Problem loading surface based parcellation

Dear All,

I am having some difficulty in using the Gordon parcellation ( for surface based connectivity (specifically the 164K surface version)

If I view this parcellation using connectome workbench it looks as one would expect:

However if I view it using nilearn:

from nilearn import plotting, surface, datasets
parcellation = surface.load_surf_data(atlas_l_path)
fsaverage = datasets.fetch_surf_fsaverage(mesh='fsaverage')
plotting.plot_surf_roi(fsaverage['pial_left'], roi_map=parcellation,
                       hemi='left', view='lateral',
                       bg_map=fsaverage['sulc_left'], bg_on_data=True,

The rois are broken up and shuffled across the cortex,
Screenshot 2020-09-08 at 10.46.49

This is reflected in the fact that when I try and build a connectivity matrix the expected structure is not seen.

def surface_conn(sub_id, denoised_path):
    atlas_l_path = f'/home/k1201869/glu_rs/data/atlas_data/gordon/notworking'
    atlas_r_path = f'/home/k1201869/glu_rs/data/atlas_data/gordon/notworking'
    surf_image_l_path = f'{denoised_path}/sub-{sub_id}/regress/lh.sub-{sub_id}_residualised.mgz'
    surf_image_r_path = f'{denoised_path}/sub-{sub_id}/regress/rh.sub-{sub_id}_residualised.mgz'

    surf_image_l = surface.load_surf_data(surf_image_l_path)
    atlas_image_l = surface.load_surf_data(atlas_l_path)
    surf_image_r = surface.load_surf_data(surf_image_r_path)
    atlas_image_r = surface.load_surf_data(atlas_r_path)
    l_roi_timecourses = []
    # We don't include the first roi as this is background
    for i in np.unique(atlas_image_l)[1:]:
        roi_idxs = np.where(atlas_image_l==i)
        l_roi_timecourses.append(np.mean(surf_image_l[roi_idxs], axis=0))

    r_roi_timecourses = []
    for i in np.unique(atlas_image_r)[1:]:
        roi_idxs = np.where(atlas_image_r==i)
        r_roi_timecourses.append(np.mean(surf_image_r[roi_idxs], axis=0))

    bilat_timecourses = np.array(l_roi_timecourses + r_roi_timecourses)
    connectivity_matrix = np.corrcoef(bilat_timecourses)

    return connectivity_matrix

So it seems as though when loading the parcellation with nilearn the vertices are getting shuffled, I wonder if anyone has any advice about how to fix this?



Edit: I think I just need to convert from HCP to FS space following the steps here:

I’d agree with the path you suggested in your edit ! To add a bit more context: nilearn currently only works with giftis in FS space, so it wouldn’t recognize the same information in a dlabel.nii that ConnectomeWB will.

I think the steps outlined in the figshare link you shared are generally right, although I don’t think you’ll want to do the final step (converting to .annot), and instead just pass the gifti files !

Let us know how it goes !

My understanding is that the connectome WB mesh is not the fsaverage one, so you would need to resample the ROI definifiotn on fsaverage7 mesh. Is this what you mean @emdupre ?

Yes, exactly ! The figshare link contains instructions for projecting the HCP-MMP1.0 parcellation from fsLR (used across HCP) onto fsaverage (the high resolution, 164k vertices mesh).

As a follow-up: reviewing the code, I think you’re right @rob that plot_surf_roi should take the .annot file as an roi_map argument. So I’ll be curious to know if the updated files work for you !

Thanks for the input!

A few less steps are required than in the figshare. Instructions below for right hemisphere:

  1. Download from

and from


wb_command -label-resample Parcels_R.func.gii BARYCENTRIC right.fsaverage164.label.gii



I’m a bit confused about the wb_command commands to resample an hcp cifti surface data (not labels) to fsaverage, and vice-versa. I’m trying to follow the basic commands done here:


wb_command -cifti-separate rfMRI_REST1_LR_Atlas_stats.dscalar.nii COLUMN -metric CORTEX_LEFT cor_left.func.gii -metric CORTEX_RIGHT cor_right.func.gii

I believe I need to apply the following command:

wb_command -metric-resample cor_right.func.gii ??

But I’m confused which files I need to use as the current sphere and new sphere options?

Thanks in advance,


Hi @tomvanasse !

The HCP provides instructions on how to map between fsLR and fsaverage space in their wiki here.

The document linked in that answer (document link) provides step-by-step instructions on which files should go where in the wb_command -metric-resample command, as well as a link to where you can download the relevant template files.

Hope that helps !

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