AFQ.nn.synthseg
===============

.. py:module:: AFQ.nn.synthseg


Classes
-------

.. autoapisummary::

   AFQ.nn.synthseg.SynthSegLabels


Functions
---------

.. autoapisummary::

   AFQ.nn.synthseg.run_synthseg


Module Contents
---------------

.. py:class:: SynthSegLabels

   Bases: :py:obj:`enum.IntEnum`


   
   Enum where members are also (and must be) ints
















   ..
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   .. py:attribute:: BACKGROUND
      :value: 0



   .. py:attribute:: LEFT_CEREBRAL_WHITE_MATTER
      :value: 1



   .. py:attribute:: LEFT_CEREBRAL_CORTEX
      :value: 2



   .. py:attribute:: LEFT_LATERAL_VENTRICLE
      :value: 3



   .. py:attribute:: LEFT_INFERIOR_LATERAL_VENTRICLE
      :value: 4



   .. py:attribute:: LEFT_CEREBELLUM_WHITE_MATTER
      :value: 5



   .. py:attribute:: LEFT_CEREBELLUM_CORTEX
      :value: 6



   .. py:attribute:: LEFT_THALAMUS
      :value: 7



   .. py:attribute:: LEFT_CAUDATE
      :value: 8



   .. py:attribute:: LEFT_PUTAMEN
      :value: 9



   .. py:attribute:: LEFT_PALLIDUM
      :value: 10



   .. py:attribute:: THIRD_VENTRICLE
      :value: 11



   .. py:attribute:: FOURTH_VENTRICLE
      :value: 12



   .. py:attribute:: BRAIN_STEM
      :value: 13



   .. py:attribute:: LEFT_HIPPOCAMPUS
      :value: 14



   .. py:attribute:: LEFT_AMYGDALA
      :value: 15



   .. py:attribute:: CSF
      :value: 16



   .. py:attribute:: LEFT_ACCUMBENS_AREA
      :value: 17



   .. py:attribute:: LEFT_VENTRAL_DC
      :value: 18



   .. py:attribute:: RIGHT_CEREBRAL_WHITE_MATTER
      :value: 19



   .. py:attribute:: RIGHT_CEREBRAL_CORTEX
      :value: 20



   .. py:attribute:: RIGHT_LATERAL_VENTRICLE
      :value: 21



   .. py:attribute:: RIGHT_INFERIOR_LATERAL_VENTRICLE
      :value: 22



   .. py:attribute:: RIGHT_CEREBELLUM_WHITE_MATTER
      :value: 23



   .. py:attribute:: RIGHT_CEREBELLUM_CORTEX
      :value: 24



   .. py:attribute:: RIGHT_THALAMUS
      :value: 25



   .. py:attribute:: RIGHT_CAUDATE
      :value: 26



   .. py:attribute:: RIGHT_PUTAMEN
      :value: 27



   .. py:attribute:: RIGHT_PALLIDUM
      :value: 28



   .. py:attribute:: RIGHT_HIPPOCAMPUS
      :value: 29



   .. py:attribute:: RIGHT_AMYGDALA
      :value: 30



   .. py:attribute:: RIGHT_ACCUMBENS_AREA
      :value: 31



   .. py:attribute:: RIGHT_VENTRAL_DC
      :value: 32



   .. py:attribute:: BACKGROUND_PARC
      :value: 33



   .. py:attribute:: CTX_LH_BANKSSTS
      :value: 34



   .. py:attribute:: CTX_LH_CAUDALANTERIORCINGULATE
      :value: 35



   .. py:attribute:: CTX_LH_CAUDALMIDDLEFRONTAL
      :value: 36



   .. py:attribute:: CTX_LH_CUNEUS
      :value: 37



   .. py:attribute:: CTX_LH_ENTORHINAL
      :value: 38



   .. py:attribute:: CTX_LH_FUSIFORM
      :value: 39



   .. py:attribute:: CTX_LH_INFERIORPARIETAL
      :value: 40



   .. py:attribute:: CTX_LH_INFERIORTEMPORAL
      :value: 41



   .. py:attribute:: CTX_LH_ISTHMUSCINGULATE
      :value: 42



   .. py:attribute:: CTX_LH_LATERALOCCIPITAL
      :value: 43



   .. py:attribute:: CTX_LH_LATERALORBITOFRONTAL
      :value: 44



   .. py:attribute:: CTX_LH_LINGUAL
      :value: 45



   .. py:attribute:: CTX_LH_MEDIALORBITOFRONTAL
      :value: 46



   .. py:attribute:: CTX_LH_MIDDLETEMPORAL
      :value: 47



   .. py:attribute:: CTX_LH_PARAHIPPOCAMPAL
      :value: 48



   .. py:attribute:: CTX_LH_PARACENTRAL
      :value: 49



   .. py:attribute:: CTX_LH_PARSOPERCULARIS
      :value: 50



   .. py:attribute:: CTX_LH_PARSORBITALIS
      :value: 51



   .. py:attribute:: CTX_LH_PARSTRIANGULARIS
      :value: 52



   .. py:attribute:: CTX_LH_PERICALCARINE
      :value: 53



   .. py:attribute:: CTX_LH_POSTCENTRAL
      :value: 54



   .. py:attribute:: CTX_LH_POSTERIORCINGULATE
      :value: 55



   .. py:attribute:: CTX_LH_PRECENTRAL
      :value: 56



   .. py:attribute:: CTX_LH_PRECUNEUS
      :value: 57



   .. py:attribute:: CTX_LH_ROSTRALANTERIORCINGULATE
      :value: 58



   .. py:attribute:: CTX_LH_ROSTRALMIDDLEFRONTAL
      :value: 59



   .. py:attribute:: CTX_LH_SUPERIORFRONTAL
      :value: 60



   .. py:attribute:: CTX_LH_SUPERIORPARIETAL
      :value: 61



   .. py:attribute:: CTX_LH_SUPERIORTEMPORAL
      :value: 62



   .. py:attribute:: CTX_LH_SUPRAMARGINAL
      :value: 63



   .. py:attribute:: CTX_LH_FRONTALPOLE
      :value: 64



   .. py:attribute:: CTX_LH_TEMPORALPOLE
      :value: 65



   .. py:attribute:: CTX_LH_TRANSVERSETEMPORAL
      :value: 66



   .. py:attribute:: CTX_LH_INSULA
      :value: 67



   .. py:attribute:: CTX_RH_BANKSSTS
      :value: 68



   .. py:attribute:: CTX_RH_CAUDALANTERIORCINGULATE
      :value: 69



   .. py:attribute:: CTX_RH_CAUDALMIDDLEFRONTAL
      :value: 70



   .. py:attribute:: CTX_RH_CUNEUS
      :value: 71



   .. py:attribute:: CTX_RH_ENTORHINAL
      :value: 72



   .. py:attribute:: CTX_RH_FUSIFORM
      :value: 73



   .. py:attribute:: CTX_RH_INFERIORPARIETAL
      :value: 74



   .. py:attribute:: CTX_RH_INFERIORTEMPORAL
      :value: 75



   .. py:attribute:: CTX_RH_ISTHMUSCINGULATE
      :value: 76



   .. py:attribute:: CTX_RH_LATERALOCCIPITAL
      :value: 77



   .. py:attribute:: CTX_RH_LATERALORBITOFRONTAL
      :value: 78



   .. py:attribute:: CTX_RH_LINGUAL
      :value: 79



   .. py:attribute:: CTX_RH_MEDIALORBITOFRONTAL
      :value: 80



   .. py:attribute:: CTX_RH_MIDDLETEMPORAL
      :value: 81



   .. py:attribute:: CTX_RH_PARAHIPPOCAMPAL
      :value: 82



   .. py:attribute:: CTX_RH_PARACENTRAL
      :value: 83



   .. py:attribute:: CTX_RH_PARSOPERCULARIS
      :value: 84



   .. py:attribute:: CTX_RH_PARSORBITALIS
      :value: 85



   .. py:attribute:: CTX_RH_PARSTRIANGULARIS
      :value: 86



   .. py:attribute:: CTX_RH_PERICALCARINE
      :value: 87



   .. py:attribute:: CTX_RH_POSTCENTRAL
      :value: 88



   .. py:attribute:: CTX_RH_POSTERIORCINGULATE
      :value: 89



   .. py:attribute:: CTX_RH_PRECENTRAL
      :value: 90



   .. py:attribute:: CTX_RH_PRECUNEUS
      :value: 91



   .. py:attribute:: CTX_RH_ROSTRALANTERIORCINGULATE
      :value: 92



   .. py:attribute:: CTX_RH_ROSTRALMIDDLEFRONTAL
      :value: 93



   .. py:attribute:: CTX_RH_SUPERIORFRONTAL
      :value: 94



   .. py:attribute:: CTX_RH_SUPERIORPARIETAL
      :value: 95



   .. py:attribute:: CTX_RH_SUPERIORTEMPORAL
      :value: 96



   .. py:attribute:: CTX_RH_SUPRAMARGINAL
      :value: 97



   .. py:attribute:: CTX_RH_FRONTALPOLE
      :value: 98



   .. py:attribute:: CTX_RH_TEMPORALPOLE
      :value: 99



   .. py:attribute:: CTX_RH_TRANSVERSETEMPORAL
      :value: 100



   .. py:attribute:: CTX_RH_INSULA
      :value: 101



   .. py:attribute:: LEFT_HYPOTHALAMUS
      :value: 102



   .. py:attribute:: RIGHT_HYPOTHALAMUS
      :value: 103



.. py:function:: run_synthseg(ort, t1_img, model_name, onnx_kwargs, parc_cortex=False, parc_hypothalamus=False)

   
   Run the Synthseg Model












   .. rubric:: 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.

   .. only:: latex

      




   ..
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