About the MNE-Python tutorial category

Welcome to the MNE-Python tutorial!

We will be using the following Github repository for this workshop. All of the necessary code will be updated in this repo.

Instructions
You will want to git clone the repository. To do so, you can open up Terminal or the Command Prompt, navigate to where you typically like to store your code locally on your machine. Then type git clone https://github.com/maansidesai/WIRED-2024-Paris.git

  • If you do not have a GitHub account, please make sure you have created one and have basic familiarity with accessing repositories. For additional help, go the Github documentation page.

If you are unfamiliar with git, you can also go to the link above and click on the green <>Code button and download a zip file to your computer. Extract the zip file and put the directory somewhere where you will remember.

Once you have successfully cloned the tutorial repository, please go through the README. The README contains important information on the following:

  • successfully installed MNE on your machine
  • downloading the necessary BIDS dataset we will be using
  • some troubleshooting tips

It’s really important you have installed MNE prior to the tutorial. If you encounter any issues, please respond on this forum so we can try and help you beforehand.

The repository also contains all of the necessary code you will need. This is located under notebooks/

That’s it for now! If you have any questions, please respond to this post.

Looking forward to meeting you all!

Maansi, Alex, Apolline

2 Likes

Hello,
I have successfully installed all the librairies (MNE was already installed since i’m currently using it), and dowloaded all the data.
But when I try to run the first cell of the first notebook I get the error ‘No module named ‘mne_bids’’. Indeed why I check the installed libraries I cannot find mne_bids. Is there a way to install it that was not specified in the README file ?

Thank you very much!
Lou

I decided to install manually the mne_bids library using:
pip install --upgrade mne-bids[full]

It works well now.
Sorry for the inconvenience.

I’ll let the comment and response online, maybe it will be useful for somebody else :slight_smile:
Lou

1 Like

I’m glad it’s working! I’m also adding a link that describes installing MNE-bids. Installation — MNE-BIDS 0.14 documentation

For those who have trouble, you can install this library in the MNE prompt.

One quick addition here – if you are using an old version of MNE python, some of the new visualizations may not work. So you may want to install the newest version of MNE (you can have multiple versions installed at once) in order to run everything in the tutorial.

What do you mean by old ? Is the 1.6.0 version ok ? (the latest seems to be 1.6.1)
Thanks!

I recommend using the latest version of MNE (1.6.1) just to make sure that you don’t run into possible errors, such as visualizations as Liberty described above.

For correct visualisation
If you installed mne via pip, mne-qt-browser was probably not installed otgether with the package:

!pip install mne-qt-browser
mne.viz.set_browser_backend(‘qt’)

instead of: mne.viz.set_browser_backend(‘matplotlib’)

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