Version 1.8.0 Beta (Mar 13, 2021)

New Features

• BIDS-Derivatives Compatibility. C-PAC can now both ingress data and write data out according to the BIDS-Derivatives standard, enhancing interoperability with other BIDS-compatible neuroimaging packages.

  • This allows users to inject already-processed data directly into key intermediate points of the C-PAC pipeline.

  • In addition, clearer information on provenance of pipeline steps for multiple C-PAC strategies are also provided in BIDS-compatible JSON files for all output data.

  • The implementation of BIDS-Derivatives compatibility and its use flow regarding interoperability with other neuroimaging packages will continue to grow and adapt throughout later releases; stay tuned for changes and upgrades.

  • [https://bids-specification.readthedocs.io/en/latest/05-derivatives/01-introduction.html]

• Freesurfer Integration for Surface-Based Processing. The C-PAC pipeline can now run Freesurfer to generate surfaces, and to produce brain masks or tissue segmentation masks for use in the voxel-based pipeline, if the user desires.

  • Note: Due to the size of the Freesurfer installation, a separate, smaller C-PAC container without Freesurfer is also available if users wish to bypass surface-based analysis.

  • [https://surfer.nmr.mgh.harvard.edu/]

New Features - Pipeline Harmonization

• New BOLD Masking Option. A new anatomical brain mask-based BOLD masking option has been adapted from the ABCD pipeline of DCAN Labs.

  • [https://innovation.umn.edu/developmental-cognition-and-neuroimaging-lab/]

  • [https://github.com/DCAN-Labs/abcd-hcp-pipeline]

• New Frequency Filtering Option. AFNI 3dBandpass has been integrated as another option for frequency filtering of BOLD data during nuisance correction.

  • [https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dBandpass.html]

Improvements

• Memory Usage Optimization. C-PAC ’ s memory usage estimates have been improved - this should reduce the occurrence of pipeline crashes caused by exceeding the memory limits of shared computing resources.

• Cleaner Pipeline Configuration. The pipeline configuration YAML format has been upgraded to a cleaner, easier-to-read nested format.

• Pipeline Configuration Importing. If configuring your pipeline directly through a YAML file, C-PAC ’ s pre-configured pipelines can now be imported into a YAML file. This allows users to specify only small segments of the pipeline they wish to change, when basing off of a default or pre-configured pipeline.

Developer Improvements

• Modularized Pipeline Blocks. C-PAC’s workflow segments have been modularized for easier development and methods integration, and for easier testing.

Bug Fixes

• An error sometimes preventing users from supplying custom nuisance regressors to C-PAC has been resolved.

In addition, the C-PAC Docker and Singularity images, as well as the AWS AMI, have all been updated. These provide a quick way to get started.

And as always, you can contact us here for user support and discussion: https://groups.google.com/forum/#!forum/cpax_forum