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|
[main]
readme = """
:html_theme.sidebar_secondary.remove:
.. _examples:
Examples
========
.. note::
The examples here are some uses of the analysis and visualization functionality
of DIPY, with example data from actual neuroscience experiments, or with
synthetic data, which is generated as part of the example.
All the examples presented in the documentation are generated from
*fully functioning* python scripts, which are available as part of the
source distribution in the `doc/examples` folder.
If you want to replicate a particular analysis or visualization, copy
or download the relevant `.py` script, edit out
the body of the text of the example and alter it to your purpose.
.. contents::
:depth: 2
"""
position = 0 # it should always be 0
enable = true # it should always be true
files = []
[quick_start]
readme = """
Quick Start
-----------
"""
position = 1
enable = true
files = [
"quick_start.py",
"tracking_introduction_eudx.py",
]
[preprocessing]
readme = """
Preprocessing
-------------
"""
position = 4
enable = true
files = [
"brain_extraction_dwi.py",
"denoise_ascm.py",
"denoise_nlmeans.py",
"denoise_gibbs.py",
"denoise_localpca.py",
"denoise_mppca.py",
"denoise_patch2self.py",
"gradients_spheres.py",
"piesno.py",
"reslice_datasets.py",
"snr_in_cc.py",
"motion_correction.py",
]
[reconstruction]
readme = """
Reconstruction
--------------
Below, an overview of all reconstruction models available in DIPY.
.. note::
Some reconstruction models do not have a tutorial yet
.. include:: ../../reconstruction_models_list.rst
"""
position = 7
enable = true
files = [
"kfold_xval.py",
"reconst_csa.py",
"reconst_csd.py",
"reconst_cti.py",
"reconst_mcsd.py",
"reconst_dki.py",
"reconst_dki_micro.py",
"reconst_dsi.py",
"reconst_dsi_metrics.py",
"reconst_dsid.py",
"reconst_dti.py",
"reconst_forecast.py",
"reconst_fwdti.py",
"reconst_gqi.py",
"reconst_ivim.py",
"reconst_mapmri.py",
"reconst_msdki.py",
"reconst_qtdmri.py",
"reconst_shore.py",
"reconst_shore_metrics.py",
"restore_dti.py",
"reconst_sfm.py",
"reconst_sh.py",
"reconst_rumba.py",
"reconst_qti.py",
"reconst_qtiplus.py",
"histology_resdnn.py",
"reconst_bingham.py"
]
[contextual_enhancement]
readme = """
Contextual Enhancement
----------------------
"""
position = 10
enable = true
files = [
"contextual_enhancement.py",
"fiber_to_bundle_coherence.py",
]
[fiber_tracking]
readme = """
Fiber Tracking
--------------
.. include:: ../../tractography_methods_list.rst
"""
position = 13
enable = true
files = [
"tracking_bootstrap_peaks.py",
"tracking_deterministic.py",
"tracking_introduction_eudx.py",
"tracking_pft.py",
"tracking_ptt.py",
"tracking_probabilistic.py",
"tracking_sfm.py",
"tracking_stopping_criterion.py",
"tracking_rumba.py",
"linear_fascicle_evaluation.py",
"surface_seed.py",
]
[streamline_analysis]
readme = """
Streamlines Analysis and Connectivity
-------------------------------------
"""
position = 17
enable = true
files = [
"afq_tract_profiles.py",
"cluster_confidence.py",
"path_length_map.py",
"streamline_length.py",
"streamline_tools.py",
"bundle_assignment_maps.py",
"bundle_shape_similarity.py",
]
[registration]
readme = """
Registration
------------
"""
position = 20
enable = true
files = [
"affine_registration_3d.py",
"bundle_registration.py",
"bundle_group_registration.py",
"register_binary_fuzzy.py",
"streamline_registration.py",
"bundlewarp_registration.py",
"syn_registration_2d.py",
"syn_registration_3d.py",
"affine_registration_masks.py",
]
[segmentation]
readme = """
Segmentation
------------
"""
position = 23
enable = true
files = [
"bundle_extraction.py",
"segment_clustering_features.py",
"segment_clustering_metrics.py",
"segment_extending_clustering_framework.py",
"segment_quickbundles.py",
"tissue_classification_dam.py",
"tissue_classification.py",
"brain_extraction_dwi.py",
"fast_streamline_search.py",
]
[simulations]
readme = """
Simulation
----------
"""
position = 26
enable = true
files = [
"simulate_dki.py",
"simulate_multi_tensor.py",
"reconst_dsid.py",
]
[Multiprocessing]
readme = """
Multiprocessing
---------------
"""
position = 29
enable = true
files = [
"reconst_csa_parallel.py",
"reconst_csd_parallel.py",
"tracking_disco_phantom.py",
]
[file_formats]
readme = """
File Formats
------------
"""
position = 32
enable = true
files = [
"streamline_formats.py",
]
[visualization]
readme = """
Visualization
-------------
"""
position = 35
enable = true
files = [
"viz_advanced.py",
"viz_bundles.py",
"viz_roi_contour.py",
"viz_slice.py",
]
[workflows]
readme = """
Workflows
---------
"""
position = 37
enable = true
files = [
"combined_workflow_creation.py",
"workflow_creation.py",
]
|
