Quick Start Tutorial

This page describes the basic steps to run ASLPrep on a BIDS dataset. ASLPrep is containerized, and thus can be run with either Docker or Singularity. Here, we provide the most basic and user friendly workflow.

ASLPrep requires a valid BIDS dataset, like the Resting State Perfusion in Healthy Aging dataset on OpenNeuro. Using Chrome, you can download the data via the browser. Note that you might have to create a new folder into which you can download the data. You can also download the data using using datalad or aws.

This BIDS dataset should include the following file tree:


ASLPrep installation

For detailed instructions on installing ASLPrep, see Installation. Here we walk through installation with Docker.

For every new version of ASLPrep that is released, a corresponding Docker image is generated and pushed to DockerHub. In order to run ASLPrep Docker images, the Docker Engine must be installed.

We recommend using Docker or Singularity to run ASLPrep. The docker image can be pulled from the ASLPrep DockerHub using the command line.

docker pull pennlinc/aslprep:latest

Running ASLPrep

Running ASLPrep will require a FreeSurfer license file (you do not actually need Freesurfer, though), which can be requested here. Move this license to a folder in your $HOME directory (to find the path to your home directory in the terminal, echo $HOME) and call it license.txt.

In the Docker desktop application, please select Preferences > Resources > Advanced and select at least 12GB for RAM. Restart Docker.

Move the data directory to your $HOME directory (again, to find this location out, run this in the terminal: echo $HOME). Make sure it is called ds000240.

The following command, which should run in about 8 hours, can be called for a single participant:

docker run -ti -m 12GB --rm \
   -v $HOME/license.txt:/license.txt \
   -v $HOME/ds000240:/data:ro \
   -v $HOME/ds000240/derivatives:/out:rw \
   -v $HOME/tmp/ds000240-workdir:/work:rw \
   pennlinc/aslprep:latest \
   /data \
   /out/aslprep \
   participant \
   --participant-label 01 \
   --fs-license-file /license/license.txt \
   -w /work

Here is a breakdown of this command:

docker run -ti -m 12GB --rm \                   # attach to the container interactively
   -v $HOME/license.txt:/license/license.txt \  # mount the freesurfer license directory
   -v $HOME/ds000240:/data:ro \                 # mount the data directory to the container directory
   -v $HOME/ds000240-results:/out:rw \          # mount the output directory to the container directory
   -v $HOME/tmp/ds000240-workdir:/work \        # mount working directory
   pennlinc/aslprep:latest \                    # the container name, along with the version tag
   /data \                                      # the data directory
   /out/aslprep \                               # the output directory
   participant \                                # analysis type: participant
   --participant-label 01 \                     # select participant 01
   --fs-license-file /license.txt \             # setting freesurfer license file
   -w /work                                     # setting working directory

For additional options, see Usage Notes.

ASLPrep outputs

After a successful run, ASLPrep generates preprocessed ASL data, computed CBF maps, confound quality metrics, preprocessed structural images, as well as one HTML report per subject that provides visual assessment of the preprocessed data. See Outputs of ASLPrep for more information.