Tips and FAQs

Leveraging precomputed results

Whether manual intervention is required, or you want to reduce processing time, NiBabies allow the use of certain pre-computed files during processing, which can skip part of the workflow. Support is limited to the following files:

  • Anatomical mask in T1w or T2w space

  • Antomical segmentation (aseg) in T1w or T2w space

To use pre-computed results, one or more BIDS Derivatives directories must be passed in to NiBabies using the --derivatives flag. Derivative directories must include a dataset_description.json and the required fields. Additionally, files must include the space-T1w or space-T2w key-value pair in the filenames, and a matching sidecar JSON file with the SpatialReference field defined.

A sample layout of a derivatives directory can be found below:

├── dataset_description.json
└── sub-01
    └── anat
        ├── sub-01_space-T2w_desc-aseg_dseg.json
        ├── sub-01_space-T2w_desc-aseg_dseg.nii.gz
        ├── sub-01_space-T2w_desc-brain_mask.json
        └── sub-01_space-T2w_desc-brain_mask.nii.gz

and the contents of the JSON files:

{"SpatialReference": "sub-01/anat/sub-01_T2w.nii.gz"}

The SpatialReference file will be used to ensure the raw data and the derivatives are aligned and in the same space.

Multi-atlas segmentation with joint label fusion

By default, NiBabies will run FSL FAST for tissue segmentation, and Infant FreeSurfer for segmentation labels. However, you can instead use ANTs Joint Label Fusion to generate both, granted you provide multiple atlases with anatomicals / segmentations via the --segmentation-atlases-dir flag. When using this approach, there are a few assumptions being made:

  1. The anatomicals are brain masked.

  2. The labeled segmentations follow the FreeSurfer lookup table.

Here is an example layout of what the --segmentation-atlases-dir flag expects:

$ tree JLF-templates
├── Template01
│   ├── Segmentation.nii.gz
│   ├── T1w_brain.nii.gz
│   └── T2w_brain.nii.gz
└── Template02
    ├── Segmentation.nii.gz
    ├── T1w_brain.nii.gz
    └── T2w_brain.nii.gz

More context on releases

Like other NiPreps, NiBabies follows Calendar Versioning (CalVer), in format of YY.MINOR.MICRO. In short, here is a quick heuristic on how new releases should be looked at:

  1. If the YY or MINOR has changed, it is a feature release, with substantial changes to the workflow.

  2. If the YY.MINOR match the version you used, but the MICRO has changed, it is a bug-fix release. Check the release notes - if the fixes do not pertain to your data, there is no need to upgrade.

For more in-depth information, refer to the NiPreps release documentation.