23.1.0

[mgxd]

Release Notes

The next minor release of NiBabies, this release includes a number of new goodies, including:

New Surface Reconstruction

M-CRIB-S (Adamson et al.), has shown to improve performance in participants under 9 months. If you would like to try this method, add the following to your command: --surface-recon-method mcribs.

*Currently, a T2w image and pre-computed segmentation derivative must be provided to run mcribs.

Improved batch processing

NiBabies now automatically parses the BIDS directory for participant ages, first searching in the
participant's session.tsv, and falling back to participants.tsv. This simplifies batch submissions including multiple subjects & sessions. As a result, the --age-months flag has been deprecated, and will be removed in a later release.

Goodvoxels projection

An option to determine and exclude high-variance voxels from being projected to the surface when creating CIFTI files. To enable this, add --project-goodvoxels to your command.

Single anatomical processing

Running NiBabies is now less restrictive, and will still process data missing either a T1w / T2w image. However, for best results, it is recommended to collect and include both for processing.

Anat-specific derivatives inputs

Previous, NiBabies expected input from the --derivatives flag to be in T1w space, using the entity space-orig. This has now been changed to support derivatives in either T1w or T2w space. For more information, please see https://nibabies.readthedocs.io/en/23.1.0/faqs.html#leveraging-precomputed-results

Changelog

• CI: Purge codecov python package (MAINT: Purge removed codecov python package #282)
• DKR: Upgrade Docker base, c3d (MNT: Upgrade Docker base, c3d #275)
• DKR: Add M-CRIB-S to Docker container (ENH: Add M-CRIB-S surface processing #283)
• DKR: Update dependencies, split into multi-stage build
• ENH: Add option to exclude projecting high variance voxels to surface (ENH: Add option to exclude projecting high variance voxels to surface #278)
• ENH: Resample morphometrics to fsLR CIFTI-2 files when outputing CIFTIs (ENH: Resample morphometrics to fsLR dscalar CIFTI-2 files if --cifti-output is used #279)
• ENH: Add MCRIBReconAll as alternative surface reconstruction method (ENH: Add M-CRIB-S surface processing #283)
• ENH: Reorder anatomical processsing, run ANTs DenoiseImage on anatomicals (RF: Anatomical processing #286)
• ENH: Extract participant ages from BIDS sources, deprecate --age-months (ENH: Extract participant ages from BIDS sources #287)
• ENH: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2star map estimation (ENH: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2* map estimation #296)
• ENH: Allow precomputed derivatives in T1w or T2w space (ENH+RF: Allow precomputed derivatives in T1w or T2w space #305)
• ENH: Add separate workflow for single anatomical processing (ENH: Add separate workflow to run with a single anatomical #316)
• FIX: Improve free memory estimation (FIX: Estimate free memory with available, not free #284)
• FIX: Ensure age is extracted from sessions file (FIX: Ensure age from sessions file is not overriden #291)
• FIX: Restore CIFTI medial wall masking, subcortical volume LAS reorientation (FIX: restore cifti medial wall masking, subcortical volume LAS reorientation #298)
• FIX: Recify "goodvoxels" surface projection (FIX: Goodvoxel projection #301)
• FIX: Connect derivatives mask to mcribs recon (FIX: Connect derivatives mask to mcribs recon #323)
• MAINT: Drop TemplateFlowSelect patches (MNT: Drop templateflow patches after smriprep changes #290)

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This discussion was created from the release 23.1.0 .