clpipe 1.9.1

1.9.1 (Dec 7, 2023)

Enhancements

• convert2bids - This command will now detect whether dcm2bids or heudiconv is being used based on the extension type of the conversion config file. dcm2bids is used when a .json file is given, and heudiconv is used when .py. The -heudiconv
• clpipe - When creating a new project, a .clpipe folder is now created which houses
  a batch_config.json file. This allows users to easily update batch config defaults
  without having to create their own batch_config.json file. This file is referenced
  from the users standard clpipe_config.json file. The .clpipe folder will
  be used in the future to store any additional files that apply to an entire project.
• clpipe - Stack trace is now hidden again when -debug is not being used, like in
  older versions of clpipe (< v1.6)
• postprocess - Indexing / query time slightly improved through use of pattern-based indexing exceptions

Bug Fixes

• postprocess - Image scrubbing node now properly persists header information
• bids_validate - Fixed issue where SLURM logs did not save to log folder after 1.9
• preprocess - Fixed issue where SLURM logs did not save to log folder
  after 1.9
• N_threads not being passed in from the configuration file when running preprocessing.
• Fix a bug where email addresses were not being properly formatted in slurm command.
• Update mem_use in ROI extract to use correct config value.
• Add transform method to convert between snake_case and camelCase to support camelCase legacy. Supposed to be slowly deprecated and replaced with snake_case eventually, but this acts as a bridge in the meanwhile.
• Fix mem/threads/time usage in job manager.
• Update custom atlas help documentation to say "sphere" instead of "spheres".

Development

• job_manager - Introduced JobManagerFactory for streamlined job manager selection and instantiation to replace the old BatchManager with BatchJobManager and LocalJobManager, enhancing job submission flexibility and configuration options.
• job_manager - Upgraded job submission mechanism from os.system to subprocess.run for better process handling and output capture, especially when jobs are run locally.

Documentation

• Updated flywheel_sync.rst to include links and a section to use flywheel_sync with an example script.
• Added an image and more text to bids_convert.rst.
• Updated dicom2bids_tutorial.md to add more helpful information and hyperlinks.