Release clpipe 1.9.0 · cohenlabUNC/clpipe

1.9.0 (Sep 15, 2023)

postprocess - postprocess2 is now named postprocess, replacing the original postprocessing functionality
postprocess - Wildcards can now be used in the target_variables of the scrub configuration to select multiple columns with similar names, such as non_steady_state_outliers*
postprocess - BIDS index now saves to the user's working directory
postprocess - Logs now saved in folders according to stream, like the output and working directories
postprocess - Distributor-level slurm jobs removed, simplifying job structure and removing the distributor log folder
postprocess - Individual images now get their own rolling log files
postprocess - Slurm output files are now saved to a separate slurm_out folder
postprocess - There are now a default processing streams setup and named specifically for the GLM and functional connectivity analyses
glm - GLM setup command now completely removed, in favor of using the GLM postprocessing stream
documentation - Expanded documentation for Postprocessing section
documentation - Sections reorganized and made more consistent with each other.
project_setup - Now prompts for name of project if not given.
config update - Converts config to new format and offers to backup old version

postprocess - Fixed an issue where postprocess took excessively long to index large datasets due to a bug in pybids
postprocess - Issue where streams did not properly update postprocessing config fixed
documentation - path to HNG modules directory corrected - missing the 's' at the end

postprocess - Removed original postprocessing command
postprocess - Removed original susan command; now a step of postprocess
postprocess - Disabled fmri-process-check report for now, pending rework
postprocess - The stream file "processing_description.json" has been moved to the stream working directory and is now called "run_config.json"

convert2bids - dcm2bids v2.1.9 now enforced to prevent update to v3, which uses a newer version of BIDS incompatible with fMRIPrep <= v23
convert2bids - heudiconv v12.2 now enforced to prevent update to v13, which for mysterious reasons does not work in our environment
other - all other top-level dependencies locked in for now to prevent breaking updates

configuration - Dataclass-based configuration has been applied to all major clpipe commands
configuration - Configuration is now serialized/deserialized with Marshmallow, which allows both JSON and YAML file types to be used
postprocess - Global workflow now constructs image and confounds workflows on its own