Is it necessary for loading aseg atlas one by one?

Discussions
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1

Hi, I'm doing the Volume source estimation for the subcortical areas which follows the guide:
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource. However, when I load the Aseg atlas like below:

image
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Is it necessary for me to load the atlas subject by subject without any scripts in Brainstorm?
Thanks

2

It is possible to automate importing the ASEG anatomical atlas as Scout atlas.

From the two available options: No overlap and Dilated which one are you using?
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_atlases

Asking, as if you are using the No overlap option, it is simpler to import the anatomical atlas from the one already imported in the Brainstorm when the segmented MRI was imported

3

I used the dilated option as below:

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4

@qjliu, thanks for the extra info.

With Brainstorm open, you can automatically load the aseg.mgz atlases with the code below.

Notes

  • Update your Brainstorm instance before trying this code.
  • Replace the PairsInfo with your data paths
  • You just one source file per Subject as the Atlases are common for all source files for a Subject
  • You can obtain the VolumeSourceFile in the GUI with right-click on the sources, then File > Copy file path to clipboard
% PairsInfo is a [Nx2] cell, where each row is for one subject, and is defined as:
% {VolumeSourceFile, FullPathAsegMgz}

PairsInfo = {'link|Subject01/Study01/results_MN_MEG_KERNEL.mat|Subject01/Study01/data_001.mat', ...
            '/home/user/subject01/anatomy/mri/aseg.mgz'; ...
            'link|Subject02/Study01/results_MN_MEG_KERNEL.mat|Subject02/Study01/data_001.mat', ...
            '/home/user/subject02/anatomy/mri/aseg.mgz'}

for iPair = 1 : size(PairsInfo, 1)
    % Open volume sources on MRI 3D slices
    view_surface_data([], PairsInfo{iPair, 1});
    % Import Atlas from aseg.mgz file
    % 'MRI-MASK' means 'Volume mask or atlas (dilated, subject space)'
    panel_scout('LoadScouts', PairsInfo{iPair, 2}, 1, 'MRI-MASK');
end
5

Thank you very much! I will try it later.

6

By the way, if I choose the overlap option, can I also use the script to load the ASEG atlas?

7

Absolutely, just replace 'MRI-MASK' with ''MRI-MASK-NOOVERLAP''