flywheel/c-pac repository overview

⁠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.