You will find below the steps for installing Clinica on Linux or Mac. Please do not hesitate to contact us on the forum if you encounter any issues with the installation of Clinica.
Installation of Clinica¶
You will need a Python environment to run Clinica. To do that, we advice you to download Miniconda allows you to install, run, and update Python packages and their dependencies. To install Miniconda, open a new terminal and type the following commands:
If you are on Linux:
curl https://repo.continuum.io/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.continuum.io/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 (just in case). 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.
Depending on the pipeline that you want to use, you need to install Pipeline-specific interfaces. Not all the dependencies are necessary to Clinica. Please refer to this section to determine which third-party libraries you need to install.
Clinica can be installed using the Conda package manager. If you want to try the last release of Clinica you can install it by typing the following command in your command line session:
conda create --name clinicaEnv python=2.7 clinica -c Aramislab -c conda-forge
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.
Running the Clinica environment¶
Activation of the Clinica environment¶
Now that we have created the Clinica environment, you can finally activate it:
source activate clinicaEnv activate-global-python-argcomplete --user
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. 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, you are ready to run any of the pipelines proposed by Clinica.
It should display a help describing the different categories of command line (see Interacting with Clinica for further explanations).
Deactivation of the Clinica environment¶
At the end of your session, remember to deactivate your Conda environment:
If you plan to contribute to Clinica or 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 our GitLab repository
git clone https://gitlab.icm-institute.org/aramislab/clinica.git.
Then, we suggest to create a custom Conda environment and install Clinica using the YAML file to guarantee the dependencies:
cd clinica conda env create -f environment.yml
By default, the environment name is
clinica_env but you can choose a different name by adding the option
Once the environment is created, Clinica can be installed inside. Remember to activate the environment before proceeding
source activate clinica_env pip install -e . activate-global-python-argcomplete --user
If everything goes well, type
clinica and you should the help message which is displayed above.
At the end of your session, you can deactivate your Conda environment:
Remember that Clinica will be only available inside of your Conda environment.