.. _home:

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Diffusion Imaging In Python
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Dipy_ is a **free** and **open source** software project focusing mainly on **diffusion** *magnetic resonance imaging* (dMRI) analysis.
Nonetheless, as we solve problems in dMRI some of the solutions are applicable to the greater medical imaging and image processing communities.
See for example our registration and denoising tutorials.


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Highlights
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**Dipy 0.8** is now available for :ref:`download <installation>`. The new
release contains state-of-the-art algorithms for diffusion MRI registration, reconstruction, denoising, statistical evaluation, fiber tracking and validation of tracking.

For more information about Dipy_, read the `dipy paper`_  in Frontiers in Neuroinformatics.

.. raw :: html

	<div style="width: 80% max-width=800px">
		<a href="http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2014.00008/abstract" target="_blank"><img alt=" " class="align-center" src="_static/dipy_paper_logo.jpg" style="width: 90%;max-height: 90%">
        </a>
	</div>

So, how similar are your bundles to the real anatomy? Learn how to optimize your analysis as we did to create the fornix of the figure above, by reading the tutorials in our :ref:`gallery <examples>`.

See :ref:`older highlights <old_highlights>`.


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Announcements
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- The creators of Dipy_ will attend both ISMRM and HBM 2015. Come and meet us!
- **Dipy 0.8.0** released, 6 January, 2015.
- Dipy_ will be an official exhibitor in `HBM 2015 <http://ohbm.loni.usc.edu>`_. Don't miss our booth!
- Dipy was featured in `The Scientist Magazine <http://www.the-scientist.com/?articles.view/articleNo/41266/title/White-s-the-Matter>`_, Nov, 2014.
- `Dipy paper`_ accepted in Frontiers of Neuroinformatics, 22 January, 2014.
- **Dipy 0.7.1** Released!, 16 January, 2014.
- **Dipy 0.7.0** Released!, 23 December, 2013.
- A team of Dipy developers **wins** the `IEEE ISBI HARDI challenge <http://hardi.epfl.ch/static/events/2013_ISBI/workshop.html#results>`_, 7 April, 2013.
- **Dipy 0.6.0** Released!, 30 March, 2013.

See some of our :ref:`past announcements <old_news>`


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Getting Started
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Here is a simple example showing how to calculate `color FA`. We
use a single Tensor model to reconstruct the datasets which are saved in a
Nifti file along with the b-values and b-vectors which are saved as text files.
In this example we use only a few voxels with 101 gradient directions::

    from dipy.data import get_data
    fimg, fbval, fbvec = get_data('small_101D')

    import nibabel as nib
    img = nib.load(fimg)
    data = img.get_data()

    from dipy.io import read_bvals_bvecs
    bvals, bvecs = read_bvals_bvecs(fbval, fbvec)

    from dipy.core.gradients import gradient_table
    gtab = gradient_table(bvals, bvecs)

    from dipy.reconst.dti import TensorModel
    ten = TensorModel(gtab)
    tenfit = ten.fit(data)

    from dipy.reconst.dti import fractional_anisotropy
    fa = fractional_anisotropy(tenfit.evals)

    from dipy.reconst.dti import color_fa
    cfa = color_fa(fa, tenfit.evecs)

As an exercise try to calculate the `color FA` with your datasets. Here is how
a slice should look like.

.. image:: _static/colorfa.png
    :align: center

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Next Steps
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You can learn more about how you to use Dipy_ with  your datasets by reading the examples in our :ref:`documentation`.

.. We need the following toctree directive to include the documentation
.. in the document hierarchy - see http://sphinx.pocoo.org/concepts.html
.. toctree::
   :hidden:

   documentation
   stateoftheart




.. include:: links_names.inc
