tedana: TE Dependent ANAlysis

The tedana package is part of the ME-ICA pipeline, performing TE-dependent analysis of multi-echo functional magnetic resonance imaging (fMRI) data.

Citations

When using tedana, please include the following citations:

Kundu, P., Inati, S.J., Evans, J.W., Luh, W.M. & Bandettini, P.A. (2011). Differentiating BOLD and non-BOLD signals in fMRI time series using multi-echo EPI. NeuroImage, 60, 1759-1770.

License Information

tedana is licensed under GNU Lesser General Public License version 2.1. All trademarks referenced herein are property of their respective holders.

Copyright © 2011-2017, Prantik Kundu. All rights reserved.

Introduction

tedana works by decomposing multi-echo BOLD data via PCA and ICA. These components are then analyzed to determine whether they are TE-dependent or -independent. TE-dependent components are classified as BOLD, while TE-independent components are classified as non-BOLD, and are discarded as part of data cleaning.

Derivatives

• medn

  ‘Denoised’ BOLD time series after: basic preprocessing, T2* weighted averaging of echoes (i.e. ‘optimal combination’), ICA denoising. Use this dataset for task analysis and resting state time series correlation analysis.

• tsoc

  ‘Raw’ BOLD time series dataset after: basic preprocessing and T2* weighted averaging of echoes (i.e. ‘optimal combination’). ‘Standard’ denoising or task analyses can be assessed on this dataset (e.g. motion regression, physio correction, scrubbing, etc.) for comparison to ME-ICA denoising.

• *mefc

  Component maps (in units of delta S) of accepted BOLD ICA components. Use this dataset for ME-ICR seed-based connectivity analysis.

• mefl

  Component maps (in units of delta S) of ALL ICA components.

• ctab

  Table of component Kappa, Rho, and variance explained values, plus listing of component classifications.

Installation

We recommend running containerized versions of tedana to avoid dependency issues. The Docker Engine appropriate for your system (i.e., linux, Mac OSX, or Windows) is required to access and run the container.

It is also possible to run a local or “bare-metal” tedana if your system has AFNI and python 2.7 or 3.4+ installed. With a local python installation, we recommend using the Anaconda or Miniconda package manager, as these allow for the creation of virtual environments.

Containerized versions

To access a containerized version of tedana simply pull the latest Docker image. This can be accomplished with the following command:

docker pull emdupre/meica-docker:0.0.3

Local installation

Local installation requires the following dependencies:

• Python 2.7 or 3.4+
• AFNI

You can clone the latest version of tedana directly from GitHub. To do so, git clone https://github.com/me-ica/tedana.git.

API

tedana.model: Modeling TE-dependence

tedana.model
tedana.model.fit_decay(data, tes, mask, …)	Fit voxel-wise monoexponential decay models to data
tedana.model.fit_decay_ts(data, mask, tes, …)	Fit voxel- and timepoint-wise monoexponential decay models to data
tedana.model.fitmodels_direct(catd, mmix, …)	Fit models directly.
tedana.model.make_optcom(data, t2s, tes, …)	Optimally combine BOLD data across TEs.
tedana.model.monoexponential	Functions to estimate S0 and T2* from multi-echo data.
tedana.model.fit	Fit models.
tedana.model.combine	Functions to optimally combine data across echoes.

tedana.decomposition: Data decomposition

tedana.decomposition
tedana.decomposition.tedpca(catd, OCcatd, …)	Use principal components analysis (PCA) to identify and remove thermal noise from multi-echo data.
tedana.decomposition.tedica(n_components, …)	Performs ICA on dd and returns mixing matrix
tedana.decomposition._utils	Utility functions for tedana decomposition

tedana.selection: Component selection

tedana.selection
tedana.selection.selcomps(seldict, mmix, …)	Labels components in mmix
tedana.selection._utils	Utility functions for tedana.selection

tedana.workflows: Common workflows

tedana.workflows
tedana.workflows.tedana(data, tes[, mixm, …])	Run the “canonical” TE-Dependent ANAlysis workflow.
tedana.workflows.t2smap(data, tes[, …])	Estimate T2 and S0, and optimally combine data across TEs.

tedana.utils: Utility functions

tedana.utils
tedana.utils.io	Functions to handle file input/output
tedana.utils.utils	Utilities for tedana package

Contributing to tedana

This document explains how to set up a development environment for contributing to tedana and code style conventions we follow within the project. For a more general guide to the tedana development, please see our contributing guide.

Development in docker is encouraged, for the sake of consistency and portability. By default, work should be built off of emdupre/meica-docker:0.0.3 (see the Installation guide for grabbing the docker image).

Style Guide

Code

Docstrings should follow numpydoc convention. We encourage extensive documentation.

The code itself should follow PEP8 convention as much as possible, with at most about 500 lines of code (not including docstrings) per script.

Pull Requests

We encourage the use of standardized tags for categorizing pull requests. When opening a pull request, please use one of the following prefixes:

• [ENH] for enhancements
• [FIX] for bug fixes
• [TST] for new or updated tests
• [DOC] for new or updated documentation
• [STY] for stylistic changes
• [RF] for refactoring existing code

Pull requests should be submitted early and often! If your pull request is not yet ready to be merged, please also include the [WIP] prefix. This tells the development team that your pull request is a “work-in-progress”, and that you plan to continue working on it.

Usage

tedana minimally requires:

1. acquired echo times (in milliseconds), and
2. 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.

Indices and tables

• Index
• Module Index
• Search Page