Installation🔗

FreeSurfer License🔗

This software includes a FreeSurfer 5.3.0 installation. A FreeSurfer License, available separately, is required to run.

Follow this link for a FreeSurfer License

Using Docker🔗

Before running, you will need to load the image onto your Docker service by running the following command:

docker pull dcanumn/abcd-hcp-pipeline

If you receive a "no space left on device" error during this pull process, you may need to clean up any old/dangling images and containers from the docker registry, and possibly increase the amount of space allocated to Docker.

Using Singularity🔗

You can either pull the image from the Docker repository, or build it from the repository for the image to be saved in the working directory.

singularity pull docker://dcanumn/abcd-hcp-pipeline

singularity build abcd-hcp-pipeline.sif docker://dcanumn/abcd-hcp-pipeline

These are essentially the same, but in the latter case you have control over the name of the .sif file.

Installing and running the pipeline from source is not recommended, but it is an option if Docker and Singularity are not available on your system. This requires installing the dependencies specified in the pipeline Dockerfile, including the contents of the DCAN internal-tools and DCAN external-software Dockerfiles.

Environment variables must be set in accordance with /app/SetupEnv.sh; then the pipeline may be run with python3 /app/run.py <args>