Setting up your environment for processing

We recommend to install MNE as a standalone installer.

The data of the MNE environment will be under C:\ProgramData\mne-python\1.6.1_0

You can setup Pycharm to use this environment as a Python environment for your pipeline project.

The configuration file for setting SUBJECTS_DIR, the directory to the data of your subject, can be set in: C:\Users\user_name\.mne\mne-python.json

Installing freesurfer on windows

Configure WSL2 on windows Access the files of the ubuntu distribution by typing \\wsl$\Ubuntu in the file explorer in windows.

Install freesurfer following their documentation page. https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wsl_ubuntu