.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        Click :ref:`here <sphx_glr_download_auto_examples_utils_mni_to_subject.py>`     to download the full example code
    .. rst-class:: sphx-glr-example-title

    .. _sphx_glr_auto_examples_utils_mni_to_subject.py:


===================================
Transform from MNI to Subject Space
===================================

Pycortex has built-in functionality for linearly transforming data to and from
standard atlas spaces (e.g. MNI-152). This functionality is built on top of FSL.

This example shows how to create a transform from some subject functional space
to MNI space (the same as in subject_to_mni.py), and how to use that to put data
into subject space from MNI space.


.. code-block:: default

    import cortex

    # First let's do this "manually", using cortex.mni
    from cortex import mni

    import numpy as np
    np.random.seed(1234)


    # This transform is gonna be from one specific functional space for a subject
    # which is defined by the transform (xfm)
    s1_to_mni = mni.compute_mni_transform(subject='S1', xfm='fullhead')
    # s1_to_mni is a 4x4 array describing the transformation in homogeneous corods

    # Transform data from MNI to subject space
    # first we will create a dataset to transform
    # this uses the implicitly created "identity" transform, which is used for data
    # in the native anatomical space (i.e. same dims as the base anatomical image,
    # and in the same space as the surface)
    data = cortex.Volume.random('MNI', 'identity')

    # then transform it into the space defined by the 'fullhead' transform for 'S1'
    subject_data = mni.transform_mni_to_subject('S1', 'fullhead', 
                                                data.data, s1_to_mni)
    # subject_data is a nibabel Nifti1Image

    subject_data_vol = mni_data.get_data() # the actual array, shape=(100,100,31)

    # That was the manual method. pycortex can also cache these transforms for you
    # if you get them using the pycortex database
    s1_to_mni_db = cortex.db.get_mnixfm('S1', 'fullhead')
    # this is the same as s1_to_mni, but will return instantly on subsequent calls

.. rst-class:: sphx-glr-timing

   **Total running time of the script:** ( 0 minutes  0.000 seconds)


.. _sphx_glr_download_auto_examples_utils_mni_to_subject.py:


.. only :: html

 .. container:: sphx-glr-footer
    :class: sphx-glr-footer-example



  .. container:: sphx-glr-download sphx-glr-download-python

     :download:`Download Python source code: mni_to_subject.py <mni_to_subject.py>`



  .. container:: sphx-glr-download sphx-glr-download-jupyter

     :download:`Download Jupyter notebook: mni_to_subject.ipynb <mni_to_subject.ipynb>`


.. only:: html

 .. rst-class:: sphx-glr-signature

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