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Merge pull request #813 from contsili/cuttingeegx-workshop
OPM tutorial for CuttingEEG X
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‎workshop/cuttingeegx.md

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@@ -9,7 +9,207 @@ CuttingEEG is turning 10 years old! This milestone calls for a special edition,
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Alongside the [CuttingEEG X](https://cuttingeegx.org) conference we will be organizing some local workshops in the morning.
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- Who: Julia Chauvet, Konstantinos Tsilimparis, Britta Westner, Tilman Stephani, Robert Oostenveld
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- When: 30 to 31 October 2024
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- Who: Konstantinos Tsilimparis, Robert Oostenveld. Jan-Mathijs Schoffelen
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- When: 31 October 2024
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- Where: Nijmegen
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- See <https://cuttingeegx.org/registration/#Nijmegen> for more details
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## The tutorial
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We will run a tutorial on [preprocessing and coregistration of SQUID-based and OPM-based data](/workshop/cuttingeegx/squids_vs_opms). We will explore the differences in data analysis between the two MEG systems.
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## Getting started with the hands-on session
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In this workshop you will work on your own laptop computer. It will be an in-person event with no possibilities for hybrid or online attendance.
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### Wifi access
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If you don't have a eduroam account through your institution, it is possible to get a visitor access. Please let us know if you need a visitor access at the day of the workshop.
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### MATLAB
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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).
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### FieldTrip
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To get the most recent copy of FieldTrip, you can follow this [link](https://github.com/fieldtrip/fieldtrip/releases/tag/20240916), download the zip-file, and unzip it at a convenient location on your laptop's hard drive.
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Alternatively, you could do the following in the MATLAB command window (less work and faster downloading):
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```
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% create a folder that will contain the code and the data, and change directory
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mkdir('cuttingeegx');
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cd('cuttingeegx');
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% download and unzip fieldtrip into the newly created folder
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url_fieldtrip = 'https://github.com/fieldtrip/fieldtrip/archive/refs/tags/20240916.zip';
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unzip(url_fieldtrip);
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```
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Upon completion of this step, the folder structure should look something like this:
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```bash
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cuttingeegx/
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|-- fieldtrip-20240916
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|-- bin
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|-- compat
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|-- connectivity
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|-- contrib
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|-- external
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|-- fileio
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|-- forward
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|-- inverse
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|-- plotting
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|-- preproc
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|-- private
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|-- qsub
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|-- realtime
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|-- specest
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|-- src
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|-- statfun
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|-- template
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|-- test
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|-- trialfun
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|-- utilities
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```
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{% include markup/red %}
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Downloading and unzipping can take up to ~10 minutes, so please download and unzip FieldTrip prior to the workshop.
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{% include markup/end %}
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{% include markup/red %}
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If you have downloaded and unzipped by hand, it could be that there's an 'extra folder layer' in your directory structure. We recommend that you remove this extra layer, i.e. move all content one level up.
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{% include markup/end %}
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### Test your installation in advance
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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](/workshop/cuttingeegx/test_installation).
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## The data used in this tutorial
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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](https://download.fieldtriptoolbox.org/workshop/cuttingeegx). You can either ‘click around’ using web browsers and/or explorer windows to grab the data that are needed, or instead (less work, at least if it works) execute the MATLAB code below.
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Please ensure that your present working directory is the ``'cuttingeegx'`` folder, which you created in the previous step. Open a new .m file in the text editor and run the following (Note: do not use the command line window):
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```
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% create a folder (within cuttingeegx) that will contain the data
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mkdir('data');
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cd('data');
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% Download the SQUID and OPM dataset
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url = 'https://download.fieldtriptoolbox.org/workshop/cuttingeegx';
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recursive_download(url, pwd)
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function recursive_download(webLocation, localFolder)
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% RECURSIVE_DOWNLOAD downloads a complete directory from a RESTful web service
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%
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% Use as
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% recursive_download(webLocation, localFolder)
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%
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% See also WEBREAD, WEBSAVE, UNTAR, UNZIP, GUNZIP
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% Copyright (C) 2023, Konstantinos Tsilimparis
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%
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% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
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% for the documentation and details.
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%
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% FieldTrip is free software: you can redistribute it and/or modify
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% it under the terms of the GNU General Public License as published by
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% the Free Software Foundation, either version 3 of the License, or
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% (at your option) any later version.
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%
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% FieldTrip is distributed in the hope that it will be useful,
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% but WITHOUT ANY WARRANTY; without even the implied warranty of
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% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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% GNU General Public License for more details.
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%
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% You should have received a copy of the GNU General Public License
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% along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.
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%
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% $Id$
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% Read the HTML content of the URL
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htmlContent = webread(webLocation);
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pattern = '<a href="([^"]+)">';
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matches = regexp(htmlContent, pattern, 'tokens');
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% Iterate over the matches
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for i = 2:numel(matches) % Ignore i=1, which is the parent directory link: '../'
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item = matches{i}{1};
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if endsWith(item, '/') % It is a folder
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% Create the necessary directories if they do not exist
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subfolder = fullfile(localFolder, item);
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if ~isfolder(subfolder)
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mkdir(subfolder);
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end
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% Recursively download the subfolder
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subWebLocation = strcat(webLocation, '/', item);
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recursive_download(subWebLocation, subfolder);
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else % It is a file
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% Create the necessary directories if they do not exist
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if ~isfolder(localFolder)
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mkdir(localFolder);
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end
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% Download the file
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fileUrl = strcat(webLocation, '/', item);
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localFilePath = fullfile(localFolder, item);
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websave(localFilePath, fileUrl);
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end
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end
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end
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```
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At this stage, you ideally have a directory structure that looks like the following one:
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```bash
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cuttingeegx/
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|-- data
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|-- sub-001
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|-- anat
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|-- meg
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|-- opm
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|-- squid
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|-- fieldtrip-20240916
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|-- bin
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|-- compat
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|-- connectivity
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|-- contrib
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|-- external
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|-- fileio
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|-- forward
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|-- inverse
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|-- plotting
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|-- preproc
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|-- private
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|-- qsub
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|-- realtime
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|-- specest
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|-- src
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|-- statfun
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|-- template
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|-- test
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|-- trialfun
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|-- utilities
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```
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Whenever starting a fresh MATLAB session, to configure the right FieldTrip paths, execute the following:
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```
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% change into the 'cuttingeegx' folder and then do the following
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restoredefaultpath
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addpath('fieldtrip-20240916');
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addpath(genpath('data'));
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ft_defaults;
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```
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`ft_defaults` command ensures that all of FieldTrip's required subdirectories are added to the path.
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{% include markup/red %}
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Furthermore, please do NOT add FieldTrip with all subdirectories, subdirectories will be added automatically when needed, and only when needed (see this [FAQ](/faq/installation)).
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{% include markup/end %}

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