C-PAC Version 1.8.1 Beta

This version of C-PAC is deprecated due to a bug in single_step_resampling. Unless you have a specific reason to use this version of C-PAC, we recommend upgrading to at least version 1.8.4. See https://fcp-indi.github.io/docs/latest/user/release_notes/v1.8.4 for more information about C-PAC v1.8.4. To use this version anyway, you can pull fcpindi/c-pac:release-v1.8.1-DEPRECATED from Docker Hub.

Critical Alert for fMRIPrep-Options in C-PAC v1.8.1 - v1.8.3

• Fixed a bug that was causing single_step_resampling, when combined with certain other configurations, to inadvertently cause unexpected forks in the pipeline past transform application.

  • This bug caused any affected fmriprep-options-based pipeline configurations (including fx-options and rbc-options) to produce BOLD time series write-outs to the output directory in template space which were not nuisance regressed or filtered, for C-PAC versions 1.8.1 through 1.8.3.

  • Although these outputs were not expressly labeled as nuisance regressed or filtered, they were labeled as preprocessed with desc-preproc and were the only functional data transformed to template space and used for downstream processing, such as ROI-based timeseries extraction.

  • If you are unsure if you have been affected, you can check the side-car JSON for your template-space BOLD data from these versions for those pipeline configurations, as the JSON will still accurately reflect what operations had been performed on the data.

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New Features & Pipeline Harmonization

• ABCD-BIDS Pipeline Harmonization.
  • The ABCD-BIDS pipeline of the ABCD study can now be reproduced by running the abcd-options preconfig in C-PAC.
• 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

• NOTE: The C-PAC default pipeline has been updated to use the whole-head T1w image as the input (moving) image for ANTs T1w-to-template registration. Comparisons with previous versions of C-PAC will show this change.
• 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.