Bump tedana from 23.0.2 to 24.0.0

[dependabot[bot]]

Bumps tedana from 23.0.2 to 24.0.0.

Release notes

Sourced from tedana's releases.

24.0.0

Release Notes

Summary

We have continued to make under-the-hood changes and improvements to documentation. Several key changes may be noticable to users.

• By default, tedana has been saving 4D volumes of the high-kappa components Accepted_bold.nii.gz and the low-kappa components 'Rejected_bold.nii.gzeven though very few people use them and they use a lot of space. These will now only be saved if the program is run with--verbose. Additionally our final denoised time series was called desc-optcomDenoised_bold.nii.gzand this created confusion. It is now calleddesc-denoised_bold.nii.gz`. This will break pipelines that looked for a file with the previous name. ME-ICA/tedana#1033
• We noticed a small difference between the decision tree implemented in MEICA v2.5 and the tree we were calling kundu. We have renamed our existing tree tedana_orig and there is now a meica tree that should match the MEICA method. In practice, the results will be identical or meica will accept additional components. The additionally accepted components can have substantive variance and, upon visual inspection usually looked like they should have been rejected. Therefore, we've kept the same default, but give both options to users. #952
• Different metrics, like kappa and rho, are calculated for each ICA component. While the code allowed for a range of different metrics, the list that was calculated when tedana was run was impossible to change without editing the code. The metrics that were already specified in the decision tree json files will now be the ones calculated. The actual metric calculations still need to be defined within the code, but this change makes it practical to add a range of additional metrics that can vary by decision tree. #969
• The tedana_report.html file now includes the mean T2* and S0 maps used in calculations #1040, consistent orientations for all images of brain slices #1045, version numbers for key python packages used during execution #1014, and the reference list is now properly rendered #1001.

Changes

• Remove accepted and rejected time series from the standard file outputs and change denoised time series name (updated) by @​martaarbizu and @​handwerkerd in ME-ICA/tedana#1033
• Generate metrics based on decision tree by @​tsalo and @​handwerkerd in ME-ICA/tedana#969
• Align with old meica by @​handwerkerd and @​tsalo in ME-ICA/tedana#952
• Add T2* and S0 figures by @​tsalo in ME-ICA/tedana#1040
• Improve component plots by @​tsalo in ME-ICA/tedana#1045
• Adding python library version numbers by @​handwerkerd in ME-ICA/tedana#1014
• Fix Bibtex rendering in reports by @​eurunuela @​martaarbizu and @​martinezeguiluz in ME-ICA/tedana#1001
• Fixed Inappropriate Logical Expression by @​fazledyn-or in ME-ICA/tedana#1012
• Document decision tree steps in report and remove log_extra_report by @​handwerkerd and @​tsalo in ME-ICA/tedana#1043
• Fixing ica_reclassify CLI documentation typo by @​handwerkerd in ME-ICA/tedana#1010
• [DOC] Replaced newsletter with Google Groups by @​goodalse2019 in ME-ICA/tedana#1017
• Reformat with new version of black by @​tsalo in ME-ICA/tedana#1020
• Add Dependabot config and switch Release Drafter to Changelog config by @​tsalo in ME-ICA/tedana#1024
• Fix error on empty input file & pre-commit updated to black version 24.2.0 by @​martinezeguiluz and @​handwerkerd in ME-ICA/tedana#1031
• docs: add effigies as a contributor for code by @​allcontributors in ME-ICA/tedana#1004
• docs: add bpinsard as a contributor for code by @​allcontributors in ME-ICA/tedana#1003
• docs: add goodalse2019 as a contributor for doc, ideas, and question by @​allcontributors in ME-ICA/tedana#1018

... (truncated)

Commits

• f084dc4 Align with old meica (#952)
• 9cbd484 Generate metrics based on decision tree (#969)
• a21d65e Update nibabel requirement from <=5.2.0,>=2.5.1 to >=2.5.1,<=5.2.1 (#1055)
• 7c0b91f Improve component plots (#1045)
• 8d7e5ff Add T2* and S0 figures (#1040)
• 62ed3c1 Update pandas requirement from <=2.2.0,>=2.0 to >=2.0,<=2.2.1 (#1048)
• 1f1845b Document decision tree steps in report and remove log_extra_report (#1043)
• d0298f2 docs: add martaarbizu as a contributor for code (#1039)
• d5512f7 Update nilearn requirement from <=0.10.2,>=0.7 to >=0.7,<=0.10.3 (#1038)
• 0d66342 Remove accepted and rejected time series from the standard file outputs and c...
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