FCP-INDI/C-PAC: CPAC Version 1.0.3 Beta

• Field map distortion correction via FSL FUGUE has been introduced as a pre-processing option. Users can provide the phase difference and magnitude files required to generate the field map (if applicable) through the data configuration (participant list) builder. See the User Guide section about distortion correction for more information.

• The data configuration (participant list) builder has been significantly upgraded:

  • The Subject/Participant list YAML file has been renamed the "Data Configuration" file. What used to be named the "data config", which contains the presets used to generate the participant list, has been renamed the "Data Settings" file. This also makes the main CPAC interface consistent with the CPAC BIDS-App. See the User Guide section about building a data configuration file for more information.
  • The layout and naming of fields in the data configuration builder GUI are now clearer.
  • A new script called cpac_data_config_setup.py has been introduced, which allows users to quickly and easily create a data settings template for modification, and then use this data settings file to generate their data configuration. This script does the same thing that the data configuration builder GUI does, except without needing to be able to open the GUI (for example, when SSHing into a server).
  • Input data can now be filtered by site, session, and series.
  • Support for BIDS-protocol scan parameter reading from JSON files has been introduced.
  • More informative status messages have been introduced detailing the data configuration building process (progress, amount of input data found, etc.).
  • A bug sometimes causing some scans to not be included in a participant entry has been fixed.
  • Data configuration files (participant lists) are now ordered by site, and then participant ID, for easier searching and navigation when manually viewing or editing the YAML file.

• The bug in the group-level analysis model builder GUI reported earlier, where the ordering of the contrasts in the contrast matrix provided to FSL FLAME did not always match the order in which they were specified in the group model builder GUI, has been fixed.

• Fixed a bug where sometimes de-spiking could cause a crash if no volumes are marked for excessive motion.

The following updates from the 1.0.2a hotfix are also included in the 1.0.3 release:

• An error introduced in v1.0.2 that was causing the CompCor nuisance regression strategy to not run even if it was selected, has been fixed.
• Logging can now be disabled by entering "run_logging: False" in your pipeline configuration YAML file.
• The formatting of the motion parameters CSV file has been fixed.