This repository defines a Docker image containing XCP-D and example data. When you run the Docker image, it will apply XCP-D to the example data and write out XCP-D derivatives.
The example data are located in /data/EF/derivatives/fmriprep
within the Docker image.
NOTE: You will need to provide your own FreeSurfer license (labeled <path_to_Freesurfer_license_file>
below).
- Open terminal
- Navigate to where you want your XCP-D outputs to be generated (labeled
<path_to_test_folder>
below). - Download the container:
- For Singularity:
singularity build xcp_walkthrough.sif docker://pennlinc/xcp_walkthrough:main
- For Docker:
docker pull pennlinc/xcp_walkthrough:main
- For Singularity:
- Run the walkthrough!
#$ -l h_vmem=40G # Allot at least 40G; this is the format for submitting via an SGE cluster
singularity run --cleanenv \
-B <path_to_test_folder> \
<path_to_test_folder>/xcp_walkthrough.sif \
/data/EF/derivatives/fmriprep \
<path_to_test_folder>/output \
--fs-license-file <path_to_Freesurfer_license_file> \
participant \
-vv
docker run --rm -ti \
-v <path_to_test_folder>:/out \
-v <path_to_Freesurfer_license_file>:/license.txt \
pennlinc/xcp_walkthrough:main \
/data/EF/derivatives/fmriprep \
/out \
--fs-license-file /license.txt \
participant \
-vv