23.0

[effigies]

23.0.0

Release Notes

New feature release in the 23.0.x series.

This release adds improvements for workflows targeting the fsLR grayordinate space. Namely, morphometric (curvature, sulcal depth and cortical thickness) measures are output as .dscalar.nii files and high-variance voxels can be excluded from the resampling step using --project-goodvoxels.

Additionally, T2w images are now resampled to the T1w-defined subject space if FreeSurfer reconstruction is used. If multiple T2w images are provided, they are merged into a single image first.

PEPolar fieldmaps with R/L phase-encoding directions or in non-standard orientations are now better supported. We continue to work toward better support for more SDC configurations.

23.0.0 supports FreeSurfer 7.3.2, which is now bundled in the Docker image.

ICA-AROMA support will be removed in 23.1.0.

With thanks to Thomas Madison, Greg Conan, Celine Provins, Robert Smith and Yaroslav Halchenko for contributions.
Thanks also to Steve Giavasis and colleagues at the Child Mind Institute for feedback on SDC processing.

Changes

• FIX: Pass reference image to unwarp_wf, use reference fieldwarp for single shot (FIX: Pass reference image to unwarp_wf, use reference fieldwarp for single shot #2945)
• FIX: Pass fmap filters to sdcflows (FIX: Pass fmap filters to sdcflows #2932)
• ENH: Resample morphometrics to fsLR dscalar CIFTI-2 files if --cifti-output is used (ENH: Resample morphometrics to fsLR dscalar CIFTI-2 files if --cifti-output is used #2959)
• ENH: Add option to exclude projecting high variance voxels to surface (update of ENH: Add option to exclude projecting high variance voxels to surface #2855) (ENH: Add option to exclude projecting high variance voxels to surface (update of #2855) #2956)
• ENH: Separate deep from shallow WM+CSF in the carpetplot (ENH : separate deep from shallow WM+CSF in the carpetplot #2744)
• ENH: Merge T2w images and coregister to T1w template (ENH: Merge T2w images and coregister to T1w template  #2941)
• RF: Use DataFrame.rename instead of ad hoc process (RF: Use DataFrame.rename instead of ad hoc process #2937)
• DOC: Update the description of the carpetplot in the sample report (DOC: update the description of the carpetplot in the sample report #2950)
• DOC: Altered CLI option grouping (DOC: Altered CLI option grouping #2944)
• DOC: Update lesion ROI documentation, warn in docs and app about upcoming changes (DOC: Update lesion ROI documentation, warn in docs and app about upcoming changes #2943)
• DOC: Update docs following read-through (DOC: Update docs following read-through #2930)
• DOC: Update carpetplot in "Outputs of fMRIPrep" (DOC: Update carpetplot in "Outputs of fMRIPrep" #2923)
• MNT: Codespell config, action + some typo fixups (codespell: config, action + some typo fixups #2958)
• MNT: Warn that AROMA support will be removed in a future version (MNT: Warn that AROMA support will be removed in a future version #2940)
• MNT: Update Ubuntu, FreeSurfer, AFNI and Convert3D (MNT: Update Ubuntu, FreeSurfer, AFNI and Convert3D #2931)
• MNT: Switch to hatch build backend and update package metadata (MNT: Switch to hatch build backend and update package metadata #2914 + FIX: Build leftovers #2939)
• MNT: Rotate CircleCI secrets and setup up org-level context (MAINT: Rotate CircleCI secrets and setup up org-level context #2928)
• CI: Minor updates to CircleCI config to improve resilience (CI: Minor updates to CircleCI config to improve resilience #2957)
• CI: Weekly docker build from scratch (CI: Weekly docker build from scratch #2938)

New Contributors

• @Lestropie made their first contribution in DOC: Altered CLI option grouping #2944
• @madisoth made their first contribution in ENH: Add option to exclude projecting high variance voxels to surface (update of #2855) #2956

Full Changelog: 22.1.1...23.0.0

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This discussion was created from the release 23.0.0.

[effigies]

23.0.1

Release Notes

Bug fix release in the 23.0.x series.

This release fixes issues with detecting partial fieldmaps, emitting a warning instead of an error. A small change in sMRIPrep fixes the name of a workflow, which may cause a duplication in a reused work directory from 23.0.0, but should not break any workflows or produce a change in derivatives.

Changes

• DOC: Add TemplateFlow's citation into bibtex file by @oesteban in DOC: Add TemplateFlow's citation into bibtex file #2969

Full Changelog: 23.0.0...23.0.1

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This discussion was created from the release 23.0.1.

[effigies]

23.0.2

Release Notes

This release fixes issues with _phase1+2, _phasediff and _fieldmap fieldmap files that are found with an orientation other than RAS.

See SDCflows 2.4.3 for changes.

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This discussion was created from the release 23.0.2.