tedana.workflows
.tedana_workflow¶
-
tedana_workflow
(data, tes, mask=None, mixm=None, ctab=None, manacc=None, strict=False, gscontrol=True, kdaw=10.0, rdaw=1.0, conv=2.5e-05, ste=-1, combmode='t2s', dne=False, cost='logcosh', stabilize=False, filecsdata=False, wvpca=False, label=None, 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. - strict (
bool
, optional) – Ignore low-variance ambiguous components. Default is False. - gscontrol (
bool
, optional) – Control global signal using spatial approach. Default is True. - kdaw (
float
, optional) – Dimensionality augmentation weight (Kappa). Default is 10. -1 for low-dimensional ICA. - rdaw (
float
, optional) – Dimensionality augmentation weight (Rho). Default is 1. -1 for low-dimensional ICA. - conv (
float
, optional) – Convergence limit. Default is 2.5e-5. - 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).
- dne (
bool
, optional) – Denoise each TE dataset separately. Default is False. - cost ({'logcosh', 'exp', 'cube'} str, optional) – Cost function for ICA
- stabilize (
bool
, optional) – Stabilize convergence by reducing dimensionality, for low quality data. Default is False. - filecsdata (
bool
, optional) – Save component selection data to file. Default is False. - wvpca (
bool
, optional) – Whether or not to perform PCA on wavelet-transformed data. Default is False. - label (
str
orNone
, optional) – Label for output directory. Default is None.
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, which are written out to a folder named TED.[ref_label].[label] if
label
is provided and TED.[ref_label] if not.ref_label
is determined based on the name of the firstdata
file. For a complete list of the files generated by this workflow, please visit https://tedana.readthedocs.io/en/latest/outputs.html- data (