Running xcp_d via Singularity containers

If the data to be preprocessed is also on the HPC or a personal computer, you are ready to run xcp_d.

$ singularity run --cleanenv xcp_d.simg \
    path/to/data/fmri_dir  path/to/output/dir \
    --participant-label label

Relevant aspects of the $HOME directory within the container. By default, Singularity will bind the user’s $HOME directory on the host into the /home/$USER directory (or equivalent) in the container. Most of the time, it will also redefine the $HOME environment variable and update it to point to the corresponding mount point in /home/$USER. However, these defaults can be overwritten in your system. It is recommended that you check your settings with your system’s administrator. If your Singularity installation allows it, you can work around the $HOME specification, combining the bind mounts argument (-B) with the home overwrite argument (--home) as follows:

$ singularity run -B $HOME:/home/xcp --home /home/xcp \
      --cleanenv xcp_d.simg <xcp_d arguments>