23.1

[effigies]

23.1.0

Release notes

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.

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.

Changes

• FIX: Raise RuntimeError at build if echos have mismatched shapes (FIX: Raise RuntimeError at build if echos have mismatched shapes #3028)
• FIX: Inconsistent fmapless estimation when ignoring fieldmaps (FIX: Inconsistent fmapless estimation when ignoring fieldmaps #2994)
• FIX: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2* map estimation (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" (FIX: Estimate free memory with "available", not "free" #2985)
• ENH: Add --me-t2s-fit-method parameter (Add --me-t2s-fit-method parameter #3030)
• ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate (ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate #3011)
• ENH: Allow SBref+EPI PEPolar fieldmaps to correct BOLD series (ENH: Allow SBref+EPI PEPolar fieldmaps to correct BOLD series #3008)
• ENH: Remove ICA-AROMA from workflow and docs (ENH: Remove ICA-AROMA from workflow and docs #2966)
• RF: Filter fieldmaps based on whether they will be used to correct a BOLD series (RF: Filter fieldmaps based on whether they will be used to correct a BOLD series #3025)
• MNT: Update ANTs pin in Docker image (MNT: Update ANTs pin in Docker image #3016)
• MNT: Update governance docs (MNT: Update governance docs #2992)
• MNT: Refactor Docker build process (MNT: Refactor Docker build process #2982)
• MNT: Pin conda environment more strictly (DOCKER: Pin conda environment more strictly #2853)
• MNT: Require niworkflows ~1.3.6 (FIX: Set pixdim[4] (repetition time) in seconds #2740)
• CI: Use registry for layer caching (CI: Use registry for layer caching #3012)
• CI: Upgrade docker orb (CI: Upgrade docker orb #2865)

Full Changelog: 23.0.2...23.1.0

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This discussion was created from the release 23.1.0.

[effigies]

23.1.1

Release notes

Bug fix release in the 23.1.x series.

This release corrects a small error that prevented the "goodvoxels" mask from being placed in the output directory if no FreeSurfer output spaces were specified.

Changes

• FIX: Remove bad metadata input from ds_goodvoxels_mask by @effigies in FIX: Remove bad metadata input from ds_goodvoxels_mask #3037

Full Changelog: 23.1.0...23.1.1

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This discussion was created from the release 23.1.1.

[effigies]

23.1.2

Release notes

Bug fix release in the 23.1.x series.

Changes

This release correctly generates *_space-fsLR_desc-reg_sphere.surf.gii, which was previously a copy of the standard *_desc-reg_sphere.surf.gii. Additionally, warnings are now correctly emitted when AROMA-related CLI options are used.

• CI: Clean up pre-release builds (CI: Clean up pre-release builds #3040)

Full Changelog: 23.1.1...23.1.2

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This discussion was created from the release 23.1.2.

[effigies]

23.1.3

Release notes

Bug fix release in the 23.1.x series.

In rare cases where Freesurfer is unable to align to its default atlas in Talairach registration, it was unable to fall back to the Schwartz atlas because we were not including it in the Docker image. This release exists to provide an updated Docker image, and no upgrade is needed for users not encountering this issue.

Changes

• DOCKER: Include 3T18yoSchwartzReactN32 FreeSurfer atlas in image (DOCKER: Include 3T18yoSchwartzReactN32 FreeSurfer atlas in image #3049)

Full Changelog: 23.1.2...23.1.3