Version 1.8.2 Beta (Dec 02, 2021)

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-v1.8.2-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.

  • Usability testing and optimization for the following minimal processing pipelines employed in the Li et al., Milham manuscript (BioRxiv) is complete and they are available:

    • CPAC:CCS

    • CPAC:ABCD-BIDS

    • CPAC:fMRIPrep

    • CPAC:Default

  • The ABCD-BIDS surface-based postprocessing pipeline is implemented, though final usability testing and optimization is pending and will be in next release.

Added

  • Added FSL-TOPUP as an option for distortion correction.

  • Added changelog

  • Added CHD8 mouse template (/cpac_templates/chd8_functional_template_noise_mask_ag.nii.gz)

  • Added commandline flags --T1w_label and --bold_label

  • Added the ability to ingress an entire FreeSurfer output directory to bypass surface analysis if already completed elsewhere

  • Added AFNI and Nilearn implementations of Pearson and partial correlation matrices

Changed

  • Expanded meta-data ingress for EPI field maps to include more fields when parsing BIDS sidecar JSONs.

  • Updated possible inputs for T2w processing and ACPC-alignment blocks to increase the modularity of these pipeline options.

  • master branch renamed main

  • Packaged templates in https://github.com/FCP-INDI/C-PAC_templates

Deprecated

  • master branch name (renamed main)

Fixed

  • Fixed bug in which the preprocessed T2w data would not be found in the resource pool when expected.

  • Fixed bug in which distortion correction-related field map ingress would raise IndexError: list index out of range when ingressing the field maps.

  • Fixed bug in which some nodes would raise KeyError: 'in_file' when estimating memory allocation

  • Improved memory management for multi-core node allocation.

  • Fixed bug where --participant_label [A B C] would skip first and last labels (A and C).

  • Stripped the ABI tag note (which was preventing the library from loading dynamically on some host operating systems) from libQt5Core.so.5 in the ABCD-HCP variant image.

  • Fixed an issue blocking non-C-PAC output data from being read in without sidecar meta-data.