Brain Storm for ECoG

[I]Hi, My name is Diana and I am new to Brainstorm. I would like to use this software for ECoG analysis and would really appreciate some guidance. For now, three questions:

  1. Is there a tutorial specifically for ECoG ?
  2. Which of the following softwares would be the best to use to extract the cortex envelope: FreeSurfer, BrainSuite, BainVISA and CIVET. I previously used MRIcron but I tried with Brainsuite and it took more than one hour to get the results (without the label option). When I tried to import this to Brainstorm I wasn’t able to (message and folder for images attached). Any suggestions on what went wrong?
  3. The neuronavigation system I am using doesn’t allow me to get the exact coordinates so I can only have the snapshots of the individual electrodes and intra-op photos. In the Brainstorm software I will have to manually located the electrodes on the 3D model, right? And can I correlate with the 3D photos?

Thank you in advance,
Diana [/I]

Hi Diana,

  1. I’m sorry, there is no ECoG or sEEG tutorial yet.

  2. There is a great deal of personal preferences in this selection. The advantages of BrainSuite and FreeSurfer are the anatomical atlases they generate. FreeSurfer is more automatic, BrainSuite is faster (FreeSurfer can take 12-24hrs to run).
    I’m not sure I can help you with this error, I will forward your question to the BrainSuite developers.
    What version of BrainSuite are you using?

  3. There is not really any automated procedure for positioning the electrodes in the MRI. If you have the 3D positions of the electrodes in a text file, you can import them in Brainstorm, if not you have to mark them manually with the MRI Viewer.

Let us know if you need more help with the placement of the electrodes.


Hi Diana,
About your question 2, you have to run BrainSuite with Surface and Volume labeling option selected. Please follow the steps in
This sequence can take upto 2 hours. Please make sure that you follow the steps shown at the above mentioned link and check the outputs.

Hi, thank you very much for the replies. I am using Brainsuite 15 b and I redid the steps as per your suggestion. Nonetheless, I still wasn’t able to import the results (photo attached below). Please let me know what you think, Diana

BrainStorm is looking for file T1004.nii.gz . Can you please make sure that this file is also available in the same folder?

FYI: We improved significantly the tools available in Brainstorm for processing and visualizing SEEG and ECOG data, including new options for volume coregistration. They are now documented in a new tutorial: