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Website update #514

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Website update #514

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1f0650d
DOC: repositioned tracking quick start in examples_index
Garyfallidis Dec 20, 2014
556f28c
DOC: added proper reference link from tracking_quick_start to new tra…
Garyfallidis Dec 20, 2014
bc262e7
DOC: added contents and highlighted new example sections
Garyfallidis Dec 20, 2014
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11 changes: 5 additions & 6 deletions doc/examples/tracking_quick_start.py
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Expand Up @@ -3,12 +3,6 @@
Tracking Quick Start
====================

.. NOTE::
Dipy has updated tools for fiber tracking. Our new machinery for fiber
tracking is featured in the example titled Introduction to Basic Tracking.
The tools demonstrated in this example are no longer actively being
maintained and will likely be deprecated at some point.

This example shows how to perform fiber tracking using Dipy.

We will use Constrained Spherical Deconvolution (CSD) [Tournier07]_ for local
Expand Down Expand Up @@ -194,6 +188,11 @@
.. [Garyfallidis12] Garyfallidis E., "Towards an accurate brain tractography", PhD thesis, University of Cambridge, 2012.
.. [Tournier07] J-D. Tournier, F. Calamante and A. Connelly, "Robust determination of the fibre orientation distribution in diffusion MRI: Non-negativity constrained super-resolved spherical deconvolution", Neuroimage, vol. 35, no. 4, pp. 1459-1472, 2007.

.. NOTE::
Dipy has a new and very modular fiber tracking machinery. Our new machinery
for fiber tracking is featured in the example :ref:`example_tracking_quick_start`.


.. include:: ../links_names.inc

"""
52 changes: 33 additions & 19 deletions doc/examples_index.rst
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Expand Up @@ -9,12 +9,16 @@ Examples

note_about_examples

.. contents::
:depth: 2


-----------
Quick Start
-----------

- :ref:`example_quick_start`
- :ref:`example_introduction_to_basic_tracking`
- :ref:`example_tracking_quick_start`

-------------
Preprocessing
Expand Down Expand Up @@ -96,44 +100,53 @@ Sparse Fascicle Model

- :ref:`example_sfm_reconst`


-------------------------------------
Statistical evaluation and validation
-------------------------------------
Statistical evaluation
~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_kfold_xval`
- :ref:`example_linear_fascicle_evaluation`


--------------
Fiber tracking
--------------
------------------------------------
Fiber tracking (NEW - Experimental)
------------------------------------

- :ref:`example_introduction_to_basic_tracking`
- :ref:`example_probabilistic_fiber_tracking`
- :ref:`example_sfm_tracking`

Old tracking examples
~~~~~~~~~~~~~~~~~~~~~
---------------
Fiber tracking
---------------

- :ref:`example_tracking_quick_start`
- :ref:`example_tracking_eudx_tensor`
- :ref:`example_tracking_eudx_odf`
- :ref:`example_probabilistic_tracking_odfs`

-------------------
Streamline analysis
-------------------
-------------------------------------
Fiber tracking validation (NEW)
-------------------------------------

- :ref:`example_linear_fascicle_evaluation`
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Yup. Looks good!



------------------------------------
Streamline analysis and connectivity
------------------------------------

- :ref:`example_streamline_tools`
- :ref:`example_streamline_length`

------------
Registration
------------

------------------
Registration (NEW)
------------------

Image-based Registration
~~~~~~~~~~~~~~~~~~~~~~~~~
- :ref:`example_syn_registration_2d`
- :ref:`example_syn_registration_3d`

Streamline-based Registration
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- :ref:`example_bundle_registration`

------------
Expand All @@ -147,6 +160,7 @@ Streamline Clustering

Brain Segmentation
~~~~~~~~~~~~~~~~~~

- :ref:`example_brain_extraction_dwi`

-----------
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