Create cortial and sub-cortical atlases

[sravani1]

Hi there,

I am currently utilizing the DBA tutorial for calculating sources within deep cerebral structures. I am curious if there's a method to export the time series data of sub-cortical regions once the source estimation is completed. I aim to conduct source estimation of these sub-cortical regions and utilize their time series data for further analysis with a technique we're developing. Any assistance on this matter would be greatly appreciated.

Thanks for your consideration!

Best regards,
Sravani

[Sylvain]

Please see the last post of this thread.

[vidushani]

Hi,
I have a similar question. For instance, I can see that the DKT atlas has pre-defined sub-regions. But I cannot see a way to extract the time series of these sub-regions without manually selecting the relevant scouts manually.
Is selecting the sub-regions also possible through scripting? This funuctionality would be greatly appreciated.

[Raymundo.Cassani]

@vidushani

Is selecting the sub-regions also possible through scripting? This funuctionality would be greatly appreciated.

Yes, the same scouts in the GUI are available in the process Extract > Scout time series.
Be sure that you are working with the same Source file and that the same Atlas is selected.

Once you can extract the time series with the process, you can generate its respective script as indicated in the first section of the Scripting tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting

---

In your screenshot the atlas name starts with From volume: ... which suggest that your source space is the cortical surface. Please note that create surface atlases from volume anatomical parcellations is not advised. See the exchange in this other thread:

Connectivity between functional networks

Hello I am working on functional connectivity development in children's brains using EEG. I have a question To calculate the functional connectivity between brain networks, how can we adjust and select the scouts based on functional networks such as DMN, CEN, salience and etc.? I would be grateful if you could help me With respect,

[vidushani]

@Raymundo.Cassani

Once you can extract the time series with the process, you can generate its respective script as indicated in the first section of the Scripting tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting

Hi,

Thank you for your helpful comments. Just to confirm, if I want to extract the scouts on the occipital region, I would have to manually define the scouts within the region as follows, and cannot extract the regions (eg. parietal, occipital etc) automatically?

            sFiles_sc_ts = bst_process('CallProcess', 'process_extract_scout', loaded_sFile, [], ...                    
                'scouts',         {'DKT', {'cuneus L', 'cuneus R', 'lateraloccipital L', 'lateraloccipital R', 'lingual L', 'lingual R', 'pericalcarine L', 'pericalcarine R'}}, ...                    
                'scoutfunc',      'mean', ...  % Mean
                'isflip',         1, ...       % flipping sign of sources in same region, with opposite directions
                'concatenate',    0, ...
                'save',           1, ...
                'addrowcomment',  1, ...
                'addfilecomment', []);

[Raymundo.Cassani]

@vidushani

I would have to manually define the scouts within the region as follows, and cannot extract the regions (eg. parietal, occipital etc) automatically?

That is right, you need to create a Scout for your different regions of interests. They can be easily created as based on an existent atlas:

1. Create a copy the existent atlas:
   Menu: Atlas > New atlas > Copy current atlas
2. Merge the scouts into your regions of interests:
   Select the Scouts that correspond to one of you regions and use the menu: Scout > Merge