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The next minor release of *NiBabies*, this release includes a number of new goodies, including:
New surface reconstruction option
M-CRIB-S (Adamson et al., https://www.nature.com/articles/s41598-020-61326-2), 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`.
Note: 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
Full Changelog
* CI: Purge codecov python package (282)
* DKR: Upgrade Docker base, c3d (275)
* DKR: Add M-CRIB-S to Docker container (283)
* DKR: Update dependencies, split into multi-stage build
* ENH: Add option to exclude projecting high variance voxels to surface (278)
* ENH: Resample morphometrics to fsLR CIFTI-2 files when outputing CIFTIs (279)
* ENH: Add MCRIBReconAll as alternative surface reconstruction method (283)
* ENH: Reorder anatomical processsing, run ANTs DenoiseImage on anatomicals (286)
* ENH: Extract participant ages from BIDS sources, deprecate `--age-months` (287)
* ENH: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2star map estimation (296)
* ENH: Allow precomputed derivatives in T1w or T2w space (305)
* ENH: Add separate workflow for single anatomical processing (316)
* FIX: Improve free memory estimation (284)
* FIX: Ensure age is extracted from sessions file (291)
* FIX: Restore CIFTI medial wall masking, subcortical volume LAS reorientation (298)
* FIX: Recify "goodvoxels" surface projection (301)
* FIX: Connect derivatives mask to mcribs recon (323)
* MAINT: Drop TemplateFlowSelect patches (290)