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 (#2945)
• FIX: Pass fmap filters to sdcflows (#2932)
• 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 #2855) (#2956)
• ENH: Separate deep from shallow WM+CSF in the carpetplot (#2744)
• ENH: Merge T2w images and coregister to T1w template (#2941)
• RF: Use DataFrame.rename instead of ad hoc process (#2937)
• DOC: Update the description of the carpetplot in the sample report (#2950)
• DOC: Altered CLI option grouping (#2944)
• DOC: Update lesion ROI documentation, warn in docs and app about upcoming changes (#2943)
• DOC: Update docs following read-through (#2930)
• DOC: Update carpetplot in "Outputs of fMRIPrep" (#2923)
• MNT: Codespell config, action + some typo fixups (#2958)
• MNT: Warn that AROMA support will be removed in a future version (#2940)
• MNT: Update Ubuntu, FreeSurfer, AFNI and Convert3D (#2931)
• MNT: Switch to hatch build backend and update package metadata (#2914 + #2939)
• MNT: Rotate CircleCI secrets and setup up org-level context (#2928)
• CI: Minor updates to CircleCI config to improve resilience (#2957)
• CI: Weekly docker build from scratch (#2938)

New Contributors

• @Lestropie made their first contribution in #2944
• @madisoth made their first contribution in #2956

Full Changelog: 22.1.1...23.0.0