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Setting-up for Clinica

You will find below the steps for installing Clinica on Linux or Mac.

Prepare your Python environment with miniconda

You will need a Python environment to run Clinica.

We advise you to use Miniconda. It 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:

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

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

Installation path

Miniconda will ask you where to install it. Do not forget to copy the export PATH given at the end of the installation.

Verify your miniconda 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=3.10
conda activate clinicaEnv
pip install clinica
Conda installation

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.

Add the following to ~/.bashrc: 

eval "$(_CLINICA_COMPLETE=source_bash clinica)"

Add the following to ~/.config/fish/completions/clinica.fish: 

eval (env _CLINICA_COMPLETE=source_fish clinica)

Add the following 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

Verify Clinica installation

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

(clinicaEnv)$ clinica
Usage: clinica [OPTIONS] COMMAND [ARGS]...

Options:
  --version      Show the version and exit.
  -v, --verbose  Increase logging verbosity.
  -h, --help     Show this message and exit.

Commands:
  convert   Convert popular neuroimaging datasets to the BIDS format.
  generate  Instantiate a new pipeline from available templates.
  iotools   Tools to handle BIDS/CAPS datasets.
  run       Run pipelines on BIDS and CAPS datasets.

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 (optional)

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.

  1. Please follow these installation instructions for Poetry and verify the poetry command is correctly setup.

  2. Clone the development branch of Clinica:

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

  3. Create an environment for development:

    conda env create -f environment.yml

  4. Install Clinica with the necessary development dependencies:

    conda activate clinica_env
poetry install

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

    poetry install --extras docs

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