Workshop on the ECoG forward solution using FEMfuns in FieldTrip at the Donders
- By whom: Maria Carla Piastra, Thom Oostendorp, Geertjan Huiskamp, and Robert Oostenveld
- When: 24 November 2022
- Where: Donders Centre for Cognitive Neuroimaging (DCCN), Kapittelweg 29, Nijmegen, room 2.258
- Audience: Researchers with previous knowledge of volume conduction modeling, source reconstruction, ECoG applications, MATLAB
What is the workshop about?
This workshop is aimed at researchers who want to learn about Electrocorticography (ECoG) forward computations. It is specifically about modeling potentials and current densities in the brain that are generated by stimulating electrodes or dipolar current generators. We expect that you know the basics of MATLAB and already have experience with anatomical MRI and intracranial EEG data.
In this workshop, we will introduce FEMfuns, a state-of-the-art ECoG tool for computing forward solutions in the case of both recording and stimulating electrodes. This tool and pipeline are the results of the project “Into the Brain” which was funded by StITPro as a continuation project of NeuroCIMT. The goal of this project was to create an easy-to-use interface to FEMfuns, which has been achieved by embedding it in FieldTrip. Details about FEMfuns can be read here and about its usability and its relevance here.
The workshop will consist of a number of short theoretical introductions, followed by hands-on sessions in which you will be tutored through the complete computation of ECoG forward solutions. The focus is on the creation and visualization of meshes and on the computation of forward solutions for recording and stimulating electrodes. The attendees will be divided into two groups of equal size so that half of the attendees will deal with recording electrodes simulations and the other half with stimulating electrodes simulations. ECoG signal processing is NOT part of this workshop.
More information about the program can be found below.
How should you prepare for the workshop?
During the workshop you will be using local machines and, in principle, you do not need your laptop with you. Please note that so far the code has been tested in Ubuntu machines with MATLAB versions not higher than 2021a. If you are not familiar with MATLAB or are not certain about your MATLAB skills, please go through the “MATLAB for psychologists” tutorial here.
Please read this paper to understand the relevance of the workshop, and the FieldTrip reference paper to understand the toolbox design. Here you can find the main output of the Into the Brain project.
We will start after lunch, at 12:30 sharp, and will finish around 17:00. If you come in advance, you can join us for a free lunch in the DCCN canteen, which is downstairs in the Trigon building.
Schedule.
| 12:00-12:30 | Lunch offered at Trigon Welcome |
| 12:30-12:45 | Welcome and get started: Thom Oostendorp (15mins): the project Into the Brain, technical details on installation/cloning |
| 12:45-13:30 | Introduction: Maria-Carla Piastra (15mins): what is the ECoG forward problem? what is FEMfuns? Geertjan Huiskamp (15mins): applications in epilepsy |
| 13:30-14:00 | Hands-on: creating and visualizing the mesh |
| 14:00-15:15 | Group1-Hands-on: compute and visualize potential with recording electrodes Group2-Hands-on: compute and visualize potential with stimulating electrodes |
| 15:15-15:30 | Break |
| 15:30-16:00 | Hands-on (exercises): what if the electrode size changes? which electrodes are injecting current? |
| 16:00-17:00 | Hands-on: try your own geometry/MRI data and ECoG electrode position |