TE-Dependent Analysis (tedana) of multi-echo functional magnetic resonance imaging (fMRI) data.
tedana: TE Dependent ANAlysis
tedana) is a Python library for denoising multi-echo functional magnetic resonance imaging (fMRI) data.
tedana originally came about as a part of the ME-ICA pipeline, although it has since diverged.
An important distinction is that while the ME-ICA pipeline originally performed both pre-processing and TE-dependent analysis of multi-echo fMRI data,
tedana now assumes that you're working with data which has been previously preprocessed.
More information and documentation can be found at https://tedana.readthedocs.io.
If you use
tedana, please cite the following papers, as well as our most recent Zenodo release:
- DuPre, E. M., Salo, T., Ahmed, Z., Bandettini, P. A., Bottenhorn, K. L., Caballero-Gaudes, C., Dowdle, L. T., Gonzalez-Castillo, J., Heunis, S., Kundu, P., Laird, A. R., Markello, R., Markiewicz, C. J., Moia, S., Staden, I., Teves, J. B., Uruñuela, E., Vaziri-Pashkam, M., Whitaker, K., & Handwerker, D. A. (2021). TE-dependent analysis of multi-echo fMRI with tedana. Journal of Open Source Software, 6(66), 3669. doi:10.21105/joss.03669.
- 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.
- Kundu, P., Brenowitz, N. D., Voon, V., Worbe, Y., Vértes, P. E., Inati, S. J., Saad, Z. S., Bandettini, P. A., & Bullmore, E. T. (2013). Integrated strategy for improving functional connectivity mapping using multiecho fMRI. Proceedings of the National Academy of Sciences, 110, 16187-16192.
tedana with your local Python environment
You'll need to set up a working development environment to use
To set up a local environment, you will need Python >=3.6 and the following packages will need to be installed:
You can then install
pip install tedana
Creating a miniconda environment for use with
tedana, you can optionally configure a conda environment.
We recommend using miniconda3.
After installation, you can use the following commands to create an environment for
conda create -n ENVIRONMENT_NAME python=3 pip mdp numpy scikit-learn scipy conda activate ENVIRONMENT_NAME pip install nilearn nibabel pip install tedana
tedana will then be available in your path.
This will also allow any previously existing
tedana installations to remain untouched.
To exit this conda environment, use
NOTE: Conda < 4.6 users will need to use the soon-to-be-deprecated option
source rather than
conda for the activation and deactivation steps.
You can read more about managing conda environments and this discrepancy here.
You can confirm that
tedana has successfully installed by launching a Python instance and running:
You can check that it is available through the command line interface (CLI) with:
If no error occurs,
tedana has correctly installed in your environment!
Use and contribute to
tedana as a developer
If you aim to contribute to the
tedana code base and/or documentation, please first read the developer installation instructions in our contributing section. You can then continue to set up your preferred development environment.
Want to learn more about our plans for developing
Have a question, comment, or suggestion?
Open or comment on one of our issues!
If you're not sure where to begin, feel free to pop into Mattermost and introduce yourself! We will be happy to help you find somewhere to get started.
If you don't want to get lots of notifications, we send out newsletters approximately once per month though our TinyLetter mailing list. You can view the previous newsletters and/or sign up to receive future ones at https://tinyletter.com/tedana-devs.
We ask that all contributors to
tedana across all project-related spaces (including but not limited to: GitHub, Mattermost, and project emails), adhere to our code of conduct.
Thanks goes to these wonderful people (emoji key):
This project follows the all-contributors specification. Contributions of any kind welcome! To see what contributors feel they've done in their own words, please see our contribution recognition page.
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