FieldTrip workshop in Krakow, Poland

Using the tutorial data and the FieldTrip version provided

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 is distributed on a USB stcik, rather than the version you might already have installed. Furthermore, the tutorial data does not have to be downloaded but will also be distributed on the USB stick.

  1. Copy the complete Krakow directory from the USB stick to your computer
  2. Unzip the fieldtrip-xxxxxxxx.zip file.
  3. Unzip the Subject01.zip file, you should place the contents in the tutorial directory.

Depending on the unzip program you are using (e.g. Winrar), the name of the zip file might also appear as directiory, resulting in path_to_directory/fieldtrip-xxxxxxxx/fieldtrip-xxxxxxxx, i.e. the fieldtrip directory in a fieldtrip directory. Please fix that by moving all files one level up.

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
ls
addpath(pwd)
ft_defaults

The restoredefaultpath command clears your path, keeping only the official MATLAB toolboxes.

The ls statement shows the list of files in the present directory, and you can visually check that the contents are correct and e.g. not in another subfolder. You should see a long list of ft_xxx.m functions.

The addpath(pwd) statement adds the present working directory, i.e. the directory containing the fieldtrip main funcctions. 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.

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, but only when needed.

After installing fieldtrip to your path, you change into the tutorial directory

cd path_to_directory/tutorial

In general the tutorials start by reading the raw data from “Subject01.ds”, which is a data directory. You should not go into the Subject01.ds directory, but stay at the level of the tutorial directory. If a specific tutorial instructs you to load data (and if you want the skip the step just prior to that because of time limitations), you should go into the respective tutorial subdirectory, i.e. tutorial/eventreltedaveraging.

Krakow specific information

The tutorials that we will use during this toolkit are:

Tuesday morning: Please begin with Event related averaging going up to and including the axial gradiometer section only. It is helpful to read The data set used in this tutorial prior to running the tutorial. When you reach the section on planar gradiometer, switch then to this EEG example: EEG data: reading-in trials and pre-processing. For this EEG example, you will also need the BrainVision data provided on the USB sticks.

Tuesday afternoon: Time-frequency analysis using Hanning window, multitapers and wavelets

Wednesday morning: Localizing oscillatory sources using beamformer techniques

Wednesday afternoon: Multivariate analysis of electrophysiological data

Thursday, FieldTrip Playground: If you are stuck with any .bdf specific questions, you might gain insight from the getting started with Biosemi documentation page.

workshop/krakow.txt · Last modified: 2012/06/24 14:46 by johzum

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