ASLPrep Installation

There are two ways to install ASLPrep:

Once the environment is set up (first option above), the next step is to execute aslprep on the command-line. The aslprep command-line options are documented in the Usage Notes section.:

$ aslprep <input_bids_path> <derivatives_path> <analysis_level> <named_options>

If you are using a docker or singularity image, the command-line call to ASLPrep will require binding configurations and options. The call to the docker or singularity image follows a similar format to standard installations, except that the binding configurations must be specified before the aslprep argument.

The command-line structure is as follows:

$ <container_command_and_options> <container_image> \
     <input_bids_path> <derivatives_path> <analysis_level> <ASLPrep_named_options>

Computer or HPC installation

Warning

This method is not recommended! Please check out container alternatives in Running ASLPrep via Docker containers, and Running ASLPrep via Singularity containers.

Make sure all of ASLPRep’s External Dependencies are installed. These tools must be installed and their binaries available in the system’s $PATH. A relatively interpretable description of how your environment can be set up is found in the Dockerfile. Note that FreeSurfer requires a license file, which can be requested here.

If Python 3.7 (or above) is installed, along with the pip command, ASLPRep can be installed using the following command

$ python -m pip install aslprep

Check your installation with the --version argument

$ aslprep --version

External Dependencies

ASLPRep is written using Python 3.7 (or above), and is based on nipype.

ASLPRep requires some other neuroimaging software tools that are not handled by Python’s packaging system (Pypi) used to deploy the ASLPrep package: