.. only:: html

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

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

    .. _sphx_glr_auto_examples_utils_subject_to_mni.py:


===================================
Transform from Subject to MNI 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, and how to apply that transform to a dataset.


.. 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 subject to MNI space
    # first we will create a dataset to transform
    data = cortex.Volume.random('S1', 'fullhead')

    # then transform it!
    mni_data = mni.transform_to_mni(data, s1_to_mni)
    # mni_data is a nibabel Nifti1Image

    mni_data_vol = mni_data.get_data() # the actual array, shape=(182,218,182)

    # 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_subject_to_mni.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: subject_to_mni.py <subject_to_mni.py>`



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

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


.. only:: html

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

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_