Glasser to Yeo atlas label matching

[Panos Fotiadis]

Hi all,

I am interested in assigning each ROI within the Glasser atlas (360 ROIs) to their corresponding Yeo resting state network (both the 7 Networks and the 17 Networks classification). I am attempting to do this by loading (via ciftiopen) both the Glasser atlas (file name: Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii) and the resting state fs32k dlabel file available at https://balsa.wustl.edu/study/show/WG33 (file name: RSN-networks.32k_fs_LR.dlabel.nii) in MATLAB. The total number of vertices in each case are slightly different, however, presumably due to the inclusion of the medial wall in the latter file (Glasser atlas file: 59412 vertices; RSN file: 64984 vertices). 

Therefore, I was wondering: Is there a way to either convert the Glasser atlas file to its 64984 vertices version, or the RSN file to its 59412 vertices version, so that when I load both files on MATLAB there is a 1-1 correspondence between their vertices?

Thanks in advance!

Panos

[Coalson, Timothy Scott (S&T-Student)]

Two ways to do this: if you are using https://github.com/Washington-University/cifti-matlab , you can use cifti_struct_dense_extract_surface_data() to isolate one hemisphere while adding the medial wall indices back in (and the matching _replace_ function to do the reverse with whatever data you want to save back out).

Or, use wb_command -cifti-create-dense-from-template , using one file as the template, and use the other in a -cifti argument.

Tim

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Sent: Thursday, October 28, 2021 10:59 PM
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Subject: [hcp-users] Glasser to Yeo atlas label matching

 

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[Panos Fotiadis]

Works great, thank you Tim!

Panos

[Tamás Andrei Földes]

Dear Panos,

Could I ask you to share how you did this? I'm not familiar with working with surface files and would like to get the same type of label matching done ...

Thanks in advance!

Tamas

[Panagiotis Fotiadis]

Hi Tamás,

Yeah, absolutely, and apologies for the delayed response. The command I used was:

wb_command -cifti-create-dense-from-template RSN-networks.32k_fs_LR.dlabel.nii Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR_64984_vertices.dlabel.nii -cifti Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii

In order to run this, you would need to download the RSN-networks.32k_fs_LR.dlabel.nii file from: https://balsa.wustl.edu/study/show/WG33 

and the Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii file from: https://balsa.wustl.edu/file/3VLx 

This command will give you the output file: Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR_64984_vertices.dlabel.nii which is the Glasser atlas in its 64984 vertices version, and matching the number of vertices in the Yeo resting state networks file (RSN-networks.32k_fs_LR.dlabel.nii).

Cheers,

Panos

--

Panagiotis Fotiadis

Ph.D. Candidate | Neuroscience Graduate Group

Perelman School of Medicine, University of Pennsylvania

B.Sc. Mathematical Biology, 2012 | University of Michigan, Ann Arbor

Email: pfo...@gmail.com

[Tamás Andrei Földes]

Thank you. Would it be too much to ask you for a table (.csv?) of the Glasser labels matched up with the Yeo 7 and 17 networks as a backup in case I horribly mess up without noticing?

Thank you in advance,

Tamas

[Harms, Michael]

 

I don’t know if anyone has gone through the process/effort of assigning the Glasser parcels to either the Yeo 7 or 17 networks.

 

A network assignment of the Glasser parcels was done in this paper https://www.ncbi.nlm.nih.gov/pubmed/30291974

which has a GitHub with their assignments available here: https://github.com/ColeLab/ColeAnticevicNetPartition

 

 

-- 

Michael Harms, Ph.D.

-----------------------------------------------------------

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.                        Tel: 314-747-6173

St. Louis, MO  63110                          Email: mha...@wustl.edu

 

From: Tamás Andrei Földes <foldes...@gmail.com>
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Date: Friday, January 27, 2023 at 7:04 AM
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Cc: Panos Fotiadis <pfo...@gmail.com>, HCP-Users <hcp-...@humanconnectome.org>, "tsc...@mst.edu" <tsc...@mst.edu>, Tamás Andrei Földes <foldes...@gmail.com>
Subject: Re: [hcp-users] Glasser to Yeo atlas label matching

 

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