cohenlabUNC/clpipe: clpipe v1.7.0

CLI Updates clpipe's subcommands have been reorganized / renamed to make them (hopefully) more intuitive. Please note that the original commands (e.g. project_setup, convert2bids, etc.) still remain and probably wouldn't be removed without several versions containing deprecation warnings, perhaps in prelude to clpipe 2.0.0 ordering of main clpipe menu now reflects order of processing steps (e.g. setup, bids, preprocess, postprocess) ordering of glm sub-menu now reflects order of processing steps (e.g. setup, fsl_onset_extract, l1_prepare_fsf, etc.) clpipe sub-commands "convert2bids" and "bids_validate" are now part of the clpipe sub-command "bids" as "convert" and "validate," respectively clpipe sub-command "fmriprep_process" renamed to "preprocess" to generalize the step clpipe sub-command "project_setup" shortened to "setup" clpipe sub-command "apply_mumford_workaround" shortened to "apply_mumford" Usage: clpipe [OPTIONS] COMMAND [ARGS]... Welcome to clpipe. Please choose a processing command. Options: -v, --version Display clpipe's version. --help Show this message and exit. Commands: setup Set up a clpipe project bids BIDS Commands preprocess Submit BIDS-formatted images to fMRIPrep postprocess Additional preprocessing for connectivity analysis postprocess2 Perform additional processing on fMRIPrepped data glm GLM Commands status Check the status of your project Usage: clpipe glm [OPTIONS] COMMAND [ARGS]... GLM Commands Options: --help Show this message and exit. Commands: setup Prepare task images and confound files for GLM analysis fsl_onset_extract Convert onset files to FSL's 3 column format l1_prepare_fsf Propagate an .fsf file template for L1 GLM analysis launch Launch all prepared .fsf files for L1 or L2 GLM... apply_mumford Apply the Mumford registration workaround to L1 FEAT... l2_prepare_fsf Propagate an .fsf file template for L2 GLM analysis report_outliers Generate a confound outliers report. Return of Heudiconv Heudiconv has returned to clpipe as an alternative to dcm2bids for handling more complicated BIDS conversions that cannot be adequately handled with a conversion_config.json file. It is accessed through the same command as dcm2bids, clpipe bids convert Example (note the abbreviate forms of -config_file and submit to -c and -s, respectively): clpipe bids convert -heudiconv -c path/to/my/config.json -s The heuristic.py file is given in the same place that your conversion_config file would go in the DICOMToBIDSOptions: "DICOMToBIDSOptions": { ... "ConversionConfig": "/path/to/project/heuristic.py", ... Update to Python 3.7 To support heudiconv v11, an update to Python > 3.7 was necessary. This is also the recommended minimum version for nypipe, a large dependency of clpipe. Misc Updates bids convert Fix a bug where values in the configuration file were being updated with values given in the CLI options Command now takes multiple subjects as arguments instead of the previous -subject option. The -subject option now warns users that they can use subject arguments. This brings its functionality in line with how the postprocessing scripts handle subjects. clpipe bids convert 111 222 -config_file /path/to/project/clpipe_config.json -submit glm apply_mumford Automatically create reg folder if it doesn't exist (such as when you don't use FEAT for preprocessing) Added debug option Increased verbosity of outputs glm l1_prepare_fsf Added additional outputs No longer eats uncaught errors when not in debug mode postproc2 Cleaned up folder organization of log files for distributed tasks Defer creation of folders until necessary, to prevent empty folders from being created when an error occurs before processing starts "Debug" option now propagates down to distributed jobs ApplyAROMA implementation "fsl_regfilt_R" is now platform independent (previously the R package installation path was hard-coded to work with UNC longleaf) Other Fix a bug in bids validate where the submission message was double printed Added output messages / logging to project setup command Updated documentation to use auto-generated click CLI documentation Added documentation page for unified CLI Add a simple bash build scrip