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Alexandre Routier edited this page Jul 10, 2020 · 10 revisions

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.

Quick start

Installation of Clinica

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.

Clinica can be installed either by using the conventional PyPI package manager or by using the Conda package manager. In both cases, it is a good idea to create an isolated environment if you want to preserve other already installed Python libraries.

Using Conda

The latest release of Clinica can be installed using Conda as follows:

conda create --name clinicaEnv python=3.6 clinica -c Aramislab -c conda-forge

It will download all the needed packages and create the Clinica environment.

!!! info This command will create an environment called clinicaEnv. Clinica is already installed inside it. The option -c Aramislab tells Conda to search the package on the Aramis conda channel.

Using pip

The latest release of Clinica can be installed using pip as follows:

conda create --name clinicaEnv python=3.6
conda activate clinicaEnv
pip install 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.

Running 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: ```bash (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](../InteractingWithClinica).

Deactivation of the Clinica environment

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

conda deactivate

Developer installation

If you plan to contribute to Clinica or if you want to have the current development version, you can either:

  • Download the tarball for a specific version from our repository. Then decompress it.
  • Clone Clinica's repository from GitHub:
git clone https://github.com/aramis-lab/clinica.git

We suggest creating a custom Conda environment and installing Clinica using the provided YML file:

cd clinica
conda env create -f environment.yml

By default, the environment is named clinica_env. You can choose a different name by adding the option --name my_clinica_environment.

Clinica is installed within the environment created. Remember to activate the environment before proceeding:

conda activate clinica_env
pip install -e . # Only the first time you activate the environment
activate-global-python-argcomplete --user # Only the first time you activate the environment
eval "$(register-python-argcomplete clinica)"

If everything goes well, type clinica and you should see the help message which is displayed above.

At the end of your session, you can deactivate your Conda environment:

conda deactivate

Remember that Clinica will be only available inside your Conda environment.

!!! warning "In case your face ResolvePackageNotFound: python==3.6 error" When installing Clinica with conda, you may see the following error: ``` Collecting package metadata (repodata.json): done Solving environment: failed

ResolvePackageNotFound:
- python==3.6
```
This is caused by newer version of conda. This has been corrected recently in the `dev` branch on Clinica.
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