cohenlabUNC/clpipe: clpipe v1.7.3

Enhancements

• setup: the "SourceOptions" block for dicom flywheel_sync is now included in the default configuration file
• setup: more modality examples added to conversion_config.json starter file (T1w and fmap)
• setup: conversion_config.json starter file now includes dcm2niix customization line which sets its search depth to its maximum value, allowing dcm2bids to work with flywheel's DICOM sync directory
• setup: the default .bidsignore file now includes scans.json, a file generated by heudiconv which would cause validation to fail otherwise
• bids validate: In clpipe_config.json, Moved BIDSValidatorImage from PostprocessingOptions block to BIDSValidationOptions block. The command will still look for the image in its old location if it can't find it in BIDSValidationOptions, maintaining backwards compatibility with < 1.7.3 config files
• preprocess: Leaving the [TemplateFlowPath] empty no longer results an unhelpful message
• glm prepare: improved logging messages
• glm prepare : changed how file copying works so only file contents are copied, not their permissions, making the command easier to run in a shared environment
• clpipe: -config_file/-c is now a required argument in most commands to prevent unhelpful error output if no config file given, and to steer clpipe more towards being configuration file driven
• clpipe: ignore writing to clpipe.log if the user does not have permission to do so
• clpipe: clpipe.log file now includes usernames
• clpipe: clpipe.log file is written with group write permission by default

• setup: generated glm_config.json file's [GLMSetupOptions][LogDirectory] field is now automatically filled out. Previously it was left blank, despite the appropriate log folder being automatically created, and would throw an error in the batch manager if not filled out manually.
• reports fmriprep: fixed issue where the main .html report files were not being bundled into the output zip
• glm prepare: fixed issue where FileNotFoundErrors were not caught correctly, causing the program to exit earlier than intended