Add --me-t2s-fit-method parameter
#3030
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
mgxd
reviewed
Jun 8, 2023
effigies
added a commit
that referenced
this pull request
Jun 12, 2023
23.1.0 (June 12, 2023) New feature release in the 23.1.x series. This release substantially reworks the resampling to fsLR grayordinate space, better accounting for partial volumes and high variance voxels. If you are resampling using ``--project-goodvoxels``, we strongly recommend upgrading. Fieldmap handling is improved, with better preference given to single-band references in both PEPolar and SyN-SDC schemes. Additionally, fMRIPrep will no longer estimate fieldmaps that are not intended to be used to correct BOLD series, reducing unneeded processing. This release removes ICA-AROMA from the fMRIPrep workflow. To use ICA-AROMA, set ``MNI152NLin6Asym:res-2`` as a target output space. MELODIC and ICA-AROMA can be run on the resulting images in a separate pipeline. For further information on the reasoning behind this change, see `GitHub issue #2936 <https://github.com/nipreps/fmriprep/issues/2936>`__. This release increments the versions of ANTs and FSL bundled in the Docker image. With thanks to Eilidh MacNicol, Basille Pinsard and Taylor Salo for contributions in fMRIPrep and SDCflows. * FIX: Raise RuntimeError at build if echos have mismatched shapes (#3028) * FIX: Inconsistent fmapless estimation when ignoring fieldmaps (#2994) * FIX: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2* map estimation (#2986) * FIX: Estimate free memory with "available", not "free" (#2985) * ENH: Add ``--me-t2s-fit-method`` parameter (#3030) * ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate (#3011) * ENH: Allow SBref+EPI PEPolar fieldmaps to correct BOLD series (#3008) * ENH: Remove ICA-AROMA from workflow and docs (#2966) * RF: Filter fieldmaps based on whether they will be used to correct a BOLD series (#3025) * MNT: Update ANTs pin in Docker image (#3016) * MNT: Update governance docs (#2992) * MNT: Refactor Docker build process (#2982) * MNT: Pin conda environment more strictly (#2853) * MNT: Require niworkflows ~1.3.6 (#2740) * CI: Use registry for layer caching (#3012) * CI: Upgrade docker orb (#2865)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Closes #3029.
Changes proposed in this pull request
--me-t2s-fit-method, to control how T2* and S0 will be estimated with tedana. The default, "curvefit", is slower and more memory intensive, which has led to out-of-memory errors for some users. The new option, "loglin", shouldn't result in the same memory issues, but it also may produce less accurate estimates.Documentation that should be reviewed
I added a couple of sentences on the new parameter to the "T2*-driven echo combination" section of
workflows.rst.