Package: tedana
tedana: TE Dependent ANAlysisTE-dependentanalysis (tedana) is a Python library for denoising multi-echo functional magnetic resonance imaging (fMRI) data.tedanaoriginally came about as a part of theME-ICApipeline, 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,tedananow assumes that you're working with data which has been previously preprocessed.More information and documentation can be found athttps://tedana.readthedocs.io.CitingtedanaIf you usetedana, please cite the following papers, as well as ourmost 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.InstallationUsetedanawith your local Python environmentYou'll need to set up a working development environment to usetedana.
To set up a local environment, you will need Python >=3.8 and the following packages will need to be installed:numpyscipyscikit-learnnilearnnibabelmapcaYou can then installtedanawithpipinstalltedanaCreating a miniconda environment for use withtedanaIn usingtedana, you can optionally configurea conda environment.We recommend usingminiconda3.
After installation, you can use the following commands to create an environment fortedana:condacreate-nENVIRONMENT_NAMEpython=3pipmdpnumpyscikit-learnscipy
condaactivateENVIRONMENT_NAME
pipinstallnilearnnibabel
pipinstalltedanatedanawill then be available in your path.
This will also allow any previously existingtedanainstallations to remain untouched.To exit this conda environment, usecondadeactivateNOTE: Conda < 4.6 users will need to use the soon-to-be-deprecated optionsourcerather thancondafor the activation and deactivation steps.
You can read more about managing conda environments and this discrepancyhere.You can confirm thattedanahas successfully installed by launching a Python instance and running:importtedanaYou can check that it is available through the command line interface (CLI) with:tedana--helpIf no error occurs,tedanahas correctly installed in your environment!Use and contribute totedanaas a developerIf you aim to contribute to thetedanacode base and/or documentation, please first read the developer installation instructions inour contributing section. You can then continue to set up your preferred development environment.Getting involvedWe :yellow_heart: new contributors!
To get started, check outour contributing guidelinesand ourdeveloper's guide.Want to learn more about our plans for developingtedana?
Have a question, comment, or suggestion?
Open or comment on one ofour issues!If you're not sure where to begin, feel free to pop intoMattermostand 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 theprevious newslettersand/or sign up to receive future ones athttps://tinyletter.com/tedana-devs.We ask that all contributors totedanaacross all project-related spaces (including but not limited to: GitHub, Mattermost, and project emails), adhere to ourcode of conduct.ContributorsThanks goes to these wonderful people (emoji key):Logan Dowdle💻💬🎨🐛👀Elizabeth DuPre💻📖🤔🚇👀💡⚠️💬Marco Flores-Coronado🤔📖Javier Gonzalez-Castillo🤔💻🎨Dan Handwerker🎨📖💡👀💻Prantik Kundu💻🤔Ross Markello💻🚇💬Pete Molfese💻Neha Reddy🐛📖🤔💬👀Taylor Salo💻🤔📖✅💬🐛⚠️👀Joshua Teves📆📖👀🚧💻Kirstie Whitaker📖📆👀📢Monica Yao📖⚠️Stephan Heunis📖Benoît Béranger💻Eneko Uruñuela💻👀🤔Cesar Caballero Gaudes📖💻Isla👀mjversluis📖Maryam📖aykhojandi📖Stefano Moia💻👀📖Zaki A.🐛💻📖Manfred G Kitzbichler💻giadaan📖This project follows theall-contributorsspecification. Contributions of any kind welcome!
To see what contributors feel they've done in their own words, please see ourcontribution recognition page.