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https://github.com/hoechenberger/pybrain_mne

Material for Pybrain 2020 MNE-Python workshop
https://github.com/hoechenberger/pybrain_mne

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Material for Pybrain 2020 MNE-Python workshop

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README 

        

![MNE-Python Logo](https://mne.tools/stable/_static/mne_logo.svg "MNE-Python")



# Pybrain 2020: M/EEG analysis with MNE-Python



## Preparations



To participate in the workshop, you will need to set up a Python environment with a number of dependencies. The following instructions will guide you through the process.



**The notebooks will be made available in this GitHub repository at the beginning of the workshop.**



### Download & install Anaconda



We will work with the Anaconda Python distribution.



- [Installation instructions for Windows](https://docs.continuum.io/anaconda/install/windows/)

- [Installation instructions for macOS](https://docs.continuum.io/anaconda/install/mac-os/)

- [Installation instructions for Linux](https://docs.continuum.io/anaconda/install/linux/)



### Install MNE-Python



- [Open an Anaconda prompt](https://docs.continuum.io/anaconda/install/verify-install/#conda)

- Follow the [MNE-Python installation instructions for your operating system](https://mne.tools/stable/install/mne_python.html#for-3d-plotting-and-source-analysis)

- Activate your newly-installed MNE-Python environment by typing into the Anaconda prompt:

  ```

  conda activate mne

  ```

- Verify your MNE-Python installation by running in the Anaconda prompt:

  ```

  mne sys_info

  ```

  The output should look similar to the following:

  ```

    Platform:      macOS-10.15.7-x86_64-i386-64bit

    Python:        3.8.5 (default, Sep  4 2020, 02:22:02)  [Clang 10.0.0 ]

    Executable:    /Users/richard/miniconda3/envs/mne-new/bin/python

    CPU:           i386: 4 cores

    Memory:        8.0 GB



    mne:           0.21.1

    numpy:         1.19.2 {blas=mkl_rt, lapack=mkl_rt}

    scipy:         1.5.2

    matplotlib:    3.3.2 {backend=MacOSX}



    sklearn:       0.23.2

    numba:         0.51.2

    nibabel:       3.2.0

    cupy:          Not found

    pandas:        1.1.3

    dipy:          1.3.0

    mayavi:        4.7.2

    pyvista:       0.27.2 {pyvistaqt=0.2.0, OpenGL 4.1 INTEL-14.7.8 via Intel HD Graphics 5000 OpenGL Engine}

    vtk:           9.0.1

    PyQt5:         5.13.2

    ```



### Install JupyterLab



We will use the Jupyter Lab environment to run our workshop notebooks. Inside the Anaconda prompt, run:

```

conda activate mne

conda install -y jupyterlab

```



Then, run:

```

jupyter lab

```

If the installation was successful, your browser should open. You may close it again, and stop the JupyterLab process in the Anaconda prompt by pressing the keys `Ctrl` and `C` simultaneously and then enterying `y` when asked if you're sure.



### Install MNE-BIDS



To readand write [BIDS data](https://bids-specification.readthedocs.io/en/stable/), we will use MNE-BIDS. To install it, run the following commands inside the Anaconda prompt:



```

conda activate mne

pip install mne-bids nibabel pybv

```



### Download MNE-Python sample data



We will work with some sample data that can be easily retrieved via MNE-Python. Open an Anaconda prompt and run:



```

conda activate mne

python -c "import mne; mne.datasets.sample.data_path()"

```

This will retrieve about 1.5 GB of data, so it might take a while if your internet connection is slow.



## Workshop summary



The workshop will cover a broad range of topics to help you get to know all essential parts of MNE-Python for conducting MEG and EEG data analysis:



- loading, filtering, and inspecting raw data

- working with BIDS data

- epoching and artifact correction

- creating and visualizing evoked responses (ERP / ERF)

- contrasting evoked responses of different experimental conditions

- decoding neural responses (machine learning)

- performing time-frequency analysis

- estimating and visualizing cortical sources (source localization)

- conducting a group analysis



We will start with a **30 min warm-up at  9:00 a.m.** UTC on both days. During this warm-up, we can resolve technical difficulties you might be experiencing. **The actual workshop will start at 9:30.**



Lunch break is from 12 to 1, and we will continue until 3:30 or longer if need be (to hopefully address all open questions).