AFQ.nn.synthseg#

Classes#

SynthSegLabels

Enum where members are also (and must be) ints

Functions#

run_synthseg(ort, t1_img, model_name, onnx_kwargs[, ...])

Run the Synthseg Model

Module Contents#

class AFQ.nn.synthseg.SynthSegLabels[source]#

Bases: enum.IntEnum

Enum where members are also (and must be) ints

BACKGROUND = 0[source]#

LEFT_CEREBRAL_WHITE_MATTER = 1[source]#

LEFT_CEREBRAL_CORTEX = 2[source]#

LEFT_LATERAL_VENTRICLE = 3[source]#

LEFT_INFERIOR_LATERAL_VENTRICLE = 4[source]#

LEFT_CEREBELLUM_WHITE_MATTER = 5[source]#

LEFT_CEREBELLUM_CORTEX = 6[source]#

LEFT_THALAMUS = 7[source]#

LEFT_CAUDATE = 8[source]#

LEFT_PUTAMEN = 9[source]#

LEFT_PALLIDUM = 10[source]#

THIRD_VENTRICLE = 11[source]#

FOURTH_VENTRICLE = 12[source]#

BRAIN_STEM = 13[source]#

LEFT_HIPPOCAMPUS = 14[source]#

LEFT_AMYGDALA = 15[source]#

CSF = 16[source]#

LEFT_ACCUMBENS_AREA = 17[source]#

LEFT_VENTRAL_DC = 18[source]#

RIGHT_CEREBRAL_WHITE_MATTER = 19[source]#

RIGHT_CEREBRAL_CORTEX = 20[source]#

RIGHT_LATERAL_VENTRICLE = 21[source]#

RIGHT_INFERIOR_LATERAL_VENTRICLE = 22[source]#

RIGHT_CEREBELLUM_WHITE_MATTER = 23[source]#

RIGHT_CEREBELLUM_CORTEX = 24[source]#

RIGHT_THALAMUS = 25[source]#

RIGHT_CAUDATE = 26[source]#

RIGHT_PUTAMEN = 27[source]#

RIGHT_PALLIDUM = 28[source]#

RIGHT_HIPPOCAMPUS = 29[source]#

RIGHT_AMYGDALA = 30[source]#

RIGHT_ACCUMBENS_AREA = 31[source]#

RIGHT_VENTRAL_DC = 32[source]#

BACKGROUND_PARC = 33[source]#

CTX_LH_BANKSSTS = 34[source]#

CTX_LH_CAUDALANTERIORCINGULATE = 35[source]#

CTX_LH_CAUDALMIDDLEFRONTAL = 36[source]#

CTX_LH_CUNEUS = 37[source]#

CTX_LH_ENTORHINAL = 38[source]#

CTX_LH_FUSIFORM = 39[source]#

CTX_LH_INFERIORPARIETAL = 40[source]#

CTX_LH_INFERIORTEMPORAL = 41[source]#

CTX_LH_ISTHMUSCINGULATE = 42[source]#

CTX_LH_LATERALOCCIPITAL = 43[source]#

CTX_LH_LATERALORBITOFRONTAL = 44[source]#

CTX_LH_LINGUAL = 45[source]#

CTX_LH_MEDIALORBITOFRONTAL = 46[source]#

CTX_LH_MIDDLETEMPORAL = 47[source]#

CTX_LH_PARAHIPPOCAMPAL = 48[source]#

CTX_LH_PARACENTRAL = 49[source]#

CTX_LH_PARSOPERCULARIS = 50[source]#

CTX_LH_PARSORBITALIS = 51[source]#

CTX_LH_PARSTRIANGULARIS = 52[source]#

CTX_LH_PERICALCARINE = 53[source]#

CTX_LH_POSTCENTRAL = 54[source]#

CTX_LH_POSTERIORCINGULATE = 55[source]#

CTX_LH_PRECENTRAL = 56[source]#

CTX_LH_PRECUNEUS = 57[source]#

CTX_LH_ROSTRALANTERIORCINGULATE = 58[source]#

CTX_LH_ROSTRALMIDDLEFRONTAL = 59[source]#

CTX_LH_SUPERIORFRONTAL = 60[source]#

CTX_LH_SUPERIORPARIETAL = 61[source]#

CTX_LH_SUPERIORTEMPORAL = 62[source]#

CTX_LH_SUPRAMARGINAL = 63[source]#

CTX_LH_FRONTALPOLE = 64[source]#

CTX_LH_TEMPORALPOLE = 65[source]#

CTX_LH_TRANSVERSETEMPORAL = 66[source]#

CTX_LH_INSULA = 67[source]#

CTX_RH_BANKSSTS = 68[source]#

CTX_RH_CAUDALANTERIORCINGULATE = 69[source]#

CTX_RH_CAUDALMIDDLEFRONTAL = 70[source]#

CTX_RH_CUNEUS = 71[source]#

CTX_RH_ENTORHINAL = 72[source]#

CTX_RH_FUSIFORM = 73[source]#

CTX_RH_INFERIORPARIETAL = 74[source]#

CTX_RH_INFERIORTEMPORAL = 75[source]#

CTX_RH_ISTHMUSCINGULATE = 76[source]#

CTX_RH_LATERALOCCIPITAL = 77[source]#

CTX_RH_LATERALORBITOFRONTAL = 78[source]#

CTX_RH_LINGUAL = 79[source]#

CTX_RH_MEDIALORBITOFRONTAL = 80[source]#

CTX_RH_MIDDLETEMPORAL = 81[source]#

CTX_RH_PARAHIPPOCAMPAL = 82[source]#

CTX_RH_PARACENTRAL = 83[source]#

CTX_RH_PARSOPERCULARIS = 84[source]#

CTX_RH_PARSORBITALIS = 85[source]#

CTX_RH_PARSTRIANGULARIS = 86[source]#

CTX_RH_PERICALCARINE = 87[source]#

CTX_RH_POSTCENTRAL = 88[source]#

CTX_RH_POSTERIORCINGULATE = 89[source]#

CTX_RH_PRECENTRAL = 90[source]#

CTX_RH_PRECUNEUS = 91[source]#

CTX_RH_ROSTRALANTERIORCINGULATE = 92[source]#

CTX_RH_ROSTRALMIDDLEFRONTAL = 93[source]#

CTX_RH_SUPERIORFRONTAL = 94[source]#

CTX_RH_SUPERIORPARIETAL = 95[source]#

CTX_RH_SUPERIORTEMPORAL = 96[source]#

CTX_RH_SUPRAMARGINAL = 97[source]#

CTX_RH_FRONTALPOLE = 98[source]#

CTX_RH_TEMPORALPOLE = 99[source]#

CTX_RH_TRANSVERSETEMPORAL = 100[source]#

CTX_RH_INSULA = 101[source]#

LEFT_HYPOTHALAMUS = 102[source]#

RIGHT_HYPOTHALAMUS = 103[source]#

AFQ.nn.synthseg.run_synthseg(ort, t1_img, model_name, onnx_kwargs, parc_cortex=False, parc_hypothalamus=False)[source]#

Run the Synthseg Model

References

[1] Billot, Benjamin, et al. “Robust machine learning segmentation: for large-scale analysis of heterogeneous clinical brain MRI datasets.” Proceedings of the National Academy of Sciences 120.9 (2023): e2216399120.
[2] Billot, Benjamin, et al. “SynthSeg: Segmentation of brain MRI scans: of any contrast and resolution without retraining.” Medical image analysis 86 (2023): 102789.