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C-PAC Version 1.8.0 Beta
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@sgiavasis sgiavasis released this 13 Mar 01:03
v1.8.0
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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

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