FieldTrip Workshop in Marseille

Together with Jean-Michel Badier and Christian Benar from the MEG laboratory in Marseille, we will run a FieldTrip workshop.

• Who: Robert Oostenveld with help from local staff
• When: 11-13 January 2016
• Where: You should have received detailed instructions on the venue at INSERM Marseille. If you have questions, please contact demat-form.dr-marseille@inserm.fr.

We will keep this page up to date and post new information here when available.

Please download the ft_connectivitysimulation data here: data.mat.

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.

Furthermore, we recommend you to watch the following online videos prior to the workshop. Note that these video lectures cannot be quickly glanced over. You should plan ahead and take your time to go through them.

• Fieldtrip toolbox introduction, 1 hour
• MEG basics and instrumentation, 15 minutes

The content of the shorter second lecture is also covered in the first, but presented differently and therefore possibly useful to get a good understanding of the signals that we deal with.

In the first workshop hands-on session we will start with preprocessing MEG 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 and you should go through the MEG preprocessing tutorial. Depending on your understanding of MATLAB and MEG, you can simply read the preprocessing tutorial (which will take you 30 minutes) or download the example data and go through it step by step (which will take you 2 hours).

We will start each day at 9:00 sharp and will finish around 17:00 on Monday and Tuesday, and around 12:30 on Wednesday.

• morning
  • 1h Lecture on frequency analysis slides
  • 2h handson Sensor-level ERF, TFR and connectivity analyses
• afternoon
  • 1h Lecture on source reconstruction using beamforming slides
  • 2h handson Localizing visual gamma and cortico-muscular coherence
  • wrap up of the day
• evening
  • dinner (not included, i.e. on own costs)

• morning
  • 1h Lecture on connectivity analysis slides
  • 2h hands on Analysis of sensor- and source-level connectivity
• afternoon
  • 1h Lecture on nonparametric statistics using clustering slides
  • 2h hands on Cluster-based permutation tests on ERFs or on Cluster-based permutation tests on time-frequency data
  • wrap up of the day
• evening
  • pub (not included, i.e. on own costs)

• Playground in which you will be working on own data (under supervision)
• Wrap up of the workshop

For the playground you should bring your own data. In case you don't have a suitable dataset for analysis (yet), we will provide you with a dataset and details on the experiment and analysis options.

The data and FieldTrip have been installed on the computers at the workshop venue.

cd /usr/local/fieldtrip-20151216/toolbox_FieldTrip/fieldtrip-20151216/
ft_defaults
cd ../../sensor_analysis/

For the hands-on sessions you have to start MATLAB. To ensure that everything runs smooth, we will work with a clean and well-tested version of FieldTrip that we have installed on all computers and that we will bring on on a USB stick. Importantly, the tutorial data does not have to be downloaded but will also be distributed on the computers and available on the USB stick.

If you work on your own laptop:

1. Copy the complete contents of the USB stick to your computer.
2. Unzip the fieldtrip-xxxxxxxx.zip file.
3. Put Subject01.zip in a directory called 'tutorial'.

After copying all files to your computer and unzipping then, you start MATLAB. To ensure that the right version of fieldtrip is used, and not another version (such as the one included in SPM or EEGLAB), you type in the MATLAB command window

restoredefaultpath
cd path_to_directory/fieldtrip-xxxxxxxx
addpath(pwd)
ft_defaults

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 change into the tutorial directory

cd path_to_directory/tutorial