tedana.workflows.ica_reclassify_workflow

ica_reclassify_workflow(registry, accept=[], reject=[], tag_accept=[], tag_reject=[], out_dir='.', config='auto', convention='bids', prefix='', tedort=False, mir=False, no_reports=False, png_cmap='coolwarm', verbose=False, overwrite=False, debug=False, quiet=False, reclassify_command=None)

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.

• tag_accept (:obj: list) – A list of classification tags to add to accepted components. Will be applied to all listed accepted components, even if they were already accepted.

• tag_reject (:obj: list) – A list of classification tags to add to rejected components. Will be applied to all listed rejected components, even if they were already rejected.

• 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’.

• verbose (bool, optional) – Generate intermediate and additional files. Default is False.

• 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

[1]

DuPre, E. M., Salo, T., Ahmed, Z., Bandettini, P. A., Bottenhorn, K. L., Caballero-Gaudes, C., Dowdle, L. T., Gonzalez-Castillo, J., Heunis, S., Kundu, P., Laird, A. R., Markello, R., Markiewicz, C. J., Moia, S., Staden, I., Teves, J. B., Uruñuela, E., Vaziri-Pashkam, M., Whitaker, K., & Handwerker, D. A. (2021). TE-dependent analysis of multi-echo fMRI with tedana. Journal of Open Source Software, 6(66), 3669. doi:10.21105/joss.03669.