Version 1.7.0 Beta (Jul 23, 2020)

New Features

• New Command Line Interface. The cpac pip-installable package is now available. This CLI allows you to use C-PAC from the command line without interacting via container-based (Docker, Singularity) CLI commands.

• Anatomical Longitudinal Pipeline. C-PAC can now explicitly handle longitudinal data. The dedicated anatomical pipeline generates robust participant-specific templates that improve the registration of longitudinal data and increase reliability.

  • [https://www.sciencedirect.com/science/article/pii/S1053811912002765?via%3Dihub]

• Prior-Based Segmentation. DCAN Labs ANTS prior-based tissue segmentation is now available. This approach is thought to be advantageous in the segmentation of the non-human primate brain.

  • DCAN Labs

  • nhp-ABCD-BIDS-pipeline

• Physiological Noise Filtering for Motion Estimates. Adapted from DCAN Labs, C-PAC can now apply a notch filter to mitigate respiratory artifacts that may present issues in motion estimation.

  • DCAN Labs

  • https://www.biorxiv.org/content/10.1101/337360v1.full.pdf

• Tissue Mask Ingress. In an increase of pipeline flexibility, C-PAC can now intake pre-existing anatomical tissue masks if desired, bypassing tissue segmentation. This is particularly important for researchers using manual or manually edited segmentations.

Improvements

• Pipeline speed increase: Motion correction using AFNI 3dvolreg can now be completed faster by dedicating multiple CPUs to each participant. This can provide a major speed increase in data with many TRs, as motion correction is often one of the processing time bottlenecks in a pipeline.

• C-PAC now writes out smoothed functional time series, when spatial smoothing is chosen (previously smoothing was only applied to derivatives).

Documentation Improvements

• The C-PAC User Guide now features versioned access! You can now view the user guide for any current or previous supported version (1.5+) of C-PAC.

Error Fixes

• A memory error triggered by aCompCor DetrendPC in nuisance regression has been resolved.

• An error that sometimes prevented the pipeline from starting when censoring was enabled has been resolved.

• An error that would prevent data configuration generation from finishing if hidden files were in the data directory has been resolved.

• The “SameFileError” crash has been resolved. This error did not have any impact, but it would cause many crash files to be generated.

Coming Soon

• Pipeline Dashboard

• Surface-Based Processing

• BIDS-Derivatives Compatibility

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