January 25, 2024 tedana newsletter
tedana-newsletter
We have been using TinyLetter to send out this very infrequent newsletter regarding https://tedana.readthedocs.io/. TinyLetter is shutting down at the end of February so we need to move this newsletter. We decided to move it to https://groups.google.com/g/tedana-newsletter We will add everyone directly receiving this message to the new list. If you don’t want your email transferred, please unsubscribe from the TinyLetter list before Feb 5. The unsubscription link is at the bottom of this message.
We will similarly use the new Google Group as an infrequent newsletter and not a discussion board. Questions about multi-echo fMRI and tedana usage or development can be posted at https://neurostars.org with tedana or multi-echo tags or as an issue or discussion at https://github.com/ME-ICA/tedana or https://mattermost.brainhack.org/brainhack/channels/tedana. We actively monitor all three message boards and try to efficiently respond.
If you know others who might appreciate receiving this tedana newsletter, please share the Google Groups link with them.
Version 23.0.1 was a major change that modularized the “decision tree” code that is used to classify ICA components as accepted or rejected and allows for user-generated new decision trees as inputs. Since then we’ve completed many standing issues that benefited from that major change. This includes:
- To improve reproducibility, logging the python version and hardware information when tedana is run. The most recent version of tedana on GitHub and our next release will also record version numbers of key Python modules.
- Multiple updates to our documentation.
- Fixing a bug where the number of PCA components could be defined by total variance explained within Python, but not from the command line.
- Cleaning up code in several places where we were unnecessarily using old versions of Python modules. This should make it easier to install tedana in multi-use Python environments.
- Tedana can now run with Python version 3.12.
A full list of changes are found here: https://github.com/ME-ICA/tedana/releases/tag/23.0.2
We are actively working on several additions where more contributors are welcome. This includes both direct contributions to the code, educational material, and documentation, as well as people who run new versions of the code on their data to make sure tedana runs as expected across a wider range of data sets. Active areas of work include:
- Adding in a more stable version of ICA which might include a more stable estimate of the total number of components.
- Correlating user-provided time series to each component so that measures like head motion can be included in the decision tree process for classifying accepted or rejected components.
- Dividing tedana into core and ICA subpackages, to reduce dependencies for downstream tools that only use a subset of tedana’s functionality (e.g., fMRIPrep).
A tedana-centered poster was just accepted for the Organization for Human Brain Mapping 2024 meeting. We will continue our practice of sharing a list of all multi-echo content at the conference (2023, 2022, 2021, 2020, 2019) and will try to organize a formal or informal event for multi-echo users. If you have content you want included or want to be in-the-loop, let us know.
Contributors
We are excited to welcome new contributors: @bpinsard, @effigies, and @fazledyn-or. We continue to thank all of our contributors for their continued input and help with tedana. We always look forward to seeing more new faces! If you’re not sure where to start, please feel free to open an issue on github, ask a question on neurostars with the ‘tedana’ or ‘multi-echo’ tag, join our next monthly developer’s call, or join the tedana mattermost channel.