ASLPrep Installation
There are two ways to install ASLPrep:
within a Computer or HPC installation
using container technologies (RECOMMENDED), such as Running ASLPrep via Docker containers or Running ASLPrep via Singularity containers.
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
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:
FSL (version 6.0.2)
ANTs (version 2.2.0 - NeuroDocker build)
AFNI (version Debian-16.2.07)
C3D (version 1.0.0)
FreeSurfer (version 6.0.1)
bids-validator (version 1.1.0)
connectome-workbench (version Debian-1.3.2)