Tested on Windows 10 and Ubuntu 22.04 LTS.
The environment contains mne + some useful packages (numpy, matplotlib, etc). Change to the folder that contains the environment.yml file and run
conda env create
Install the spyder package + some optional dependencies recommended by the author.
conda create -n spyder spyder numpy scipy pandas matplotlib sympy cython
On Ubuntu, add PyQtWebEngine to the list of packages to be installed
conda create -n spyder spyder numpy scipy pandas matplotlib sympy cython PyQtWebEngine
Open spyder. From the miniconda prompt run
conda activate spyder
spyder
Setup Spyder to use python interpreter from the mne environment. In Spyder: Tools -> Preferences -> Python interpreter -> Use the following Python intepreter -> select the interpreter for the mne environment.
Setup Spyder to plot graphs in separate windows: In Spyder: Tools -> Preferences -> IPython console -> Graphics -> Backend -> Qt5.
Restart Spyder.
Doesn't work on Windows. Install tcsh
sudo apt install tcsh
Download freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz to ~/opt
cd ~/opt
tar -zxpf freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz
Copy the .license file to ~/opt/freesurfer
Move the subjects dir to ~/freesurfer_subjects
mv ~/opt/freesurfer/subjects ~/freesurfer_subjects
Add the following lines to ~/.bashrc
export FREESURFER_HOME=$HOME/opt/freesurfer
export SUBJECTS_DIR=$HOME/freesurfer_subjects
source $FREESURFER_HOME/SetUpFreeSurfer.sh