Visualizing hemispheric differences- sans freesurfer

[liamc]

Hey Francois!

Is it possible to use Brainstorm to produce the following without Freesurfer, using the default anatomy?

3 separate diagrams showing hemispheric differences for various regions in volume, surface area, and cortical thickness. Being able to isolate, for example, the left hippocampus, color it a given color and label it, all the while the rest of the brain is still visible (albeit transparent to show this subcortical region)?

I've tried accomplishing this using the default anatomy's ICBM152 with not much luck

Is there a specific package or atlas I need to download, or tutorial I'm not understanding?

I have extremely layman experience in this but want to self-teach to be able to produce diagrams capturing the above. Any feedback or pointers would be greatly appreciated!

Thanks!!
Liam

[Francois]

@liamc

Being able to isolate, for example, the left hippocampus, color it a given color and label it, all the while the rest of the brain is still visible (albeit transparent to show this subcortical region)?

You could try the following:

1. Create a subject with NO default anatomy
2. Right-click on the subject > Use template > MNI > ICBM152
3. Run CAT12 on the ICBM152 MRI:
   https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12
4. Use one of the output atlases that include the regions you are interested in (e.g. AAL3):
   https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12#Volume_parcellations
5. For using as scouts:
   https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_atlases
6. For obtaining surfaces: Creating surfaces is not possible directly, but you can do the following:
   • Right-click on the volume parcellation of interest > Export to file > .nii
   • Right-click on the subject > Import surfaces > Select exported .nii with file format: Volume mask or atlas (subject space)
   • Then manage this just like the ASEG surface in the FreeSurfer output (extract only the regions of interest and merge them with the cortex):
     • https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Subcortical_structures:_aseg_atlas
     • https://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas#Select_deep_structures
     • https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#Subcortical_regions:_Surface

Example obtained for the hippocampus:

[liamc]

This is incredible! Thanks for getting back to me. I'm giving this a try now and will circle back with any additional questions.

Thanks again!
-Liam

[liamc]

I should have mentioned that I don't have Freesurfer, have downloaded the MATLAB 2020a package, and am using a Windows machine. Am I still able to do the above? I'm having a similar issue as another thread.

I downloaded the standalone version of cat12, but Brainstorm's toolbar ribbon isn't allowing me to specify the plugin's location with "Custom Install" as the CAT12 tutorial suggests, or by automatically having the plugin installed like this tutorial outlines: https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins

[Francois]

CAT12 is not available in the compiled version of Brainstorm, which you are apparently running.
If you have Matlab installed on your computer, run Brainstorm from Matlab instead of the compiled packaged.

If you don't then you need to find information on how to run the compiled version of CAT12 on your computer, run it on the MRI, then import the output in your Brainstorm database with the menu "Import anatomy folder", just like in the introduction tutorials.

[Francois]

@liamc

Being able to isolate, for example, the left hippocampus, color it a given color and label it, all the while the rest of the brain is still visible (albeit transparent to show this subcortical region)?

I've added a new menu to make this process much easier, documented here:

Select deep structures/cerebellum in script

Then, I used the "aseg atlas" from the default anatomy and combined it with the generated cortex from CAT12. This is definitely not a good idea. If Brainstorm can generate "cortex_cereb" without FreeSurfer, is there a way to do it without using the default anatomy? I added a new menu "Create surfaces", when you right-click on an atlas: https://github.com/brainstorm-tools/brainstorm3/commit/efb5c4a472b687e8fd24f87501a982d55c9e638a Start by updating Brainstorm. After the CAT12 segmentatio…