NextBrain is a probabilistic atlas of the entire human brain derived from histology images.
Casamitjana, A., Mancini, M., Robinson, E., Peter, L. et al. A probabilistic histological atlas of the human brain for MRI segmentation. Nature (2025). https://doi.org/10.1038/s41586-025-09708-2
It can be used by an accompanying software to segment any brain scan into more than 300 anatomical regions at sub-millimeter resolution.
Puonti, O., Nolan, J., Dicamillo, R., Balbastre, Y., et al. Fast segmentation with the NextBrain histological atlas. bioRxiv (2025). https://doi.org/10.1101/2025.09.22.673638
The NextBrain subcortical labels follow the Allen Brain ontology. The Allen Human Brain Atlas is a reference anatomical atlas of the human brain drawn on a single specimen.
Ding, S.-L., Royall, J.J., Sunkin, S.M., Ng, L. et al. Comprehensive cellular-resolution atlas of the adult human brain. The Journal of Comparative Neurology (2016). https://doi.org/10.1002/cne.24080
The tools provided in this package allow NextBrain label maps to be converted to Allen Brain label maps. It also allows Allen Brain label maps to be simplified by collapsing labels along levels of its ontology.
nextbrain-utils combine \
-l seg.left.nii.gz \
-r seg.right.nii.gz \
-o seg.both.nii.gz \
-m sides.nii.gz
nextbrain-utils allen \
-i seg.both.nii.gz \
-o seg.allen.nii.gzNote that some of the Allen Brain labels are pretty large and cannot be encoded in a 16 bit integer. This means that Freeview does not properly display them, even if an appropriate lookup table is used. As a workaround, "large" Allen labels can be mapped to a lower range. Specifically, we
- map the range [146035001, 146035199] to [1, 199]
- map the range [146034600, 146034999] to [600, 999]
- map the range [266441000, 266441999] to [3000, 3999]
- map the range [267499000, 267499999] to [9000, 9999]
nextbrain-utils allen \
-i seg.both.nii.gz \
-o seg.allen.nii.gz \
-s16
By default, this function approximately maps the Desikan-Killiany cortical labels generated by Freesurfer/NextBrain to Allen's gyral labels. It uses the following mapping:
2000 ctx-unknown -> 12112 cerebral gyri and lobules
2001 ctx-bankssts -> 12112 cerebral gyri and lobules
2002 ctx-caudalanteriorcingulate -> 12158 cingulate gyrus, caudal (posterior) part
2003 ctx-caudalmiddlefrontal -> 12116 middle frontal gyrus
2005 ctx-cuneus -> 12150 cuneus
2006 ctx-entorhinal -> 12163 anterior parahippocampal gyrus
2007 ctx-fusiform -> 12152 occipitotemporal (fusiform) gyrus, occipital part
2008 ctx-inferiorparietal -> 12134 inferior parietal lobule
2009 ctx-inferiortemporal -> 12142 inferior temporal gyrus
2010 ctx-isthmuscingulate -> 12158 cingulate gyrus, caudal (posterior) part
2011 ctx-lateraloccipital -> 12148 occipital lobe
2012 ctx-lateralorbitofrontal -> 12125 lateral orbital gyrus
2013 ctx-lingual -> 12151 lingual gyrus
2014 ctx-medialorbitofrontal -> 12121 gyrus rectus (straight gyrus)
2015 ctx-middletemporal -> 12141 middle temporal gyrus
2016 ctx-parahippocampal -> 12164 posterior parahippocampal gyrus
2017 ctx-paracentral -> 12138 paracentral lobule, rostral part
2018 ctx-parsopercularis -> 12119 inferior frontal gyrus, opercular part
2019 ctx-parsorbitalis -> 12120 inferior frontal gyrus, orbital part
2020 ctx-parstriangularis -> 12118 inferior frontal gyrus, triangular part
2021 ctx-pericalcarine -> 12148 occipital lobe
2022 ctx-postcentral -> 12132 postcentral gyrus
2023 ctx-posteriorcingulate -> 12158 cingulate gyrus, caudal (posterior) part
2024 ctx-precentral -> 12114 precentral gyrus
2025 ctx-precuneus -> 12137 precuneus
2026 ctx-rostralanteriorcingulate -> 12157 cingulate gyrus, rostral (anterior) part
2027 ctx-rostralmiddlefrontal -> 12116 middle frontal gyrus
2028 ctx-superiorfrontal -> 12115 superior frontal gyrus
2029 ctx-superiorparietal -> 12133 supraparietal lobule
2030 ctx-superiortemporal -> 12140 superior temporal gyrus
2031 ctx-supramarginal -> 12135 supramarginal gyrus
2032 ctx-frontalpole -> 146034888 frontal pole
2033 ctx-temporalpole -> 12146 temporal pole
2034 ctx-transversetemporal -> 12144 transverse temporal gyrus (Heschl's gyrus)
2035 ctx-insula -> 12176 insular lobe
This mapping is imperfect and cannot be totally trusted. It is possible to preserve the Desikan-Killiany labels (IDs in range [2000, 2035]).
nextbrain-utils allen \
-i seg.both.nii.gz \
-o seg.allen.nii.gz \
-c dk
Alternatively, the Desikan-Killiany labels can be collapsed into coarse "developmental" cortical regions.
nextbrain-utils allen \
-i seg.both.nii.gz \
-o seg.allen.nii.gz \
-c dev
This uses the following mapping:
10160 neocortex (isocortex) <- 2000 ctx-unknown
10161 frontal neocortex <- 2003 ctx-caudalmiddlefrontal
<- 2012 ctx-lateralorbitofrontal
<- 2014 ctx-medialorbitofrontal
<- 2017 ctx-paracentral
<- 2018 ctx-parsopercularis
<- 2019 ctx-parsorbitalis
<- 2020 ctx-parstriangularis
<- 2024 ctx-precentral
<- 2027 ctx-rostralmiddlefrontal
<- 2028 ctx-superiorfrontal
<- 2032 ctx-frontalpole
10208 parietal neocortex <- 2008 ctx-inferiorparietal
<- 2022 ctx-postcentral
<- 2025 ctx-precuneus
<- 2029 ctx-superiorparietal
<- 2031 ctx-supramarginal
10235 temporal neocortex <- 2001 ctx-bankssts
<- 2007 ctx-fusiform
<- 2009 ctx-inferiortemporal
<- 2015 ctx-middletemporal
<- 2030 ctx-superiortemporal
<- 2033 ctx-temporalpole
<- 2034 ctx-transversetemporal
10268 occipital neocortex <- 2005 ctx-cuneus
<- 2011 ctx-lateraloccipital
<- 2013 ctx-lingual
<- 2021 ctx-pericalcarine
10288 insular neocortex <- 2035 ctx-insula
10314 periarchicortex <- 2006 ctx-entorhinal
<- 2016 ctx-parahippocampal
nextbrain-utils simplify \
-i seg.allen.nii.gz \
-o seg.simple.nii.gz \
-l AMY ATA EXA Ca Pu NAC GP Cla BF THM SubTH HTH HIPThe list of labels to collapse can be long names, acronyms or IDs from
the Allen ontology. If the Allen map uses S16-compatible labels, please
use the -s16 option here as well.
Then Allen ontology can br browsed online:
nextbrain-utils aseg \
-i seg.both.nii.gz \
-o seg.aseg.aparc.nii.gz \
-s sides.nii.gz
An ASeg label map contains the following labels (+ the AParc/Desikan-Killiany labels):
0 Unknown 0 0 0 0
2 Left-Cerebral-White-Matter 245 245 245 0
3 Left-Cerebral-Cortex 205 62 78 0
4 Left-Lateral-Ventricle 120 18 134 0
5 Left-Inf-Lat-Vent 196 58 250 0
7 Left-Cerebellum-White-Matter 220 248 164 0
8 Left-Cerebellum-Cortex 230 148 34 0
10 Left-Thalamus 0 118 14 0
11 Left-Caudate 122 186 220 0
12 Left-Putamen 236 13 176 0
13 Left-Pallidum 12 48 255 0
14 3rd-Ventricle 204 182 142 0
15 4th-Ventricle 42 204 164 0
16 Brain-Stem 119 159 176 0
17 Left-Hippocampus 220 216 20 0
18 Left-Amygdala 103 255 255 0
24 CSF 60 60 60 0
26 Left-Accumbens-area 255 165 0 0
28 Left-VentralDC 145 42 42 0
41 Right-Cerebral-White-Matter 245 245 245 0
42 Right-Cerebral-Cortex 205 62 78 0
43 Right-Lateral-Ventricle 120 18 134 0
44 Right-Inf-Lat-Vent 196 58 250 0
46 Right-Cerebellum-White-Matter 220 248 164 0
47 Right-Cerebellum-Cortex 230 148 34 0
49 Right-Thalamus 0 118 14 0
50 Right-Caudate 122 186 220 0
51 Right-Putamen 236 13 176 0
52 Right-Pallidum 13 48 255 0
53 Right-Hippocampus 220 216 20 0
54 Right-Amygdala 103 255 255 0
58 Right-Accumbens-area 255 165 0 0
60 Right-VentralDC 165 42 42 0
nextbrain-utils supersynth \
-i seg.both.nii.gz \
-o seg.supersynth.nii.gz \
-s sides.nii.gz
A SuperSynth label map contains the following labels:
0 Unknown 0 0 0 0
2 Left-Cerebral-White-Matter 245 245 245 0
3 Left-Cerebral-Cortex 205 62 78 0
4 Left-Lateral-Ventricle 120 18 134 0
5 Left-Inf-Lat-Vent 196 58 250 0
7 Left-Cerebellum-White-Matter 220 248 164 0
8 Left-Cerebellum-Cortex 230 148 34 0
10 Left-Thalamus 0 118 14 0
11 Left-Caudate 122 186 220 0
12 Left-Putamen 236 13 176 0
13 Left-Pallidum 12 48 255 0
14 3rd-Ventricle 204 182 142 0
15 4th-Ventricle 42 204 164 0
16 Brain-Stem 119 159 176 0
17 Left-Hippocampus 220 216 20 0
18 Left-Amygdala 103 255 255 0
26 Left-Accumbens-area 255 165 0 0
41 Right-Cerebral-White-Matter 245 245 245 0
42 Right-Cerebral-Cortex 205 62 78 0
43 Right-Lateral-Ventricle 120 18 134 0
44 Right-Inf-Lat-Vent 196 58 250 0
46 Right-Cerebellum-White-Matter 220 248 164 0
47 Right-Cerebellum-Cortex 230 148 34 0
49 Right-Thalamus 0 118 14 0
50 Right-Caudate 122 186 220 0
51 Right-Putamen 236 13 176 0
52 Right-Pallidum 13 48 255 0
53 Right-Hippocampus 220 216 20 0
54 Right-Amygdala 103 255 255 0
58 Right-Accumbens-area 255 165 0 0
77 WM-hypointensities 200 70 255 0
85 Optic-Chiasm 234 169 30 0
99 Lesion 255 165 0 0
# sclimbic
819 Left-HypoThal-noMB 0 80 0 0 2
820 Right-HypoThal-noMB 15 165 15 0 2
821 Left-Fornix 0 255 255 0 3
822 Right-Fornix 27 187 253 0 3
843 Left-MammillaryBody 178 255 80 0 2
844 Right-MammillaryBody 25 246 80 0 2
865 Left-Basal-Forebrain 170 85 0 0 2
866 Right-Basal-Forebrain 139 69 19 0 2
869 Left-SeptalNuc 255 170 255 0 2
870 Right-SeptalNuc 191 127 191 0 2
nextbrain-utils lut \
-o AllenBrainLUT.txt \
-l allen+dkBy default, this lookup table uses long names for each region. Acronyms can be used instead.
nextbrain-utils lut \
-o AllenBrainLUT.txt \
-l allen+dk \
-aIf S16-compatible labels are used, use the -s16 option here as well.
nextbrain-utils lut \
-o AllenBrainLUT.txt \
-l allen+dk \
-s16The ASeg and SuperSynth label maps can be displayed using the default freesurfer lookup table. Nonetheless, compact lookup tables that only contain labels present in a ASeg+AParc or SuperSynth label map can be generated. Possible LUT options are
allen: Labels from the Allen Brain developmental ontologyallen+dk: Allen + append Desikan-Killiany cortical labelsnextbrain: NextBrainaseg: ASeg+AParc/SynthSegsupersynth: SuperSynthsupersynth-cerebrum: SuperSynth (cerebrum mode)supersynth-exvivo: SuperSynth (exvivo mode)freesurfer: Complete FreeSurfer colormap