OPM tutorial for CuttingEEG X

workshop/cuttingeegx.md

@@ -9,7 +9,139 @@ CuttingEEG is turning 10 years old! This milestone calls for a special edition,
 
 Alongside the [CuttingEEG X](https://cuttingeegx.org) conference we will be organizing some local workshops in the morning.
 
-- Who: Julia Chauvet, Konstantinos Tsilimparis, Britta Westner, Tilman Stephani, Robert Oostenveld
-- When: 30 to 31 October 2024
+- Who: Konstantinos Tsilimparis, Robert Oostenveld
+- When: 31 October 2024
 - Where: Nijmegen
 - See <https://cuttingeegx.org/registration/#Nijmegen> for more details
+
+
+## Getting started with the hands-on session
+
+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.
+
+### 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](https://intranet.donders.ru.nl/index.php?id=eva).
+
+### MATLAB
+
+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). 
+
+### FieldTrip
+
+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. 
+
+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('cuttingeegx');
+cd('cuttingeegx');
+
+% download and unzip fieldtrip into the newly created folder
+url_fieldtrip = 'https://github.com/fieldtrip/fieldtrip/releases/tag/20240916.zip';
+unzip(url_fieldtrip);
+```
+
+Upon completion of this step, the folder structure should look something like this: 
+
+```bash
+cuttingeegx/
+|-- fieldtrip-20240916
+    |-- bin
+    |-- compat
+    |-- connectivity
+    |-- contrib
+    |-- external
+    |-- fileio
+    |-- forward
+    |-- inverse
+    |-- plotting
+    |-- preproc
+    |-- private
+    |-- qsub
+    |-- realtime
+    |-- specest
+    |-- src
+    |-- statfun
+    |-- template
+    |-- test
+    |-- trialfun
+    |-- utilities
+```
+
+{% include markup/red %}
+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.
+{% include markup/end %}
+
+### Test your installation in advance
+
+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/toolkit2024/test_installation).
+
+## The data used in this tutorial
+
+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.
+
+Please ensure that your present working directory is the ```cuttingeegx``` folder, which you created in the previous step.
+
+```
+% create a folder (within cuttingeegx) that will contain the data, to keep a clean structure
+mkdir('data');
+cd('data');
+
+% create a folder and download the SQUID and OPM dataset
+url_tutorial = 'https://download.fieldtriptoolbox.org/workshop/cuttingeegx';
+fnames = {''};
+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:
+
+```bash
+cuttingeegx/
+|-- data
+    |-- opm
+    |-- squid
+    |-- mri
+|-- fieldtrip-20240916
+    |-- bin
+    |-- compat
+    |-- connectivity
+    |-- contrib
+    |-- external
+    |-- fileio
+    |-- forward
+    |-- inverse
+    |-- plotting
+    |-- preproc
+    |-- private
+    |-- qsub
+    |-- realtime
+    |-- specest
+    |-- src
+    |-- statfun
+    |-- template
+    |-- test
+    |-- trialfun
+    |-- utilities
+```
+
+
+Whenever starting a fresh MATLAB session, to configure the right FieldTrip paths, execute the following: 
+
+```
+% change into the 'cuttingeegx' folder and then do the following
+restoredefaultpath
+addpath('fieldtrip-20240417');
+addpath(genpath('data'));
+ft_defaults;
+```
+
+ `ft_defaults` command ensures that all of FieldTrip's required subdirectories are added to the path.
+
+{% include markup/red %}
+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).
+{% include markup/end %}