pmacsPreps

*prep wrapper scripts for the PMACS cluster

Usage

The executable scripts are stored in bin/, eg

bin/runprep.sh [args]

runs a container of the form containers/modalityprep-version.sif.

The containers are not included in this repository.

The generic script runprep.sh is designed to run any prep; more specialized, specific scripts may be added later.

Container information

The shared installation on

/project/ftdc_pipeline/pmacsPreps

contains Singularity images built directly from DockerHub images, on a Ubuntu VM. Details can be found by running

singularity inspect containers/container-version.sif

This container information is written to the standard output at run time, and will be available in job logs.

templateflow

The compute nodes cannot access the Internet, so templateflow must be installed locally and the desired templates must be pre-fetched. A shared installation for FTDC users is used by default, which contains the 'tpl-MNI152NLin2009cAsym' (for normalization) and 'tpl-OASIS30ANTs' (for brain extraction).

Container sources

Current containers installed in

/project/ftdc_pipeline/pmacsPreps/containers

include:

• fmriprep from nipreps
• qsiprep from pennbbl