Version 1.8.1 Beta (Sep 17, 2021)¶

New Features & Pipeline Harmonization

  • ABCD-BIDS Pipeline Harmonization.

  • CCS Pipeline Harmonization.

    • A new BOLD masking option, CCS_Anatomical_Refined, has been added. This has been adapted from the BOLD mask method from the CCS pipeline.

    • New T1 masking options using Freesurfer have been added to facilitate the harmonization with the CCS pipeline.

    • A preconfigured pipeline that reproduces the CCS pipeline is now available.

  • fmriprep Pipeline Harmonization Updated.

    • The fmriprep-options preconfigured pipeline, which reproduces the fmriprep pipeline, has been updated to reflect recent changes.

Improvements

  • Further improvements to memory management for less frequent hanging have been integrated, in an ongoing process.

  • Freesurfer’s Recon-All functionality in C-PAC has been opened to further configurability.

  • More options for selecting a reference for slice-timing correction have been added.

  • Description and other meta-data fields have been added to some output JSON sidecar files in an ongoing process to make output data descriptors clearer.

  • DVARS calculation is now performed using AFNI 3dTto1d, increasing computation speed.

  • Manually inserting input data to a C-PAC output directory for ingress is now easier. A sidecar JSON containing meta-data will be produced for the data automatically if one is not provided.

  • For developers: improvements to the codebase have streamlined the process of adding new output data types to C-PAC through a central table, in line with recent v1.8 changes and the move to BIDS-Derivatives compliance.

Bug Fixes

  • Choosing On/Off for nuisance regression once again correctly produces the non-cleaned BOLD outputs in addition to any nuisance regression strategies.

  • Forking T1 and EPI based registration while simultaneously forking ANTs and FSL registration options no longer crashes the pipeline.

  • An error where the DVARS calculation step would cause the pipeline to hang has been resolved.

  • All nuisance regression choices are now available for EPI-registration based pipelines.

  • The mem_gb input parameter for memory allocation no longer overrides other memory selections, when left unspecified.

  • The selected_volume option for motion correction reference is now working again.