NEU502B — OPM-MEG Software Setup

Follow these four parts in order. Commands are ready to copy and paste.

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Contents

• 00 · Prerequisites
• 01 · Get the mne-opm software
• 02 · Download the sample data
• 03 · Set up Jupyter notebooks
• 04 · Get the Oddball PsychoPy task

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00 · Prerequisites

🍎 Mac & Linux — Install uv

curl -LsSf https://astral.sh/uv/install.sh | sh

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🪟 Windows users

Windows users are strongly encouraged to install WSL (Windows Subsystem for Linux), which allows your machine to run Linux. Once WSL is set up, follow the Mac & Linux instructions above instead of the steps below.

From PowerShell (run as Administrator):

wsl --install

This installs WSL 2 with Ubuntu by default. A reboot is required afterward.

The steps below only apply to Windows users not running WSL.

1. Install uv

From PowerShell (you may see a security prompt — this is expected and safe to proceed through):

powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

2. Install Git

From Windows Terminal:

winget install Git.Git

3. Install Anaconda or Miniconda

Download from anaconda.com if you don't already have it, then open Anaconda Prompt and run:

conda install pyqt
conda install jupyterlab

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01 · Get the mne-opm Software

1. Clone the repository

Navigate to your preferred software location first, then clone:

git clone -b my-working-branch https://github.com/mrribbits/mne-opm.git

2. Enter the directory and sync dependencies

cd mne-opm
uv sync

3. Register the Jupyter kernel

🪟 Windows (not WSL) — from the mne-opm directory, in Anaconda Prompt:

.venv\Scripts\activate
pip install ipykernel
python -m ipykernel install --user --name mne-opm --display-name "mne-opm"

🍎 Mac or Linux (if you have kernel issues) — from the mne-opm directory:

uv run python -m ipykernel install --user --name mne-opm --display-name "mne-opm"

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02 · Download the Preprocessed Sample Data

1. Navigate to your preferred data location and download

curl -L -H "Cache-Control: no-cache" \
  -o "./MEG-for-students-preproc.zip" \
  "https://www.dropbox.com/scl/fi/mwk2xs6jcar5ppl6ahk0t/MEG-for-students-preproc.zip?rlkey=0bpthyvizakg1h8c9ncy10sp4&dl=1"

2. Unzip the file

unzip MEG-for-students-preproc.zip

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03 · Set Up the Jupyter Notebooks

1. Clone the course notebooks

git clone https://github.com/mrribbits/NEU502-2026.git meg-notebooks

2. Launch JupyterLab

Point uv at your mne-opm install location:

uv run --project /path/to/your/mne-opm jupyter lab

💡 Once open, make sure the mne-opm kernel is selected. If it isn't chosen automatically, select it from the kernel menu in JupyterLab.

3. Edit the path variables in each notebook

Open each notebook and update the directory variables to match your local setup:

Variable	Set in	Description	Example
DERIV_DIR	Notebooks 1–4	Preprocessed derivatives folder	~/classes/neu502/oddball/data/oddball/bids/derivatives/analysis1__/sub-001/ses-01/meg
RAW_DIR	Notebook 1	Raw BIDS data folder	~/classes/neu502/oddball/data/oddball/bids/sub-001/ses-01/meg
SUBJECTS_DIR	Notebook 3	FreeSurfer subjects directory	~/classes/neu502/oddball/data/oddball/bids/derivatives/freesurfer
PROJECT_ROOT	Notebook 5	Top-level project folder	~/classes/neu502/oddball

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04 · Get the Oddball PsychoPy Task

curl -L -H "Cache-Control: no-cache" \
  -o "./Psychopy-oddball-task.zip" \
  "https://www.dropbox.com/scl/fi/3x7r53n3js3i0hdv75p13/Psychopy-oddball-task.zip?rlkey=2e7zj1rkgol4t2ukz21748nml&dl=1"