ME-ICA/tedana: 24.0.2

Release Notes

Enhancements

• Generate metrics from external regressors using F stats by @handwerkerd in https://github.com/ME-ICA/tedana/pull/1064. We have added in a long-requested addition to functionality. It is now possible to provide a TSV file with time series the same length as the fMRI time series, fit those time series to each ICA component, and use that information in the process to decide which components to accept or reject. For example, it is possible to use head motion regressors, cardiac and respiratory, regressors, and region-of-interest based regressors in models. With this functionality, it is now possible to combine the echo-based methods of tedana with other ICA-based denoising methods that depend on fitting to time series. Best practices for how to apply this new functionality are still a work-in-progress, but by adding this functionality, any use can start testing and contributing to this effort without needing to edit code. More information is available in https://tedana.readthedocs.build/en/stable/building_decision_trees.html#external-regressor-configuration

• Adding robustica option to ICA decomposition to achieve consistent results by @BahmanTahayori in https://github.com/ME-ICA/tedana/pull/1013. tedana previously used a single iteration of FastICA. This works but it means that the results are sensitive to initial seed selection. We have added in an option to use RobustICA which runs FastICA multiple times and outputs more stable components. As part of this process, if the PCA step defines, X components, robustica often finds fewer stable components and will output fewer than X ICA components. A benefit of this is that our PCA-based component estimation methods sometimes fail. By giving robustica a plausible number of PCA components, it will find a stable number of ICA components leading to a more stable and less arbitrary result. We are still working on improving the stability of the step that initially defines the number of PCA components.

🐛 Bug Fixes

• Use nearest-neighbors interpolation in plot_component by @tsalo in https://github.com/ME-ICA/tedana/pull/1098
• Filter out non-diagonal affine warning by @tsalo in https://github.com/ME-ICA/tedana/pull/1103
• Refactor gscontrol module by @tsalo in https://github.com/ME-ICA/tedana/pull/1086

Documentation Changes

• Cleaning up installation instructions by @handwerkerd in https://github.com/ME-ICA/tedana/pull/1113
• Update list of multi-echo datasets by @tsalo in https://github.com/ME-ICA/tedana/pull/1115
• Link to the open-multi-echo-data website by @tsalo in https://github.com/ME-ICA/tedana/pull/1117
• documentation and resource updates by @handwerkerd in https://github.com/ME-ICA/tedana/pull/1114
• docs: add BahmanTahayori as a contributor for code, design, and ideas by @allcontributors in https://github.com/ME-ICA/tedana/pull/1123
• docs: add Lestropie as a contributor for code, design, and 2 more by @allcontributors in https://github.com/ME-ICA/tedana/pull/1124
• Update figure-generating notebook by @tsalo in https://github.com/ME-ICA/tedana/pull/1074

Other Changes

• Refactor metrics.dependence module by @tsalo in https://github.com/ME-ICA/tedana/pull/1088

New Contributors

• @BahmanTahayori made their first contribution in https://github.com/ME-ICA/tedana/pull/1013
• @Lestropie made their first contribution in https://github.com/ME-ICA/tedana/pull/1013

Full Changelog: https://github.com/ME-ICA/tedana/compare/24.0.1...24.0.2