i_gii std.141.?h.smoothwm.gii -i_gii ?h.smoothwm.gii -prefix res.141.lh -mapfile std.141.sub01_?h.niml.M2M -dset ?h.Glasser_HCP.gii -output_params NearestNode

the res.141.lh.Glasser_HCP.niml.dset that I got, will you say it’s in native space?

I compared this surface parcellation, with the surface file you uploaded yesterday, by projecting them to MNI152_a2009, and two surface looks exactly the same.

4

The standard mesh labels should apply across all datasets on a standard mesh, so results from one to another should be very, very similar.