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
orlist
ofstr
) – 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 tomdp.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
- data (