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C-PAC Version 1.8.6 Beta

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@e-kenneally e-kenneally released this 15 Jan 20:19
· 278 commits to main since this release
v1.8.6
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Learn about vigilant mode.

New Features

  • C-PAC can now ingress fMRIPrep output data.
    • Users can now perform further processing on fMRIPrep-processed data through C-PAC, using any template-space processing they wish to employ. This includes using the nuisance confounds generated by fMRIPrep to perform nuisance denoising on the preprocessed BOLD data.
    • A fMRIPrep-ingress pre-configured pipeline configuration (pre-config) has been created to make it easy to get started. This pre-config can be modified to suit a user's specific processing needs.
    • This is part of a wider project leading to the ability to easily ingress any BIDS-format output directory.

Improvements

  • The motion parameter and motion derivative outputs have been converted to BIDS-compliant formats.
  • A tip box has been added to appear when C-PAC returns with a "missing outputs" error.
  • The data configuration builder tool can now easily add FreeSurfer output directories for the purpose of ingressing FreeSurfer data into your C-PAC pipeline.
  • A large number of C-PAC's dependencies has been upgraded to more recent versions, including
    • Ubuntu (18.04 'Bionic Beaver' → 22.04 'Jammy Jellyfish')
    • Python (3.7.13 → 3.10.6)
    • AFNI (21.1.00 'Domitian' → 23.3.09 'Septimius Severus')
    • ANTs (2.3.3 'Leptomyrmex' → 2.4.3 'Emplastus')
    • FSL (5.0.9 → 6.0.6.5)
    • Nipype (1.5.1 → 1.8.6)
  • Please refer to the "Upgraded dependencies" section of the changelog for 1.8.6 or the release notes in the user guide for a full list of these upgrades.
  • torch, a large dependency that is used by U-Net and nothing else in C-PAC, has been removed from the pre-installed dependencies in the C-PAC image and is now installed in the container at runtime if U-Net is selected in the configuration being run.

Bug Fixes

  • When motion parameters are filtered, C-PAC now uses the filtered version of the motion parameters downstream - for example, in nuisance regression/denoising.
  • Fixed a bug where some connectivity matrices wouldn't generate if anatomical and functional outputs were in different resolutions.
  • Repaired the handling of 3dECM (network centrality) outputs for AFNI ≥ 21.1.1.
  • Fixed a bug (introduced in v1.8.0) where sparsity thresholds were not being scaled for network centrality.
  • Fixed a bug where calculate_motion_first would not calculate motion at all.
  • Fixed an error message that was reporting missing resources in pipeline nodeblocks, but was referring to the incorrect nodeblock in question.
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