fidoptFastSurferVINN
FastSurferVINN, three voxel-size independent 2D networks (axial, coronal, sagittal) whose views are aggregated: 95 structures of a T1-weighted brain, FreeSurfer's aseg and the 62 DKT cortical regions, run as its authors' run_fastsurfer.sh --seg_only runs it.
SegmentationGPUversion FastSurfer v2.6.0 (1dc0247), checkpoints aparc_vinn_{axial,coronal,sagittal}_v2.0.0.pkl of Zenodo 10390573 (SHA-256 checked)brain · MRApache-2.0
Run it
With its KonfAI app, at the benchmark's settings (the fidopt app repositories are private for now: a Hugging Face token with access opens them):
pip install konfai-apps konfai-apps infer fideus-labs/fidopt-segmentation:FastSurferVINN -i image.nii.gz -o out --gpu 0
The app on Hugging Face: its model, its settings and how it is scored.
Where it works
Its place on each kind of problem it has results on, among the methods ranked there. A method that leads one problem can trail another: read the one closest to yours.
| Problem | Place | Ranked | Datasets |
|---|---|---|---|
| Brain MR, segmentation | not ranked yet | 3 of 6 |
Results
| Dataset | # | Read by | Score | Failed | Time s |
|---|---|---|---|---|---|
| Baby Open Brains, 31 structures | 2 | Dice | 0.051 | 0 | 24 |
| M-CRIB neonatal brain, 94 regions | 2 | Dice | 0.106 | 0 | 34 |
| MRBrainS18 | 2 | Dice | 0.767 | 0 | 52 |
| Mindboggle-101, 62 cortical regions | 1 | Dice | 0.827 | 0 | 24 |
| UltraCortex, cortex and white matter at 9.4 T | 2 | Dice | 0.864 | 0 | 52 |
- Reference
- Henschel et al., NeuroImage 2022