How to compute cortical schaefer 300 parcellations

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Hi,

I understand that brainstorm does not currently support the Schaefer 300 parcellation options. I am trying to compute the Functional Connectivity for some EEG data, using the 7 network Schaefer 300 parcellation. Is there any way I can compute this using brainstorm.

Thank you very much!

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Unfortunately, there is not way to do it from Brainstorm.

To do so, you would need to recreate the Default anatomy by using FreeSurfer to segment the ICBM 2009c Nonlinear Asymmetric MRI file link

And once FreeSurfer finishes, run mris_ca_label link with the .gcs files that corresponds to the 300parces_7networks link

Note: mris_ca_label has to be called twice, once for each hemisphere (LH and RH).

Lastly, you can check how the current Default anatomy is processed in these links:

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Hi Raymundo,

Thank you for your quick reply.

I am not very familiar with using freesurfer. However, freesurfer was already run on the data I’m referring to, and has produced the surface files for each subject (eg. lh.sphere.reg) which I tried running with ‘mris_ca_label‘ as follows:

mris_ca_label -sdir . -orig sphere.reg Subject1 lh Subject1/surf/lh.sphere.reg lh.Schaefer2018_300Parcels_7Networks.gcs lh_300_v2.annot

Does this make sense? Or could you highlight the difference between using this reg file directly vs doing the 1st freesurfer step you mentioned previously.

And then, I tried steps on this page: How to import other brain atlases to use as scouts - #3 by Jeff_Eriksen . But I am unable to import the file successfully.

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This is correct, as you have already processed the individual's anatomy with FreeSurfer, what you describe will provide the 300Parcels_7Networks for this individual subject.

The steps I mentioned describe how to process the default anatomy so the 300Parcels_7Networks scout atlas will be available in the Default anatomy.

So, it mostly depends where (which cortex) connectivity is computed.

The simple way to import these annot files is to stored them in the label directory of the resulting files from MRI segmentation with FreeSurfer, then import the anatomy into Brainstorm. The annot files will be automatically detected and imported, more over, this atlas ( 300Parcels_7Networks) will be available for all the other cortical surfaces (e.g, surfaces with less vertices).

If you do now want (or cannot) reimport the anatomy, it is needed to import manually these annot files. Keep in mind that these annot files (L and R) are indices that make references to the full resolution cortical surfaces (L and R, with around 150K vertices each) obtained from FreeSurfer. As you, you need to:

  1. Import the Left hemisphere in Brainstorm.
    Right-click on the Subject, then Import surface , use FreeSurfer file type and select the file (e.g. lh.pial)

  2. If asked about apply the same transformation to surfaces, answer Yes.

  3. Double-click the imported surface (e.g. lh.pial)

  4. Go to the Scout label, then Atlas > Load atlas, select the FreeSurder atlas (*.annot) file type, and select the left annot: lh.Schaefer2018_300Parcels_7Networks.annot

  5. Close the figure with the surface.

  6. Repeat steps 1 to 5 for the right hemisphere files.

  7. Lastly, merge those surface. Select them both, then right-click Merge surface. Double-click the new cortex file, and check the scouts in the Scout tab.

Please note that this atlas will be available for the newly imported surface.