Volumetric ROI Overlap Using Standard Volume Atlases

Dear Francois,

I am currently computing a volumetric source localization using the default ICM152 anatomy with the cerebellum included (resolution 5mm). After my sources are computed on the volume grid I am trying to import standard volumetric ROI atlases (currently trying the AAL atlas from micron) to use for ROI analysis. I am importing the atlas ROIs as scouts using the method in this tutorial:


After the AAL atlas is loaded I noticed that the ROIs look to be correct in general but that many of the ROIs have significant overlap. I have checked this with other standard atlases as well from other software and found the issue to be consistent.

Do you know why vertices in the imported ROIs are not unique to one ROI?
Do you have any suggestions on how to import the atlases without this overlap?

It seems to me that the ROIs should have no overlap unless I am misunderstanding how these standard atlases are generated.

You are right, this is a problem.

I added two more options to the list of file formats when importing the volume atlases: "dilated" or "no overlap". Just update Brainstorm, and the former should give you what you want. Please let me know if this is not the case.

I added a section in this tutorial to explain the difference between the options:

Let me know if this is not clear enough (feel free to report any typo or syntax issues as well)

Thanks a lot. Your update fixed this issue. I have modified your tutorial text below to read a little more clearly.

When importing a volume atlas, you have the option to dilate or not to dilate each ROI mask (the voxels associated with this ROI in the input volume) before it is converted into a scout (a list of the indices of grid points). This adjusts the import method depending on what you are planning to do with these scouts.

  • No overlap : Each point of the source grid is associated with one and only one scout, as it was in the imported atlas volume. You should select this option if you want a strict parcellation of the source grid, eg. if you are using all the scouts at once, this avoids any unnecessary signal mixing between different scouts.

  • Dilated : The spatial sampling of the source grid is typically much lower (~5mm) than the resolution of the volume atlas you import (~1mm), which may cause small ROIs to disappear completely. If you are interested in one small ROI of the atlas, it might not be associated with any source point, and you wouldn't be able to retrieve any source signal for it. To ensure most ROIs are attached to at least one grid point, this option dilates each ROI before it is associated with points of the source grid. This option creates overlap between the scouts, which causes most grid points along the edges of ROIs to be associated with two or more scouts.

Thanks for proofreading! :slight_smile: