Tips and FAQs

Leveraging precomputed results

Whether to allow for manual intervention for tough cases, or simply to reduce processing time, NiBabies can allow the use of certain pre-computed files during processing. Initial support is limited to the following files:

  • Anatomical mask in T1w space

  • Antomical segmentation (aseg) in T1w 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-orig key-value pair in the name.

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

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

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.