Extended Data Tab. 1:
Dice scores between the ground truth labels of the 100 μm ex vivo brain MRI scan presented in [3] and the automated segmentations obtained with NextBrain. ROIs are listed in decreasing order of size (volume). The Dice scores are shown for segmentations obtained at two different resolutions: 200 μm (the resolution at which we created the ground truth labels) and 1 mm (which is representative of in vivo data). We note that the Dice scores are computed from labels made on the right hemisphere (since we did not label the left side of the brain). We also note that the labels "rest of hippocampus" and "rest of amygdala" correspond to voxels that did not clearly belong to any of the manually labelled nuclei, and have therefore no direct correspondence with ROIs in NextBrain.
| ROI | Dice (200 μm) | Dice (1 mm) |
|---|---|---|
| Cerebral-White-Matter | 0.90871 | 0.81367 |
| Ctx-whole | 0.89455 | 0.81493 |
| Cerebellum-Cortex | 0.93205 | 0.85472 |
| ctx-superiorfrontal | 0.77579 | 0.67069 |
| Cerebellum-White-Matter | 0.84393 | 0.65269 |
| ctx-inferiorparietal | 0.77458 | 0.68367 |
| ctx-precentral | 0.73685 | 0.65937 |
| ctx-rostralmiddlefrontal | 0.72036 | 0.66448 |
| ctx-superiortemporal | 0.78506 | 0.69595 |
| ctx-superiorparietal | 0.63853 | 0.56005 |
| ctx-middletemporal | 0.71694 | 0.67675 |
| ctx-inferiortemporal | 0.64805 | 0.65658 |
| ctx-lateraloccipital | 0.61442 | 0.57929 |
| ctx-postcentral | 0.72245 | 0.60464 |
| ctx-supramarginal | 0.78025 | 0.66091 |
| ctx-precuneus | 0.72374 | 0.61229 |
| ctx-fusiform | 0.64278 | 0.5845 |
| ctx-rh-lateralorbitofrontal | 0.69867 | 0.66915 |
| Brain-Stem | 0.65342 | 0.64177 |
| ctx-insula | 0.80767 | 0.73846 |
| ctx-caudalmiddlefrontal | 0.65308 | 0.52521 |
| ctx-medialorbitofrontal | 0.73295 | 0.62687 |
| ctx-lingual | 0.66735 | 0.59501 |
| ctx-parsopercularis | 0.70901 | 0.63893 |
| Left-Putamen | 0.9199 | 0.86072 |
| ctx-paracentral | 0.66197 | 0.58969 |
| ctx-parstriangularis | 0.68932 | 0.65785 |
| Left-Caudate | 0.91102 | 0.86814 |
| ctx-cuneus | 0.56676 | 0.52349 |
| Pons | 0.73371 | 0.6236 |
| ctx-caudalanteriorcingulate | 0.6305 | 0.56515 |
| ctx-bankssts | 0.67939 | 0.4762 |
| ctx-isthmuscingulate | 0.70825 | 0.55557 |
| ctx-parsorbitalis | 0.43236 | 0.42366 |
| Pons-nuc | 0.65229 | 0.5514 |
| ctx-rh-posteriorcingulate | 0.69731 | 0.56382 |
| ctx-rostralanteriorcingulate | 0.67935 | 0.41073 |
| ctx-pericalcarine | 0.5253 | 0.38703 |
| ctx-entorhinal | 0.72093 | 0.65273 |
| ctx-temporalpole | 0.54659 | 0.49421 |
| ctx-parahippocampal | 0.73123 | 0.66232 |
| Left-PuL | 0.76937 | 0.78917 |
| Left-external-pallidum | 0.78074 | 0.79407 |
| Left-MDl | 0.87316 | 0.86494 |
| ctx-frontalpole | 0.11589 | 0.3493 |
| ctx-transversetemporal | 0.63184 | 0.56123 |
| Left-VA | 0.6994 | 0.73112 |
| CA1 | 0.78967 | 0.60729 |
| Fornix | 0.30751 | 0.29593 |
| Claustrum | 0.48364 | 0.3618 |
| Reticular-of-thalamus | 0.2386 | 0.3239 |
| VPL | 0.57387 | 0.62796 |
| LP | 0.73933 | 0.73133 |
| molecular_layer_HP | 0.50045 | 0.50313 |
| Internal-pallidum | 0.78939 | 0.83776 |
| subiculum | 0.69842 | 0.61734 |
| Dentate-cerebellum | 0.71523 | 0.54696 |
| alveus | 0.57837 | 0.3076 |
| CA4_GC-DG | 0.75655 | 0.7136 |
| Accumbens-area | 0.77455 | 0.67541 |
| Thalamus | 0.32506 | 0.32978 |
| Lateral-nucleus | 0.8586 | 0.75999 |
| CeM | 0.6668 | 0.70489 |
| Substancia-Nigra | 0.7045 | 0.63047 |
| CA2_CA3 | 0.54381 | 0.4454 |
| AV | 0.59365 | 0.60739 |
| Basal-nucleus | 0.66909 | 0.61273 |
| SCP | 0.71921 | 0.67856 |
| hypothalamus posterior | 0.58318 | 0.53634 |
| hypothalamus_tubular_sup | 0.51626 | 0.48914 |
| Accessory-Basal-nucleus | 0.74887 | 0.78098 |
| hypothalamus_tubular_inf | 0.65529 | 0.56586 |
| PAG | 0.76829 | 0.7809 |
| Red-Nucleus | 0.83407 | 0.83386 |
| VTA | 0.67032 | 0.4751 |
| STN | 0.71496 | 0.72738 |
| Optic-Nerve | 0.58216 | 0.44427 |
| LGN | 0.64318 | 0.62109 |
| acomm | 0.44371 | 0.42966 |
| fimbria | 0.264 | 0.157 |
| MGN | 0.37669 | 0.21371 |
| VLa | 0.32691 | 0.45109 |
| LD | 0.42601 | 0.46225 |
| stria-terminals | 0.50263 | 0.30588 |
| Central-nucleus-inf-colliculus | 0.78275 | 0.72433 |
| Corticoamygdaloid-transitio | 0.58151 | 0.48352 |
| mammillary_body | 0.56602 | 0.57353 |
| DR | 0.54393 | 0.49046 |
| Inferior-olive | 0.26264 | 0.046102 |
| hypothalamus_anterior_sup | 0.54939 | 0.45936 |
| Medial-nucleus | 0.32559 | 0.33181 |
| Central-nucleus | 0.52925 | 0.48942 |
| Anterior-amygdaloid-area-AAA | 0.21345 | 0.18373 |
| zona-incerta | 0.40755 | 0.45308 |
| hypothalamus_anterior_inf | 0.36912 | 0.32702 |
| Paralaminar-nucleus | 0.14105 | 0.13123 |
| Cortical-nucleus | 0.30083 | 0.23504 |
| Rest of hippocampus | N/A | N/A |
| Rest of amygdala | N/A | N/A |