flywheel-apps / c-pac

Configurable Pipeline for the Analysis of Connectomes (C-PAC)

The C-PAC gear is now hosted on GitLab

flywheel/c-pac

Configurable Pipeline for the Analysis of Connectomes (C-PAC).

A configurable, open-source, Nipype-based, automated processing pipeline for resting state fMRI data. Designed for use by both novice users and experts, C-PAC brings the power, flexibility and elegance of Nipype to users in a plug-and-play fashion; no programming required.

Website

The C-PAC website is located here: http://fcp-indi.github.com/

Usage Notes

This gear downloads the BIDS directory structure from the associated flywheel session and processes it according to the selected parameters and the prefered pipeline configuration (default or the optional pipeline_file input).

The parameters that can be configured through the gear interface are:

• anat_only - Only run anatomical preprocessing.
• n_cpus - Number of execution resources available for the pipeline(==0: Use default).
• mem_mb - Amount of RAM available to the pipeline in megabytes. Included for compatibility with BIDS-Apps standard, but mem_gb is preferred (<=0: Use default of 6 GB).
• mem_gb - Amount of RAM available to the pipeline in megabytes. If this is specified along with mem_mb, this flag will take precedence.d (==0: Use default of 6 GB).
• save_working_dir - Save the contents of the working directory.

These are a subset of the parameters that can be specified in running the C-PAC pipeline from the command-line.

Extra parameters for troubleshooting and data-management:

• gear-save-output-on-error - Save the contents of the working directory to output on failure (can be large).
• gear-run-bids-validation - Run bids-validator on a the gear bids directory.
• gear-abort-on-bids-error - If bids-validator returns an error, abort gear execution.

For a supplied pipeline file, it is recommended to use a C-PAC configuration GUI to reduce the potential for errors.

The size of the zipped gear output will depend on the C-PAC pipeline settings. For example, the zipped output of the defaultpipeline can exceed 4 GB. However, using the --anat-only flag will reduce this to under 70 MB.