<commit_before>.. _examples:

========
Examples
========

.. toctree::
   :maxdepth: 1

   note_about_examples

.. contents::
   :depth: 2


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

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

-------------
Preprocessing
-------------

Gradients & Spheres
~~~~~~~~~~~~~~~~~~~

- :ref:`example_gradients_spheres`

Brain Extraction
~~~~~~~~~~~~~~~~

- :ref:`example_brain_extraction_dwi`

Basic SNR estimation
~~~~~~~~~~~~~~~~~~~~

- :ref:`example_snr_in_cc`


Denoising
~~~~~~~~~

- :ref:`example_denoise_nlmeans`
- :ref:`example_denoise_localpca`

Reslice
~~~~~~~

- :ref:`example_reslice_datasets`

--------------
Reconstruction
--------------

Constrained Spherical Deconvolution
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_csd`

Fiber ORientation Estimated using Continuous Axially Symmetric Tensors
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_forecast`

Simple Harmonic Oscillator based Reconstruction and Estimation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_shore`
- :ref:`example_reconst_shore_metrics`

Mean Apparent Propagator (MAP)-MRI
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_mapmri`

Studying diffusion time-dependence using qt-dMRI
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_qtdmri` 

Diffusion Tensor Imaging
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_dti`
- :ref:`example_restore_dti`
- :ref:`example_reconst_fwdti`


Diffusion Kurtosis Imaging
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- :ref:`example_reconst_dki`


Q-Ball Constant Solid Angle
~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_csa`


Diffusion Spectrum Imaging
~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_dsi`
- :ref:`example_reconst_dsi_metrics`


Generalized Q-Sampling Imaging
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_gqi`

DSI with Deconvolution
~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_dsid`

Sparse Fascicle Model
~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_sfm_reconst`

Intravoxel incoherent motion (IVIM)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_ivim`


Statistical evaluation
~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_kfold_xval`

------------------------------------------------
Contextual enhancement
------------------------------------------------

- :ref:`example_contextual_enhancement`
- :ref:`example_fiber_to_bundle_coherence`

--------------
Fiber tracking
--------------

- :ref:`example_introduction_to_basic_tracking`
- :ref:`example_probabilistic_fiber_tracking`
- :ref:`example_deterministic_fiber_tracking`
- :ref:`example_tracking_bootstrap_peaks`
- :ref:`example_tracking_tissue_classifier`
- :ref:`example_particle_filtering_fiber_tracking`
- :ref:`example_sfm_tracking`

-------------------------------------
Fiber tracking evaluation
-------------------------------------

- :ref:`example_linear_fascicle_evaluation`


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

- :ref:`example_streamline_tools`
- :ref:`example_streamline_length`
- :ref:`example_cluster_confidence`
- :ref: `example_path_length_map`


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

Image-based Registration
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- :ref:`example_affine_registration_3d`
- :ref:`example_syn_registration_2d`
- :ref:`example_syn_registration_3d`
- :ref:`register_binary_fuzzy`

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

Streamline Clustering
~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_segment_quickbundles`
- :ref:`example_segment_extending_clustering_framework`
- :ref:`example_segment_clustering_features`
- :ref:`example_segment_clustering_metrics`

Brain Segmentation
~~~~~~~~~~~~~~~~~~<commit_msg>removed syntax error (extra space) from examples index<commit_after>.. _examples:

========
Examples
========

.. toctree::
   :maxdepth: 1

   note_about_examples

.. contents::
   :depth: 2


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

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

-------------
Preprocessing
-------------

Gradients & Spheres
~~~~~~~~~~~~~~~~~~~

- :ref:`example_gradients_spheres`

Brain Extraction
~~~~~~~~~~~~~~~~

- :ref:`example_brain_extraction_dwi`

Basic SNR estimation
~~~~~~~~~~~~~~~~~~~~

- :ref:`example_snr_in_cc`


Denoising
~~~~~~~~~

- :ref:`example_denoise_nlmeans`
- :ref:`example_denoise_localpca`

Reslice
~~~~~~~

- :ref:`example_reslice_datasets`

--------------
Reconstruction
--------------

Constrained Spherical Deconvolution
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_csd`

Fiber ORientation Estimated using Continuous Axially Symmetric Tensors
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_forecast`

Simple Harmonic Oscillator based Reconstruction and Estimation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_shore`
- :ref:`example_reconst_shore_metrics`

Mean Apparent Propagator (MAP)-MRI
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_mapmri`

Studying diffusion time-dependence using qt-dMRI
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_qtdmri`

Diffusion Tensor Imaging
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_dti`
- :ref:`example_restore_dti`
- :ref:`example_reconst_fwdti`


Diffusion Kurtosis Imaging
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- :ref:`example_reconst_dki`


Q-Ball Constant Solid Angle
~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_csa`


Diffusion Spectrum Imaging
~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_dsi`
- :ref:`example_reconst_dsi_metrics`


Generalized Q-Sampling Imaging
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_gqi`

DSI with Deconvolution
~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_dsid`

Sparse Fascicle Model
~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_sfm_reconst`

Intravoxel incoherent motion (IVIM)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_reconst_ivim`


Statistical evaluation
~~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_kfold_xval`

------------------------------------------------
Contextual enhancement
------------------------------------------------

- :ref:`example_contextual_enhancement`
- :ref:`example_fiber_to_bundle_coherence`

--------------
Fiber tracking
--------------

- :ref:`example_introduction_to_basic_tracking`
- :ref:`example_probabilistic_fiber_tracking`
- :ref:`example_deterministic_fiber_tracking`
- :ref:`example_tracking_bootstrap_peaks`
- :ref:`example_tracking_tissue_classifier`
- :ref:`example_particle_filtering_fiber_tracking`
- :ref:`example_sfm_tracking`

-------------------------------------
Fiber tracking evaluation
-------------------------------------

- :ref:`example_linear_fascicle_evaluation`


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

- :ref:`example_streamline_tools`
- :ref:`example_streamline_length`
- :ref:`example_cluster_confidence`
- :ref:`example_path_length_map`


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

Image-based Registration
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- :ref:`example_affine_registration_3d`
- :ref:`example_syn_registration_2d`
- :ref:`example_syn_registration_3d`
- :ref:`register_binary_fuzzy`

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

Streamline Clustering
~~~~~~~~~~~~~~~~~~~~~

- :ref:`example_segment_quickbundles`
- :ref:`example_segment_extending_clustering_framework`
- :ref:`example_segment_clustering_features`
- :ref:`example_segment_clustering_metrics`

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