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23.1.0 release candidate 1

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@mgxd mgxd released this 10 Nov 16:09
· 294 commits to master since this release
23.1.0rc1
de1fd0e

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.

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)
  • MAINT: Drop TemplateFlowSelect patches (#290)
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