Inflated state viewing for *.gii files

AFNI Message Board
1

Hello!

I am wondering if there is any way to view an inflated version of *.gii surface files SUMA. The surface I am interested in inflating is a surface from an MEG data analysis software (Brainstorm) that I am interested in viewing in SUMA. This gii file is exported from the MEG software specifically for viewing in SPM, and it is possible to see an inflated view in SPM from this gii file, but I am not sure whether it is possible in SUMA.

At the moment, the surface loads fine into SUMA, I just can’t change viewing states.

Any guidance is appreciated!

Veronica

2

It should be doable. Can you post your commands for what you’re doing to open the files. Is there a .spec file exported from Brainstorm?

3

That’s a relief to hear! Here’s the command I use to load the file and the output that follows.

[dhcp58-238:~/Documents/SUMA_s03] etienne% suma -i_gii NewCarla_cortex.gii

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #1/1(Local Domain Parent), loading …
Warning SUMA_Make_Edge_List_eng:
Min/Max number of edge hosting triangles: [1/4]
Warning SUMA_Make_Edge_List_eng:
You have edges that belong to more than two triangles.
Bad for analysis assuming surface is a 2-manifold.
SUMA_Engine: Starting to listen …

The output from Brainstorm does not include a .spec file, but rather two .gii files and a .dat file. According to one of the designers of Brainstorm, one .gii file is the cortex surface and the other .gii file is a texture on this surface with the source values. I tried to attach the files in this post but I guess they are too large even when compressed.

The purpose of fussing with this is to compare the way SUMA and Brainstorm represent the sulci maps, because there is a distinct difference now despite the fact that both programs import from FreeSurfer-made surfaces. SUMA’s is very accurate to the FreeSurfer display, and Brainstorm’s is quite different, which we think is due to the way the surface is smoothed in their software. We were hoping to maybe get around this issue or at least diagnose the issue better by getting the Brainstorm surfaces into SUMA. Hope this helps give some context for the goal!

4

I’ll PM you upload instructions and take a look this week!

Is the eventual goal is to display the data/values on the surface within SUMA?

-Pete

5

Hi Pete,

Well, what I’m thinking is that there are two options.

One is to extract the surface from Brainstorm with the data/values on it and import into SUMA, assuming the weird smoothing that alters the sulcification isn’t imported along with it.

OR to export the data on the surface from Brainstorm as a NIfTI that’s coregistered to the subject’s anatomical used to generate the surface in the first place, then project that NIfTI data onto the SUMA surface as I’ve been doing with our fMRI data.

Do these seem like reasonable ideas? Is there something obvious to try that I’m missing?

Thank you! Veronica

6

Hi Veronica,

Those both sound plausible. I think in my mind it really depends on what type of source analysis method you’re doing… If it’s BEM, then hopefully we can get the direct to surface part working. But the NIFTI export is a good fallback if necessary.

I’ll confess, I’m an MNE user and haven’t done much with BrainStorm, so it’ll be an adventure. Upload link sent to you by email.

-Pete