Running ASLPrep via Singularity containers¶
Preparing a Singularity Image¶
Singularity version >= 2.5: If the version of Singularity installed on your HPC system is modern enough you can create a Singularity image directly on the system using the following command:
$ singularity build aslprep-<version>.simg docker://pennlinc/aslprep:<version>
<version> should be replaced with the desired version of ASLPrep that you
want to download.
Running a Singularity Image¶
If the data to be preprocessed is also on the HPC or a personal computer, you are ready to run ASLPrep.
$ singularity run --cleanenv aslprep.simg \ path/to/data/dir path/to/output/dir \ participant \ --participant-label label
Handling environment variables¶
By default, Singularity interacts with all environment variables from the host.
The host libraries could accidentally conflict with singularity variables.
To avoid such a situation, it is recommended that you sue the
--cleanenv or -e
$ singularity run --cleanenv aslprep.simg \ /work/789/asdf/ $WORK/output \ participant \ --participant-label 01
Relevant aspects of the
$HOME directory within the container.
By default, Singularity will bind the user’s
$HOME directory on the host
/home/$USER directory (or equivalent) in the container.
Most of the times, it will also redefine the
$HOME environment variable and
update it to point to the corresponding mount point in
However, these defaults can be overwritten in your system.
It is recommended that you check your settings with your system’s administrators.
If your Singularity installation allows it, you can work around the
specification combining the bind mounts argument (
-B) with the home overwrite
--home) as follows:
$ singularity run -B $HOME:/home/aslprep --home /home/aslprep \ --cleanenv aslprep.simg <aslprep arguments>