Schaefer parcellation 100Parcels_7Networks labels

Hello,
The Schaefer parcellation-100Parcels_7Networks in Brainstorm uses the labels "LH_Background+FreeSurfer_Defined_Medial_Wall," as specified in the link below:

How can I modify these labels so that I use "lymph node and vascular labels" instead of the default labels used in Brainstorm?

Thank you!

Hi @niloofar

The atlas information is stored in the surface files as a structure under the Atlas field.
If you want to edit the names, one possible option is to edit the surface file; you can export it to Matlab, edit the Atlas field, and then import it back to Brainstorm.

You can view the following, right click on the surface file, then File > View File Contents

in my example, the Schaefer parcellation-100Parcels_7Networks is saved as struct 8, you can scout you need to edit and then change the name

You can export the file to Matlab to edit: Right click > File> Export to Matlab, and then you can edit and import it back

Hi @tmedani,

Thank you for the prompt response. My question is not just about changing the labels—I also need to determine the corresponding vertices and seeds.

In Brainstorm, the Schaefer atlases in the Default anatomy are generated using the mris_ca_label command with the provided .gcs files:

How can I adapt this to identify the locations and corresponding labels for "lymph node and vascular labels" referenced in this file:
Schaefer2018_100Parcels_7Networks_order_LUT.txt?

Thanks,
Niloofar

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@Anand_Joshi do you have any recommendation?

FOr the list of vertices on each schouts, those are also in figure I shared earlier (highlighted in green here):

@niloofar, the link that you shared is for anatomical atlases (not to be confused with Scout atlases in Brainstorm), so a MRI volume would have these values (column #No. ), and the lookup table (LUT) is used to get the labels.

So, to have these labels (# lymph node and vascular labels), you would need to run the specific MRI segmentation to identify them. There is not an equivalent between Schaefer labels and those.