AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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August 14, 2017 12:11AM
Dear afni experts,

I'm using AFNI/FreeSurfer/SUMA tool chain, and CoSMoMVPA matlab package to do surface-based MVPA, and encountered a few problems. Any help would be highly appreciated.

1) According to the CoSMoMVPA demo, its surface-based searchlight routine seems to require merged hemisphere (mh, as opposed to lh+rh) format of the FS surface (in *.asc file). However, @SUMA_Make_Spec_FS generates separated (lh+rh) files. I used the following pseudo matlab code to merge the two:
[left_verts, left_faces] = read_asc('lh.asc');
[right_verts, right_faces] = read_asc('rh.asc');
right_faces(:,1:3) = right_faces(:,1:3) + size(left_verts,1);
write_asc('mh.asc', [left_verts; right_verts], [left_faces; right_faces]);
It seemed to work (but is it the correct way to do this?). But when I visualize the merged surfaces, I realized that the spatial location of the vertices from the two hemispheres in volumetric space are overlaped. Is that OK? Specifically, will that affect neighborhood definition or multiple comparison correction?

2) After I got the surface-based searchlight result with CoSMoMVPA in a *.niml.dset file, which contains the results for both hemispheres, I tried to load and visualize it with SUMA. However, with SUMA object controller, I could load the dset onto only one of the two hemispheres (either left or right, but not both). When I loaded the same dset to the second hemisphere, SUMA complained and failed.
Is there a way to visualize merged hemisphere dset with SUMA?

Thanks~
Chencan
Subject Author Posted

How to load merged hemisphere dset in SUMA?

herrlich10 August 14, 2017 12:11AM

Re: How to load merged hemisphere dset in SUMA?

Daniel Glen August 14, 2017 12:27PM

Re: How to load merged hemisphere dset in SUMA?

herrlich10 August 15, 2017 11:44AM

Re: How to load merged hemisphere dset in SUMA?

Daniel Glen August 15, 2017 03:39PM

Re: How to load merged hemisphere dset in SUMA?

nick August 22, 2017 12:21PM

Re: How to load merged hemisphere dset in SUMA?

Alireza November 03, 2021 05:10PM