Vertices number from freesurfer and Brainstorm

Discussions
1

Hi all,

I want to generate a ROI file ('.annot') including both cortical and subcortical brain regions.

In Freesurfer, based on the fsaverage dataset, I have been able to parcellate the cortical areas and get the '.annot' file which includes only the cortical regions. The vertices number for one hemisphere is 163842.

ROIs
ROIs1501×839 231 KB

It surprises me when I saw the 'FSAverage.zip' file on website https://neuroimage.usc.edu/bst/download.php. I looked into the 'tess_aseg.mat' file and tried to get the vertices' index of subcortical areas, and incorporated them to the ROIs file I made from Freesurfer.

But the vertices number of this file are only 79114 for two hemispheres, so it is very difficult to be incorporated to the ROIs file I generated from Freesurfer (163842 vertices in one hemisphere).

So is there any fast way in brainstorm that I can get the ROIs file from subcortical brain regions with the same vertices number as I got from Freesurfer so I can incorporate them together?

Very appreciated if I can get any suggestions. Thanks.

Best,
Feng

2

The .annot files need to be loaded for each hemisphere separately.
You cannot use the Brainstorm template distributed on the website, you need to re-import the FSAverage anatomy folder manually (at step 5, add your own .annot files):
https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Manual_import_of_the_anatomy

3

Hi Francois,

Thanks for your reply. However, when I opened the FSAverage anatomy folder, there was no 'lh.pial, lh.white, rh.pial, rh.white' files anymore. There were only 'cortex' file with different resolution. Is there any way we can separate the 'cortex' file back to each left and right hemisphere? Otherwise it seems like we cannot map the '.annot' files into the surface.

Best,
Feng

4

Indeed, the separate hemispheres are deleted during the automatic import (step #14) or in the template distributed on the Brainstorm website.
You need to follow step by step the instructions I sent you to import the fsaverage anatomy you can find in your freesurfer installation folder.