Exporting downsampled subject cortex to Freesurfer with two hemispheres separately

1

Dear Brainstorm community,

I am hoping to use the cortex_15002v generated for each subject by Brainstorm for an fMRI analysis (I have no idea if this is possible, but am interested). Accordingly, I exported the cortex file as a .fs file, and looked at it using freeviewer. It looked good, but as I am trying to replicate a freesurfer folder that could be imported for fMRI analysis, is there a way to export the cortex as both left and right hemispheres separately? Also, can anyone recommend or share any caveats with trying to do this analysis?

Best,
Pauk

2

If you want to export the two hemispheres separately, you need to import the FreeSurfer folder manually instead of using the menu "Import anatomy folder":
https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Manual_import_of_the_anatomy

Isn't there any tool for downsampling a surface directly in FreeSurfer?
It sounds quite cumbersome to import the surfaces in Brainstorm only to reduce the number of vertices... Maybe you could ask the FreeSurfer community?

3

Dear Francois,

thank you for the reply.

There should be a tool as you suggested in FreeSurfer which I'm currently searching for.

Ultimately, I want to relate the fMRI connectivity to the EEG source localization results, which is why I want to do both analyses in the same space using the same cortex, so I can relate the two metrics on a vertex by vertex basis.

Speaking to the fMRI connectivity community, they suggested that I first run a normal fMRI analysis pipeline, and then simply downsample the subject-specific results to the Brainstorm 15002v cortex. However, to do so, I believe I'll need the sphere.reg files for the 15002v cortex of each subject. How can I get these? I can only find how to view them the spheres. Sorry if my questions aren't making sense...

Best,
Paul

4

fMRI gives you spatial information, EEG temporal information. It can be complicated to relate the two in space, the spatial resolution of the EEG source modeling being very low. Making use of the combination of the two modalities can be done in different ways, see for instance these articles:
https://www.nature.com/articles/nn.3635
Similarity-Based Fusion of MEG and fMRI Reveals Spatio-Temporal Dynamics in Human Cortex During Visual Object Recognition | Cerebral Cortex | Oxford Academic
https://www.biorxiv.org/content/10.1101/095620v1

Speaking to the fMRI connectivity community, they suggested that I first run a normal fMRI analysis pipeline, and then simply downsample the subject-specific results to the Brainstorm 15002v cortex. However, to do so, I believe I'll need the sphere.reg files for the 15002v cortex of each subject. How can I get these?

The downsampled registered spheres are saved in the low-resolution cortex surface:
https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#On_the_hard_drive:_Surface

You could probably import the high-resolution fMRI results projected to the surface in Brainstorm similarly to the thickness maps (last steps of this section: https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Manual_import_of_the_anatomy) and then project them to the low-resolution surface (15000V).