Question about -cifti-smoothing

[Miriam Klein-Flugge]

Dear all,

I have a quick question with regards to -cifti-smoothing. I am not too familiar with how the smoothing uses the specified -right-surface and -left-surface and wondered if these need to be subject-specific and whether and how smoothing will differ when specifying e.g. midthickness versus inflated surfaces here? 

What would be your recommended way of smoothing several participants? 

Thanks a lot!

Miriam  

==========================
Miriam C Klein-Flugge
University Research Lecturer

Department of Experimental Psychology and
Wellcome Centre for Integrative Neuroimaging
University of Oxford

http://users.ox.ac.uk/~xpsy0747/
@MKFlugge

[Glasser, Matthew]

I would use ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.${Hemisphere}.midthickness${RegString}.32k_fs_LR.surf.gii.  Keep in mind our cautions about smoothing, even on the surface: https://www.pnas.org/content/115/27/E6356.short

Matt.

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

The surfaces are used to determine the distance between vertices, which is needed in order to ensure the gaussian smoothing kernels used are as round as possible, and the correct size.  Inflated surfaces are not shaped like the real anatomy, and should only be used for viewing.  We generally use midthickness, and if using a group average surface, you should also provide corrected vertex areas to approximately compensate for how averaging surfaces across subjects reduces its folding.

If you are doing a study with both adults and children, or across species, or that would be sensitive to differences in brain size for other reasons, some thought should be put into exactly what a given smoothing distance means on each subject's surface, if doing the smoothing using individuals' surfaces.  Smoothing on the group average surface avoids this problem in one way by combining the same vertices with the same weights regardless of brain size, but on the other hand it ignores the effects of things like using the same voxel resolution on different sized brains.

Tim

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From: Glasser, Matthew <glas...@wustl.edu>
Sent: Tuesday, October 13, 2020 9:00 AM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Subject: Re: [hcp-users] Question about -cifti-smoothing

 

To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/197FD765-C23A-4FD7-8B6C-2D0D30FDB118%40wustl.edu.

[Miriam Klein-Flugge]

Thanks Tim & Matt, that is really helpful to know! 

Kind regards,

Miriam 

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