Question regarding fsaverage

[Erika Nolan]

Hi there

 

I am using the HCP S1200 Freesurfer data (native data). I would like to know which fsaverage was used during recon all- to calculate the transforms and where may I find the scripts folder for each subject (as is normally an output of recon-all in the regular FS pipeline). 

 

We have some commands we usually use with the regular FS pipeline and want to apply them to HCP subjects. To do so, we need the fsaverage folder that was used during recon-all of the HCP subjects.

 

Thank you for your help! 

Erika

____________________________

Erika Nolan 

PhD Candidate, Clinical Psychology

Department of Psychology, McGill University

Department of Neurology and Neurosurgery, Montreal Neurological Institute

[Harms, Michael]

 

All the usual FS output is located in the $StudyFolder/$SubjID/T1w/$SubjID folder.

We used whatever version of ‘fsaverage’ is the default in ‘recon-all’.

 

Cheers,

-MH

 

-- 

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: Erika Nolan <erika...@mail.mcgill.ca>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, May 18, 2022 at 10:31 AM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Subject: [hcp-users] Question regarding fsaverage

 

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[Erika Nolan]

Hi everyone, 

Following-up on my previous email. I am using the HCP S1200 dataset and have manually drawn surface labels on the native surfaces. Now I need to convert these labels to fsaverage to compute a group-level analysis - does anyone know how to do this? 

I appreciate your help,

Erika

____________________________

Erika Nolan 

PhD Candidate, Clinical Psychology

Department of Psychology, McGill University

Department of Neurology and Neurosurgery, Montreal Neurological Institute

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From: Erika Nolan
Sent: May 18, 2022 11:29 AM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Subject: Question regarding fsaverage

 

[Tim Coalson]

There are three choices of registration here, MSMAll which focuses on functional alignment by using resting state data, myelin, and cortical thickness, MSMSulc which aligns folding like freesurfer but with less distortion to avoid overfitting that reduces functional alignment, and the freesurfer sulc registration.  We generally recommend MSMAll.

The MNINonLinear/Native folder should contain sphere surfaces for each of these registrations.  For MSMAll, MSMSulc, and reg.reg_LR (note: reg.reg_LR in S1200 probably used an older group registration between freesurfer and fs_LR, so it may not be the right way to use freesurfer's registration), these spheres are registered to fs_LR, not fsaverage (fs_LR uses the same vertex number for the equivalent location on the other hemisphere, fsaverage has unrelated vertex numbering across hemispheres).  If you specifically need to use the fsaverage mesh, we have a precomputed group registration from fs_LR to fsaverage in our pipelines:

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

We wrote instructions for going from fs_LR to fsaverage, and freesurfer native mesh outputs to fs_LR, as we recommend generating results in fs_LR space to make comparisons across all HCP projects easier:

https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?

It doesn't cover resampling HCP data on native mesh to fsaverage, but if that is still what you need, these instructions may be useful as examples.

If you would prefer the freesurfer registration, the sphere.reg.native.surf.gii files may be the freesurfer registration merely converted to gifti format, so you can use wb_command to do the resampling.

Tim

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