Advanced MEG/EEG toolkit at the Donders

From May 27-31 2024 we will host our annual MEG/EEG Tool-kit course in Nijmegen. During this 5-day toolkit course we will teach you advanced MEG and EEG data analysis skills. Pre-processing, frequency analysis, source reconstruction, analysis methods such as RSA and TRFs, and various statistical methods will be covered. Furthermore, we will give special attention to new opportunities in experimental design and measurements with Optically Pumped Magnetometer (OPM) systems and mobile EEG.

The toolkit consists of a number of lectures, followed by hands-on sessions in which you will be tutored through the analysis of a MEG data set using the FieldTrip toolbox. Furthermore, we will schedule time for you to work on your own data under supervision of experienced tutors.

There are only 38 places available for this toolkit and from experience we expect the course to be over-subscribed. Participants will be selected on the basis of background experience, the research interest and the expectations on what to learn (see the questions during pre-registration). We prefer the group to be reasonably homogeneous in level and expertise of the participants, as this improves the overall interaction.

You can pre-register here, the deadline for pre-registration is April 15, 2024.

We will inform you as to whether you obtained a place in this course not later than Thursday April 29, 2024.

The fee is €550 for PhD students and €750 for senior researchers. If your institute is based in a low/middle income country, you will also be able to request a discount.

Program

Note that the tentative program below still might change a bit.

Monday May 27, 2024

Tuesday May 28, 2024

Wednesday May 29, 2024

Thursday May 30, 2024

Friday May 31, 2024

Practicalities

This will be an in-person event with no possibilities for hybrid or online attendance.

Wifi access

If you need wifi access and you don’t have a eduroam account through your institution, it is possible to get a visitor access. This needs to be renewed each day. Please follow the instructions on this intranet page.

FieldTrip playground sessions: BYOD (bring-your-own-data)

A large part of the toolkit will consist of playground sessions, in which ideally you will be working on your own data. Please think a bit about what you want to achieve, and ensure that you have your data easily accessible (preferably, if possible on the laptop that you bring yourself, or on an external USB-drive). If you don’t have data to work with, please let us know in time so that we can think about an alternative. We have plenty of tutorial data available, so this can be used to practice your data analysis skills.

Test your MATLAB and FieldTrip installation in advance

For the hands-on sessions we assume that you will work on your own laptop computer. To have a smooth experience - and to avoid having to spend precious debugging time during the hands-on sessions - we recommend that you test your MATLAB and FieldTrip installation in advance, and download the data that we will need during the hands-on sessions. Before running this test, we recommend that you prepare your laptop as per the instructions in the next section, which explains in some more detail what needs to be downloaded in advance, as well as how you can easily obtain (and install) a copy of FieldTrip on your computer.

Getting started with the hands-on sessions

For the hands-on sessions we assume that you have a computer with a relatively recent version of MATLAB installed (preferably < 5 years old, >= 2019a/b).

To ensure that everything runs smoothly, we recommend that you set up your computer with a clean and well-tested version of FieldTrip, and download the data that are needed for the hands-on sessions in advance.

To get a recent copy of FieldTrip, you can follow this link, download the zip-file, and unzip it at a convenient location on your laptop’s hard drive. Alternatively, you could do the following in the MATLAB command window.

% create a folder that will contain the code and the data, and change directory
mkdir('toolkit2024');
cd('toolkit2024');

% download and unzip fieldtrip into the newly created folder
url_fieldtrip = 'https://github.com/fieldtrip/fieldtrip/archive/refs/tags/20240417.zip';
unzip(url_fieldtrip);

Upon completion of this step, the folder structure should look something like this:

fieldtrip-20240417/
|-- bin
|-- compat
|-- connectivity
|-- contrib
|-- external
|-- fileio
|-- forward
|-- inverse
|-- plotting
|-- preproc
|-- private
|-- qsub
|-- realtime
|-- specest
|-- src
|-- statfun
|-- template
|-- test
|-- trialfun
`-- utilities

Next, we proceed with downloading the relevant data. The data that are used in the hands-on sessions, are stored on the FieldTrip download-server. The tutorial documentation contains links to the relevant files, but it is easier to pre-install (and if needed to unzip) the data. To this end, you can use the recipe below. Please ensure that your present working directory is the toolkit2024 folder, which you created in the previous step.

% create a folder (within toolkit2024) that will contain the data, to keep a clean structure
mkdir('data');
cd('data');

% then download and unzip the Subject01 dataset
url_subject01 = 'https://download.fieldtriptoolbox.org/tutorial/Subject01.zip';
unzip(url_subject01);

% next, create for each of the tutorials a folder, and download the data
mkdir('eventrelatedaveraging');
cd('eventrelatedaveraging');
url_tutorial = 'https://download.fieldtriptoolbox.org/tutorial/eventrelatedaveraging';
fnames = {'dataFC_LP.mat' 'dataFIC_LP.mat' 'dataIC_LP.mat'};
for k = 1:numel(fnames)
  websave(fnames{k}, fullfile(url_tutorial, fnames{k}));
end
cd('../');

mkdir('timefrequencyanalysis');
cd('timefrequencyanalysis');
url_tutorial = 'https://download.fieldtriptoolbox.org/tutorial/timefrequencyanalysis';
fnames = {'dataFIC.mat'};
for k = 1:numel(fnames)
  websave(fnames{k}, fullfile(url_tutorial, fnames{k}));
end
cd('../');

mkdir('beamformer');
cd('beamformer');
url_tutorial = 'https://download.fieldtriptoolbox.org/tutorial/beamformer';
fnames = {'Subject01.mri' 'dataPost.mat' 'dataPre.mat' 'data_all.mat' 'freqPost.mat' 'freqPre.mat' 'headmodel.mat' 'segmentedmri.mat' 'sourcePost_con.mat' 'sourcePost_nocon.mat' 'sourcePre_con.mat' 'sourcemodel.mat'};
for k = 1:numel(fnames)
  websave(fnames{k}, fullfile(url_tutorial, fnames{k}));
end
cd('../');

mkdir('cluster_permutation_timelock');
cd('cluster_permutation_timelock');
url_tutorial = 'https://download.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock';
fnames = {'ERF_orig.mat' 'GA_ERF_orig.mat' 'dataFC_LP.mat' 'dataFIC_LP.mat' 'stat_ERF_axial_FICvsFC.mat' 'stat_ERF_planar_FICvsFC.mat'};
for k = 1:numel(fnames)
  websave(fnames{k}, fullfile(url_tutorial, fnames{k}));
end
cd('../../');

At this stage, you ideally have a directory structure that looks like the following one:

.
|-- data
|   |-- Subject01.ds
|   |-- beamformer
|   |-- cluster_permutation_timelock
|   |-- eventrelatedaveraging
|   `-- timefrequencyanalysis
`-- fieldtrip-20240417
    |-- bin
    |-- compat
    |-- connectivity
    |-- contrib
    |-- external
    |-- fileio
    |-- forward
    |-- inverse
    |-- plotting
    |-- preproc
    |-- private
    |-- qsub
    |-- realtime
    |-- specest
    |-- src
    |-- statfun
    |-- template
    |-- test
    |-- trialfun
    `-- utilities

So, if you from now on - that is for the duration of the toolkit - ALWAYS execute the following steps after starting a fresh MATLAB session, you should be all good to go:

% change into the 'toolkit2024' folder and then do the following
restoredefaultpath
addpath('fieldtrip-20240417');
addpath(genpath('data'));
ft_defaults;

The restoredefaultpath command clears your path, keeping only the official MATLAB toolboxes. The addpath statement adds the fieldtrip-20240417 directory, i.e. the directory containing the FieldTrip main functions. The other addpath statement tells MATLAB where to find the relevant data, and the ft_defaults command ensures that all of FieldTrip’s required subdirectories are added to the path.

Code of conduct

Please spend a couple of minutes to have a look at our Code of Conduct to make sure we all are taking responsibility to look after each other and make sure we are contributing towards an inclusive and supportive community. Please let us know if you have any questions regarding it. All toolkit participants are responsible to follow the rules listed here, as well as making sure that everyone in the toolkit follows it.