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C-PAC Version 1.8.3 Beta
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@shnizzedy shnizzedy released this 11 Feb 22:00
· 3125 commits to main since this release
v1.8.3
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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-v1.8.3-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.

New features

  • Added XCP-style quality control file
  • Added RBC-options pipeline preconfiguration
  • Added engine.log (when verbose debugging is on)
  • Added ability to fix random seed for
    • antsAI
    • antsRegistration
    • Atropos (fixed but not specified)
    • fslmaths
    • mri_vol2vol
    • recon-all
  • Added ability to use lateral ventricles mask in place of cerebrospinal fluid mask when when segmentation is Off, specifically for the rodent pipeline, but works on any dataset when segmentation is off

Improvements

  • In a given pipeline configuration, segmentation probability maps and binary tissue masks are warped to template space, and those warped masks are included in the output directory

    • if registration_workflows['functional_registration']['EPI_registration']['run segmentation'] is On and segmentation['tissue_segmentation']['Template_Based']['template_for_segmentation'] includes EPI_Template

      and/or

    • if registration_workflows['anatomical_registration']['run'] is On and segmentation['tissue_segmentation']['Template_Based']['template_for_segmentation'] includes T1_Template

  • Renamed connectivity matrices from *_connectome.tsv to *_correlations.tsv
  • Moved some ephemeral logging statements into pypeline.log

Bug fixes

  • Fixed bug in which working connectivity matrix filepaths were generated incorrectly, preventing generating matrices depending on container bindings
  • Fixed broken links in README
  • Fixed bug in which anatomical-only configurations required functional data directories
  • Fixed bug in which nuisance regressors would crash when segmentation is off and no CSF mask is provided
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