Obtaining 10k midthickness surf.gii files

[Thomas Nichols]

Hi HCP folks,

I'm doing work trying to reproduce results from an paper from 2019 (Hong et al, 2019) that seemed to use an initial product of the HCP Young Adult study, specifically 

Q1-Q6_R440.{L,R}.midthickness.10k_fs_LR.surf.gii

I have scoured the internet and have not found this specific file, in particular looking at 

https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/standard_mesh_atlases

but there I find (a) there are no midthickness files and (b) no 10k versions.

We did find average.R.midthickness.10k_fs_LR.surf.gii in Balsa but it is for Macaque.

I understand that you can use wb_command to resample meshes, but I am unsure -- without knowing more -- that I would be guaranteed to get the *exact* same 10k space in the file above. 

Thanks for any tips!

-Tom

Hong, Seok Jun, Reinder Vos de Wael, Richard A.I. Bethlehem, et al. ‘Atypical Functional Connectome Hierarchy in Autism’. Nature Communications 10, no. 1 (2019): 1–13. https://doi.org/10.1038/s41467-019-08944-1.

__________________________________________________________

Thomas Nichols, PhD

Professor of Neuroimaging Statistics

Associate Head, Big Data Institute

Nuffield Department of Population Health | University of Oxford
Big Data Institute | Li Ka Shing Centre for Health Information and Discovery
Old Road Campus | Headington | Oxford | OX3 7LF | United Kingdom
T: +44 1865 743590 | E: thomas....@bdi.ox.ac.uk
W: http://nisox.org | http://www.bdi.ox.ac.uk

[Glasser, Matthew]

Hi Tom,

 

We didn’t make that surface; however, I suspect it is probably the 10k icosohedron: 10242 vertices.  We have code for making arbitrary surface meshes, but I don’t think anyone else has that or is likely using it.

Matt.

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[Tim Coalson]

The help info of wb_command -surface-create-sphere has an example sequence for making left and right fs_LR-style spheres of an arbitrary resolution, which you can then treat as if they are another resolution of fs_LR.  It is somewhat likely, given that they followed fs_LR naming patterns, that this is what they did, but the only way to be sure is to contact the authors to obtain the files or instructions.  However, 10k is also one of the typical recursive icosphere resolutions, so it is possible they used sphere(s) from another source instead, in which case spheres generated by wb_command will not work (the good news is, wb_command-generated spheres have a much different vertex order than typical recursive spheres, so data displayed on the wrong type of 10k surface should look very obviously wrong).

https://www.humanconnectome.org/software/workbench-command/-surface-create-sphere

As a broader note, for people who are interested in a dimensionality reduction to something on the order of 1,000 vertices, we recommend parcellating instead (with the HCP MMP or another areal-feature-based parcellation), because severe downsampling does a lot of mixing of data between neighboring cortical areas.

Tim

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[Thomas Nichols]

OK! Thanks for speedy replies Tim, Matt!  I'll reach out to the authors and see if they have those original file

-Tom

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