tedana.workflows.ica_reclassify_workflow
- ica_reclassify_workflow(registry, accept=[], reject=[], out_dir='.', config='auto', convention='bids', prefix='', tedort=False, mir=False, no_reports=False, png_cmap='coolwarm', overwrite=False, debug=False, quiet=False, reclassify_command=None)[source]
Run the post-tedana manual classification workflow.
Please remember to cite [1].
- Parameters:
registry (
str) – The previously run registry as a JSON file.accept (:obj: list) – A list of integer values of components to accept in this workflow.
reject (:obj: list) – A list of integer values of components to reject in this workflow.
out_dir (
str, optional) – Output directory.tedort (
bool, optional) – Orthogonalize rejected components w.r.t. accepted ones prior to denoising. Default is False.mir (
bool, optional) – Run minimum image regression after denoising. Default is False.no_reports (obj:’bool’, optional) – Do not generate .html reports and .png plots. Default is false such that reports are generated.
png_cmap (obj:’str’, optional) – Name of a matplotlib colormap to be used when generating figures. Cannot be used with –no-png. Default is ‘coolwarm’.
debug (
bool, optional) – Whether to run in debugging mode or not. Default is False.overwrite (
bool, optional) – Whether to force file overwrites. Default is False.quiet (
bool, optional) – If True, suppresses logging/printing of messages. Default is False.reclassify_command (
str, optional) – The command used to run ica_reclassify. Default is None.
Notes
This workflow writes out several files. For a complete list of the files generated by this workflow, please visit https://tedana.readthedocs.io/en/latest/outputs.html
References