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FieldTrip tutorial at CuttingEEG 2021 in Aix-en-Provence |
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- Who: Jan-Mathijs Schoffelen and Robert Oostenveld
- When: 4 October 2021
- Where: Le Cube Université Aix-Marseille (AMU) and screen sharing on zoom 889 8100 0507.
- See https://cuttingeeg2021.org for more details
We will keep this page up to date and post new information here when available.
In this hands-on we will do a tutorial on time-frequency analysis on short and long timescales. The tutorial covers preprocessing and time-frequency analysis, and we will specifically look at how your selection of data segments, rereferencing, filtering and handling of artifacts can be optimized to get the best time-frequency estimates of the EEG and MEG activity.
If you are new to time-frequency analysis in general, we recommend you to watch the lecture on the fundamentals of neuronal oscillations in advance. If you are entirely new to FieldTrip, please watch the introduction lecture. An overview of all lectures is available here.
We will be using the eeg-language dataset that has been converted to BIDS. The data is available from our download server and is alternatively available from https://zenodo.org/communities/cuttingeeg.
The conversion of the 5 pilot subjects' EEG data to BIDS is fully documented on this page. You don't have to run that code, but you can use it as inspiration for organizing your own data in the BIDS format, or use it to convert the full dataset that is available from the archive of the MPI for Psycholinguistics.
The "minimal" dataset (~260MB) contains one subject and is enough to run the tutorial. The "pilot" dataset (~1.7GB) contains all 5 subjects used for the pilot analysis in the original paper; you can use that if you want to explore other subjects with this tutorial.
{% include markup/danger %} Please download and unzip a recent version of FieldTrip from https://github.com/fieldtrip/fieldtrip/releases. We will be using some cutting edge features in FieldTrip, so you should download and install release 20210928 or later. {% include markup/end %}
To get going, you need to start MATLAB. Then, you need to issue the following commands:
restoredefaultpath
cd <your_fieldtrip_location>
addpath(pwd)
ft_defaults
The <your_fieldtrip_location> is the directory in which all the code is after you have unzipped the downloaded folder.
{% include markup/danger %}
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. See also this frequently asked question. {% include markup/end %}
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 that you are in the correct 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 hands-on session.