tedana.workflows.tedana_workflow

tedana_workflow(data, tes, mask=None, mixm=None, ctab=None, manacc=None, tedort=False, gscontrol=None, tedpca='mle', ste=-1, combmode='t2s', verbose=False, stabilize=False, wvpca=False, out_dir='.', fixed_seed=42, debug=False, quiet=False)[source]

Run the “canonical” TE-Dependent ANAlysis workflow.

Parameters:
  • data (str or list of str) – Either a single z-concatenated file (single-entry list or str) or a list of echo-specific files, in ascending order.
  • tes (list) – List of echo times associated with data in milliseconds.
  • mask (str, optional) – Binary mask of voxels to include in TE Dependent ANAlysis. Must be spatially aligned with data.
  • mixm (str, optional) – File containing mixing matrix. If not provided, ME-PCA and ME-ICA are done.
  • ctab (str, optional) – File containing component table from which to extract pre-computed classifications.
  • manacc (str, optional) – Comma separated list of manually accepted components in string form. Default is None.
  • tedort (bool, optional) – Orthogonalize rejected components w.r.t. accepted ones prior to denoising. Default is False.
  • gscontrol ({None, ‘t1c’, ‘gsr’} or list, optional) – Perform additional denoising to remove spatially diffuse noise. Default is None.
  • tedpca ({'mle', 'kundu', 'kundu-stabilize'}, optional) – Method with which to select components in TEDPCA. Default is ‘mle’.
  • ste (int, optional) – Source TEs for models. 0 for all, -1 for optimal combination. Default is -1.
  • combmode ({'t2s', 'ste'}, optional) – Combination scheme for TEs: ‘t2s’ (Posse 1999, default), ‘ste’ (Poser).
  • verbose (bool, optional) – Generate intermediate and additional files. Default is False.
  • wvpca (bool, optional) – Whether or not to perform PCA on wavelet-transformed data. Default is False.
  • out_dir (str, optional) – Output directory.
Other Parameters:
 
  • fixed_seed (int, optional) – Value passed to mdp.numx_rand.seed(). Set to a positive integer value for reproducible ICA results; otherwise, set to -1 for varying results across calls.
  • debug (bool, optional) – Whether to run in debugging mode or not. Default is False.
  • quiet (bool, optional) – If True, suppresses logging/printing of messages. Default is False.

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