Installation¶

You will find below the steps for installing Clinica on Linux or Mac. Please do not hesitate to contact us on the forum or GitHub if you encounter any issues.

Prepare your Python environment¶

You will need a Python environment to run Clinica. We advise you to use Miniconda. Miniconda allows you to install, run, and update Python packages and their dependencies. It can also create environments to isolate your libraries. To install Miniconda, open a new terminal and type the following commands:

If you are on Linux:

curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o /tmp/miniconda-installer.sh
bash /tmp/miniconda-installer.sh

If you are on Mac:

curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o /tmp/miniconda-installer.sh
bash /tmp/miniconda-installer.sh

Miniconda will ask you where to install it. Do not forget to copy the export PATH given at the end of the installation. If everything went fine, open a new terminal and type conda info, it will verify if Conda is installed, check the version and show your Miniconda path.

Install Clinica¶

The latest release of Clinica can be installed by using the conventional PyPI package manager as follows:

conda create --name clinicaEnv python=3.7
conda activate clinicaEnv
pip install clinica

Info

Since Clinica v0.3.5, Conda installation is no longer available (i.e. conda create --name clinicaEnv python=3.6 clinica -c Aramislab -c conda-forge will only install Clinica v0.3.4). Pip is now the only way to install the latest version of Clinica.

Installation of the third-party software packages¶

Depending on the pipeline that you want to use, you need to install pipeline-specific interfaces. Not all the dependencies are necessary to run Clinica. Please refer to this section to determine which third-party libraries you need to install.

Shell completion (optional)¶

Shell completion for Clinica is available for Bash, Fish and Zsh.

For Bash, add this to ~/.bashrc:

eval "$(_CLINICA_COMPLETE=source_bash clinica)"

For Fish, add this to ~/.config/fish/completions/clinica.fish:

eval (env _CLINICA_COMPLETE=source_fish clinica)

For Zsh, add this to ~/.zshrc:

eval "$(_CLINICA_COMPLETE=source_zsh clinica)"

Finally, open a new shell to enable completion.

Run the Clinica environment¶

Activation of the Clinica environment¶

Now that you have created the Clinica environment, you can activate it:

conda activate clinicaEnv
activate-global-python-argcomplete --user # Only the first time you activate the environment
eval "$(register-python-argcomplete clinica)"

Success

Congratulations, you have installed Clinica! At this point, you can try the basic clinica command and get the help screen:

(clinicaEnv)$ clinica
usage: clinica [-v] [-l file.log]  ...

clinica expects one of the following keywords:

    run                 To run pipelines on BIDS/CAPS datasets.
    convert             To convert unorganized datasets into a BIDS hierarchy.
    iotools             Tools to handle BIDS/CAPS datasets.
    visualize           To visualize outputs of Clinica pipelines.
    generate            To generate pre-filled files when creating new
                        pipelines (for developers).

Optional arguments:
  -v, --verbose         Verbose: print all messages to the console
  -l file.log, --logname file.log
                        Define the log file name (default: clinica.log)

If you have successfully installed the third-party software packages, you are ready to run any of the pipelines proposed by Clinica.

You can now learn how to interact with Clinica.

Deactivation of the Clinica environment¶

At the end of your session, remember to deactivate your Conda environment:

conda deactivate

Developer instructions¶

This section is intended for users who plan to contribute to Clinica or test the current development version.

Clinica uses Poetry to manage its development environment. Please follow these installation instructions and verify the poetry command is correctly setup.

First, create a separate development environment:

conda create --name clinicaDev python=3.7
conda activate clinicaDev

Then, clone the development branch of Clinica:

git clone --branch dev https://github.com/aramis-lab/clinica.git
cd clinica

Finally, install Clinica with the necessary development dependencies:

poetry install

In case you need to test the documentation locally, install the additional dependencies with:

poetry install --extras docs