24.0.0

[tsalo]

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. Remove accepted and rejected time series from the standard file outputs and change denoised time series name (updated) #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 Remove accepted and rejected time series from the standard file outputs and change denoised time series name (updated) #1033
• Generate metrics based on decision tree by @tsalo and @handwerkerd in Generate metrics based on decision tree #969
• Align with old meica by @handwerkerd and @tsalo in Align with old meica #952
• Add T2* and S0 figures by @tsalo in Add T2* and S0 figures #1040
• Improve component plots by @tsalo in Improve component plots #1045
• Adding python library version numbers by @handwerkerd in Adding python library version numbers #1014
• Fix Bibtex rendering in reports by @eurunuela @martaarbizu and @martinezeguiluz in Fix Bibtex rendering in reports #1001
• Fixed Inappropriate Logical Expression by @fazledyn-or in Fixed Inappropriate Logical Expression #1012
• Document decision tree steps in report and remove log_extra_report by @handwerkerd and @tsalo in Document decision tree steps in report and remove log_extra_report #1043
• Fixing ica_reclassify CLI documentation typo by @handwerkerd in Fixing ica_reclassify CLI documentation typo #1010
• [DOC] Replaced newsletter with Google Groups by @goodalse2019 in [DOC] Replaced newsletter with Google Groups #1017
• Reformat with new version of black by @tsalo in Reformat with new version of black #1020
• Add Dependabot config and switch Release Drafter to Changelog config by @tsalo in Add Dependabot config and switch Release Drafter to Changelog config #1024
• Fix error on empty input file & pre-commit updated to black version 24.2.0 by @martinezeguiluz and @handwerkerd in Fix error on empty input file & pre-commit updated to black version 24.2.0 #1031
• docs: add effigies as a contributor for code by @allcontributors in docs: add effigies as a contributor for code #1004
• docs: add bpinsard as a contributor for code by @allcontributors in docs: add bpinsard as a contributor for code #1003
• docs: add goodalse2019 as a contributor for doc, ideas, and question by @allcontributors in docs: add goodalse2019 as a contributor for doc, ideas, and question #1018
• docs: add martinezeguiluz as a contributor for code by @allcontributors in docs: add martinezeguiluz as a contributor for code #1032
• docs: add martaarbizu as a contributor for code by @allcontributors in docs: add martaarbizu as a contributor for code #1039

New Contributors

• @bpinsard made their first contribution in docs: add bpinsard as a contributor for code #1003
• @fazledyn-or made their first contribution in Fixed Inappropriate Logical Expression #1012
• @goodalse2019 made their first contribution in [DOC] Replaced newsletter with Google Groups #1017
• @dependabot made their first contribution in Bump actions/setup-python from 2 to 5 #1025
• @martinezeguiluz made their first contribution in docs: add martinezeguiluz as a contributor for code #1032
• @martaarbizu made their first contribution in docs: add martaarbizu as a contributor for code #1039

Full Changelog: 23.0.2...24.0.0

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This discussion was created from the release 24.0.0.