FieldTrip workshop in Singapore

  • By whom: Maria Carla Piastra, Sophie Schrader and Simon Homölle
  • When: 17 June 2018
  • Where: Educational courses at the OHBM2018 conference in Singapore

What is the workshop about?

The course is aimed at researchers who want to learn how to do MEG and/or EEG source reconstruction. We expect that you know the basics of MATLAB and that you already have experience with MEG/EEG preprocessing and analysis.

In this intense one-day workshop we will explain state-of-the-art MEG and EEG source reconstruction methods. Special emphasis will be given to new features available now in FieldTrip to solve the EEG and MEG forward solution with advanced finite element methods. These techniques are the results with the collaboration with WWU Muenster University where the SimBio and duneuro forward problem solutions have been embedded in FieldTrip pipelines.

The workshop will consist of a number of lectures, followed by hands-on sessions in which you will be tutored through the complete analysis of a MEG, EEG and MRI data set using the FieldTrip toolbox. The focus is in source reconstruction, particularly in advanced techniques available to solve the EEG and MEG forward problem. As the focus is on source reconstruction, topics that will NOT be covered in great detail are segmenting, artifact handling, averaging, frequency and time-frequency analysis, statistics. For the hands-on sessions you should bring a laptop with MATLAB installed.

More information about the program can be found below.

The SimBio software is described in detail here. The integration with FieldTrip is described in the reference below. Please cite this reference if you use the FieldTrip-SimBio pipeline in your research.

Vorwerk, J., Oostenveld, R., Piastra, M.C., Magyari, L., & Wolters, C. H. The FieldTrip‐SimBio pipeline for EEG forward solutions. BioMed Eng OnLine (2018) 17:37. DOI: 10.1186/s12938-018-0463-y.

How should you prepare for the workshop?

In this workshop we will have a steep learning curve. We will move from basic preprocessing to source-level analysis. Given the limited amount of time, it is important that you come well prepared.

If you are not familiar with MATLAB or are not certain about your MATLAB skills, please go through the “MATLAB for psychologists” tutorial on http://www.antoniahamilton.com/matlab.html

Please read the FieldTrip reference paper to understand the toolbox design.

In the first workshop hands-on session we will start with preprocessing EEG data, but will not spend too much time on understanding how MATLAB works and how FieldTrip organizes the data. Therefore if you have never done any FieldTrip analysis in MATLAB before, you should read this introduction tutorial. We will start at 9:00 sharp and will finish around 17:30.

What is the experiment about?

The experiment that the subject performed is a slight adaptation of the classical oddball experiment. The details about the experiment can be found here.

Schedule for Sunday

08:00-08:30 Welcome and getting started
08:30-9:20 Lecture - Preprocessing
9:20-10:40 Hands on - Preprocessing
10:40-11:00 Break
11:00-12:00 Lecture - Forward problem
12:00-13:00 Lunch break
13:00-14:00 Hands on - Forward problem
14:00-14:45 Lecture - Inverse problem
14:45-15:00 Break
15:00-16:00 Hands on -Inverse problem
16:00-16:30 Wrap-up-the-day: special topics, general questions and answers

Currently, the pipeline for computing the MEG forward problem solution has been tested on Ubuntu systems, where Matlab should be started with the following command:

BLAS_VERSION=/usr/lib/libblas.so LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6 ./matlab

Once Matlab is open, you need to issue the following command

clc;
clear;
close all;

restoredefaultpath    % restore default folder for matlab
path2ft_ohbm2018 = ''; % write your path
cd(path2ft_ohbm2018)

maindir = pwd;        % keep main path

cd FieldTrip % set up the path of fieldtrip
addpath([path2ft_ohbm2018,'/external_duneuro'])
addpath(pwd)
ft_defaults

cd(maindir)           % return to main

Please do NOT use the graphical path management tool from MATLAB. In this hands-on session we’ll manage the path from the command line, but in general you are much better off using the startup.m file than the path GUI.

Please do NOT add FieldTrip with all subdirectories, subdirectories will be added automatically when needed, and only when needed.

The restoredefaultpath command clears your path, keeping only the official MATLAB toolboxes. The addpath(pwd) statement adds the present working directory, i.e. the directory containing the FieldTrip main functions. The ft_defaults command ensures that all required subdirectories are added to the path.

If you get the error “can’t find the command ft_defaults” you should check the present working directory.

After installing FieldTrip to your path, you need to change into the hands-on specific directory, containing the data that is necessary to run the specific hands-on session. These folders are located in C:\FieldTrip_workshop\OHBM2018\data.