CCEP computation with Brainstorm

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Visualization of CCEPs. The average response of a stimulation train was extracted from SEEG data using Brainstorm .

Disclaimer

The methods and software used in this tutorial have not been certified for clinical practice and should be considered for research purposes only.

About this tutorial

Electrical stimulation applied (sub)cortically can elicit CCEPs, recorded remotely from the stimulation site. The objective of this tutorial is to guide HIP users in computing the average response of a stimulation train extracted from a SEEG file using Brainstorm. It primarily consists of a video demonstration and should be viewed as an introductory tutorial because it does not go into all the intricacies of the processing steps used to compute CCEPs.

For more in-depth information regarding some of the processing steps illustrated in the video, please refer to the following official tutorials:

Requirements

There are no technical requirements to follow this tutorial because the dataset and software are available on the HIP.

HIP software used in this tutorial:

HIP dataset used in this tutorial:

  • “CCEP tutorial dataset” located in the shared tutorial_data folder.

Prepare the working environment

This tutorial relies on data available in the “CCEP tutorial dataset” located in the read-only shared folder called tutorial_data, and the following file has to be copied in your Private Space (this is demonstrated in the video tutorial):

  • sub-anon_task-stimulation_run-01.edf

This tutorial requires to use Brainstorm, which is available on the HIP, and it is advised to initiate a new Desktop. Please, refer to the How to use Desktops and run applications from the App Catalog guide if you need help with this step.

Compute cortico-cortical evoked potentials

Important

Applications running in a Desktop environment have access to your Private Space data under the /home/<HIP_USER>/nextcloud directory. Any data and/or configuration file outside of this directory will be lost when the application or desktop are closed. This is the only persistent directory as it is tied to the HIP user’s Private Space at application startup. Make sure you are always working within the /home/<HIP_USER>/nextcloud directory when using applications.

There are different ways to compute CCEPs depending on your data and the analyzes you want to perform. The processing steps used in this tutorial are derived from a pipeline developed during The Functional Brain Tractography Project (see [Trebaul_2018c] for full scientific details) which has been simplified for demonstration purposes. Notably, this tutorial shows how to: (1) import raw SEEG data into Brainstorm; (2) extract a stimulation train; (3) mark bad channels; (4) detect the stimulation artifacts (individual pulses); (5) apply bipolar montage; (6) remove stimulation artifacts; (7) apply a band-pass filter; (8) compute the average response across all pulses. Depending on your objective, some of these steps might not be relevant/necessary or might be executed in a different order.

This video tutorial (14’04’’) relies on data publicly available on the HIP and describes the different steps to compute CCEPs using Brainstorm:


References

Trebaul_2018c

Trebaul, L., Deman, P., Tuyisenge, V., Jedynak, M., Hugues, E., Rudrauf, D., Bhattacharjee, M., Tadel, F., Chanteloup-Forêt, B., Saubat, C., Reyes Mejia, G.C., Adam, C., Nica, A., Pail, M., Dubeau, F., Rheims, S., Trébuchon, A., Wang, H., Liu, S., Blauwblomme, T., Garces, M., De Palma, L., Valentín, A., Metsahonkala, E.-L., Petrescu, A.M., Landré, E., Szurhaj, W., Hirsch, E., Valton, L., Rocamora, R., Schulze-Bonhage, A., Mîndruţă, I., Francione, S., Maillard, L., Taussig, D., Kahane, P., David, O., 2018. Probabilistic functional tractography of the human cortex revisited. NeuroImage 181, 414–429. doi:10.1016/j.neuroimage.2018.07.039.