:py:mod:`AFQ.tasks.mapping`
===========================

.. py:module:: AFQ.tasks.mapping


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


Functions
~~~~~~~~~

.. autoapisummary::

   AFQ.tasks.mapping.export_registered_b0
   AFQ.tasks.mapping.template_xform
   AFQ.tasks.mapping.export_rois
   AFQ.tasks.mapping.mapping
   AFQ.tasks.mapping.sls_mapping
   AFQ.tasks.mapping.get_reg_subject
   AFQ.tasks.mapping.get_mapping_plan



Attributes
~~~~~~~~~~

.. autoapisummary::

   AFQ.tasks.mapping.logger


.. py:data:: logger

   

.. py:function:: export_registered_b0(data_imap, mapping)

   
   full path to a nifti file containing
   b0 transformed to template space
















   ..
       !! processed by numpydoc !!

.. py:function:: template_xform(mapping, data_imap)

   
   full path to a nifti file containing
   registration template transformed to subject space
















   ..
       !! processed by numpydoc !!

.. py:function:: export_rois(base_fname, output_dir, data_imap, mapping)

   
   dictionary of full paths to Nifti1Image files of ROIs
   transformed to subject space
















   ..
       !! processed by numpydoc !!

.. py:function:: mapping(base_fname, dwi_data_file, reg_subject, data_imap, mapping_definition=None)

   
   mapping from subject to template space.


   :Parameters:

       **mapping_definition** : instance of `AFQ.definitions.mapping`, optional
           This defines how to either create a mapping from
           each subject space to template space or load a mapping from
           another software. If creating a map, will register reg_subject and
           reg_template.
           If None, use SynMap()
           Default: None














   ..
       !! processed by numpydoc !!

.. py:function:: sls_mapping(base_fname, dwi_data_file, reg_subject, data_imap, tractography_imap, mapping_definition=None)

   
   mapping from subject to template space.


   :Parameters:

       **mapping_definition** : instance of `AFQ.definitions.mapping`, optional
           This defines how to either create a mapping from
           each subject space to template space or load a mapping from
           another software. If creating a map, will register reg_subject and
           reg_template.
           If None, use SynMap()
           Default: None














   ..
       !! processed by numpydoc !!

.. py:function:: get_reg_subject(data_imap, reg_subject_spec='power_map')

   
   Nifti1Image which represents this subject
   when registering the subject to the template


   :Parameters:

       **reg_subject_spec** : str, instance of `AFQ.definitions.ImageDefinition`, optional  # noqa
           The source image data to be registered.
           Can either be a Nifti1Image, an ImageFile, or str.
           if "b0", "dti_fa_subject", "subject_sls", or "power_map,"
           image data will be loaded automatically.
           If "subject_sls" is used, slr registration will be used
           and reg_template should be "hcp_atlas".
           Default: "power_map"














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       !! processed by numpydoc !!

.. py:function:: get_mapping_plan(kwargs, use_sls=False)