AFQ.nn.babyseg
==============

.. py:module:: AFQ.nn.babyseg


Attributes
----------

.. autoapisummary::

   AFQ.nn.babyseg.logger


Classes
-------

.. autoapisummary::

   AFQ.nn.babyseg.BabySegLabels


Functions
---------

.. autoapisummary::

   AFQ.nn.babyseg._get_model
   AFQ.nn.babyseg.run_babyseg
   AFQ.nn.babyseg.pve_from_babyseg


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

.. py:data:: logger

.. py:class:: BabySegLabels

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


   
   Enum where members are also (and must be) ints
















   ..
       !! processed by numpydoc !!

   .. 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_CEREBELLUM_CORTEX
      :value: 4



   .. py:attribute:: LEFT_THALAMUS
      :value: 5



   .. py:attribute:: LEFT_CAUDATE
      :value: 6



   .. py:attribute:: BRAIN_STEM
      :value: 7



   .. py:attribute:: LEFT_HIPPOCAMPUS
      :value: 8



   .. py:attribute:: LEFT_AMYGDALA
      :value: 9



   .. py:attribute:: LEFT_VENTRAL_DC
      :value: 10



   .. py:attribute:: RIGHT_CEREBRAL_WHITE_MATTER
      :value: 11



   .. py:attribute:: RIGHT_CEREBRAL_CORTEX
      :value: 12



   .. py:attribute:: RIGHT_LATERAL_VENTRICLE
      :value: 13



   .. py:attribute:: RIGHT_CEREBELLUM_CORTEX
      :value: 14



   .. py:attribute:: RIGHT_THALAMUS
      :value: 15



   .. py:attribute:: RIGHT_CAUDATE
      :value: 16



   .. py:attribute:: RIGHT_HIPPOCAMPUS
      :value: 17



   .. py:attribute:: RIGHT_AMYGDALA
      :value: 18



   .. py:attribute:: RIGHT_VENTRAL_DC
      :value: 19



   .. py:attribute:: LEFT_BASAL_GANGLIA
      :value: 20



   .. py:attribute:: RIGHT_BASAL_GANGLIA
      :value: 21



.. py:function:: _get_model(model_name)

.. py:function:: run_babyseg(ort, t1_img, onnx_kwargs)

   
   Run the BabySeg Model












   .. rubric:: References

   .. [Rcd0b7f21bbab-1] Hoffmann M, Zöllei L, Dalca AV. Deep infant brain segmentation from
          multi-contrast MRI. Asilomar Conference on Signals, Systems, and
          Computers, 2025, pp. 974-981. https://arxiv.org/abs/2512.05114
   .. [Rcd0b7f21bbab-2] Hoffmann M. Domain-randomized deep learning for neuroimage analysis.
          IEEE Signal Processing Magazine, 42(4):78-90, 2025.
          https://arxiv.org/abs/2507.13458

   .. only:: latex

      [Rcd0b7f21bbab-1]_, [Rcd0b7f21bbab-2]_




   ..
       !! processed by numpydoc !!

.. py:function:: pve_from_babyseg(babyseg_data)

   
   Compute partial volume estimates from BabySeg segmentation.


   :Parameters:

       **babyseg_data** : ndarray
           The output segmentation from BabySeg.

   :Returns:

       **pve** : ndarray
           PVE data with CSF, GM, and WM segmentations.













   ..
       !! processed by numpydoc !!