I suppose that some regions are not defined with coarse grid and surface based atlases.
Indeed, the ROIs in the Schaefer400 atlas can be smaller than the 5mm grid.
Therefore some of the Schaefer400 would be missing if you use it to define volume scouts.
So my question is : how can I have the same pre-post segmentation(volumetric or cortical) so I can export the scouts /ROIs, correctly excluding those which are removed with surgery?
In understand that you want to:
- delineate the resection in the post-surgery MRI
- get the corresponding scouts in the pre-surgery MRI
The best solution probably depends on what you want to do with this result.
a) Is it only to be able to represent the resection in a standard space (ie. the list of parcels from the Schaefer400 parcelation)? Or
b) is it for doing some ROI-based source-level analysis in Brainstorm?
First of all, I don't think that trying to run the segmentation of the post-resection MRI would help much.
If you are interested in the a list of source points that are included in the resection, you should probably try to create a new volume scout (in a new volume atlas) from a grid covering the entire head that covers the resection, by drawing it point by point on the post MRI (read the tooltip for the
Create scout button it should explain how to do this).
Then to get the list of grid points included in a scout, this is an information that you can find in the cortex surface structure (field
You can finally compare the list of vertices in this resection scout, with the list of vertices in all the scouts of the Schaefer400 atlas. This requires some Matlab scripting, the function
ismember might help.