Skip to content

23.1.0

23.1.0 (November 22, 2023)
@mgxd mgxd tagged this 22 Nov 19:51 
The next minor release of *NiBabies*, this release includes a number of new goodies, including:

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.

*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.

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.

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.

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

  * 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)
Assets 2
Loading