Installing MNE-Python

Installing Python

MNE-Python runs within Python, and depends on several other Python packages. MNE-Python 0.18 only supports Python version 3.5 or higher. We strongly recommend the Anaconda distribution of Python, which comes with more than 250 scientific packages pre-bundled, and includes the conda command line tool for installing new packages and managing different package sets (“environments”) for different projects.

To get started, follow the installation instructions for Anaconda. When you are done, if you type the following commands in a bash terminal, you should see outputs similar to the following (assuming you installed conda to /home/user/anaconda3):

$ conda --version && python --version
conda 4.6.2
Python 3.6.7 :: Anaconda, Inc.
$ which python
/home/user/anaconda3/bin/python
$ which pip
/home/user/anaconda3/bin/pip

If you see something like:

conda: command not found

It means that your PATH variable (what the system uses to find programs) is not set properly. In a correct installation, doing:

$ echo $PATH
...:/home/user/anaconda3/bin:...

Will show the Anaconda binary path (above) somewhere in the output (probably at or near the beginning), but the command not found error suggests that it is missing.

On Linux or OSX, the installer should have put something like the following in your ~/.bashrc or ~/.bash_profile (or somewhere else if you are using a non-bash terminal):

. ~/anaconda3/etc/profile.d/conda.sh

If this is missing, it is possible that you are not on the same shell that was used during the installation. You can verify which shell you are on by using the command:

$ echo $SHELL

If you do not find this line in the configuration file for the shell you are using (bash, tcsh, etc.), add the line to that shell’s rc or profile file to fix the problem.

If you see an error like:

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.

It means that you have used an old method to set up Anaconda. This means that you have something like:

PATH=~/anaconda3/bin:$PATH

in your ~/.bash_profile. You should update this line to use the modern way using anaconda3/etc/profile.d/conda.sh above.

You can also consult the Anaconda documentation and search for Anaconda install tips (Stack Overflow results are often helpful) to fix these or other problems when conda does not work.

Installing MNE-Python and its dependencies

Once you have Anaconda installed, the easiest way to install MNE-Python with all dependencies is update your base Anaconda environment:

Use the base environment file, e.g.:

$ curl --remote-name https://raw.githubusercontent.com/mne-tools/mne-python/master/environment.yml
$ conda env update --file environment.yml

Use the base environment file and then update PyQt using pip, e.g.:

$ curl --remote-name https://raw.githubusercontent.com/mne-tools/mne-python/master/environment.yml
$ conda env update --file environment.yml
$ pip install "PyQt5>=5.10"
  • Download the base environment file

  • Open an Anaconda command prompt

  • cd to the directory where you downloaded the file

  • Run conda env update --file environment.yml

If you prefer an isolated Anaconda environment, instead of usingconda env update to modify your “base” environment, you can create a new dedicated environment with conda env create --name mne --file environment.yml.

Testing MNE-Python installation

To make sure MNE-Python installed itself and its dependencies correctly, type the following command in a terminal:

$ python -c 'import mne; mne.sys_info()'

This should display some system information along with the versions of MNE-Python and its dependencies. Typical output looks like this:

Platform:      Linux-4.18.0-13-generic-x86_64-with-debian-buster-sid
Python:        3.6.8 |Anaconda, Inc.| (default, Dec 30 2018, 01:22:34)  [GCC 7.3.0]
Executable:    /home/travis/miniconda/bin/python
CPU:           x86_64: 48 cores
Memory:        62.7 GB

mne:           0.17.0
numpy:         1.15.4 {blas=mkl_rt, lapack=mkl_rt}
scipy:         1.2.0
matplotlib:    3.0.2 {backend=Qt5Agg}

sklearn:       0.20.2
nibabel:       2.3.3
mayavi:        4.7.0.dev0 {qt_api=pyqt5, PyQt5=5.10.1}
cupy:          Not found
pandas:        0.24.0
dipy:          0.15.0

If you see an error like:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'mne'

This suggests that your mne environment is not active. Try doing conda activate mne and try again. If this works, you might want to add conda activate mne to the end of your ~/.bashrc or ~/.bash_profile files so that it gets executed automatically.

If something went wrong during installation and you can’t figure it out yourself, check out the Advanced setup of MNE-Python page to see if your problem is discussed there. If not, the MNE mailing list and MNE gitter channel are good resources for troubleshooting installation problems.