Usage¶
tedana minimally requires:
- acquired echo times (in milliseconds), and
- functional datasets equal to the number of acquired echoes.
But you can supply many other options, viewable with tedana -h
.
Command line options¶
Run tedana¶
usage: tedana [-h] -d FILE [FILE ...] -e TE [TE ...] [--mix FILE]
[--ctab FILE] [--manacc MANACC] [--kdaw KDAW] [--rdaw RDAW]
[--conv CONV] [--sourceTEs STE] [--combmode {t2s,ste}]
[--initcost {tanh,pow3,gaus,skew}]
[--finalcost {tanh,pow3,gaus,skew}] [--denoiseTEs] [--strict]
[--no_gscontrol] [--stabilize] [--fout] [--filecsdata]
[--label LABEL] [--seed FIXED_SEED]
Named Arguments¶
-d | Multi-echo dataset for analysis. May be a single file with spatially concatenated data or a set of echo-specific files, in the same order as the TEs are listed in the -e argument. |
-e | Echo times (in ms). E.g., 15.0 39.0 63.0 |
--mix | File containing mixing matrix. If not provided, ME-PCA & ME-ICA is done. |
--ctab | File containing a component table from which to extract pre-computed classifications. |
--manacc | Comma separated list of manually accepted components |
--kdaw | Dimensionality augmentation weight (Kappa). Default=10. -1 for low-dimensional ICA Default: 10.0 |
--rdaw | Dimensionality augmentation weight (Rho). Default=1. -1 for low-dimensional ICA Default: 1.0 |
--conv | Convergence limit. Default 2.5e-5 Default: 2.5e-5 |
--sourceTEs | Source TEs for models. E.g., 0 for all, -1 for opt. com., and 1,2 for just TEs 1 and 2. Default=-1. Default: -1 |
--combmode | Possible choices: t2s, ste Combination scheme for TEs: t2s (Posse 1999, default), ste (Poser) Default: “t2s” |
--initcost | Possible choices: tanh, pow3, gaus, skew Initial cost function for ICA. Default: “tanh” |
--finalcost | Possible choices: tanh, pow3, gaus, skew Final cost function for ICA. Same options as initcost. Default: “tanh” |
--denoiseTEs | Denoise each TE dataset separately. Default: False |
--strict | Ignore low-variance ambiguous components Default: False |
--no_gscontrol | Disable global signal regression. Default: True |
--stabilize | Stabilize convergence by reducing dimensionality, for low quality data Default: False |
--fout | Output TE-dependence Kappa/Rho SPMs Default: False |
--filecsdata | Save component selection data Default: False |
--label | Label for output directory. |
--seed | Seeded value for ICA, for reproducibility. Default: 42 |
Run t2smap¶
usage: t2smap [-h] -d FILE [FILE ...] -e TE [TE ...] [--combmode {t2s,ste}]
[--label LABEL]
Named Arguments¶
-d | Multi-echo dataset for analysis. May be a single file with spatially concatenated data or a set of echo-specific files, in the same order as the TEs are listed in the -e argument. |
-e | Echo times (in ms). E.g., 15.0 39.0 63.0 |
--combmode | Possible choices: t2s, ste Combination scheme for TEs: t2s (Posse 1999, default), ste (Poser) Default: “t2s” |
--label | Label for output directory. |