.. _examples: ======== Examples ======== .. toctree:: :maxdepth: 1 note_about_examples .. contents:: :depth: 2 ----------- Quick Start ----------- - :ref:`example_quick_start` - :ref:`example_tracking_introduction_eudx` ------------- 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` - :ref:`example_denoise_mppca` - :ref:`example_denoise_gibbs` 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` Free-water Diffusion Tensor Imaging ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - :ref:`example_reconst_fwdti` Diffusion Kurtosis Imaging ~~~~~~~~~~~~~~~~~~~~~~~~~~ - :ref:`example_reconst_dki` - :ref:`example_reconst_msdki` White Matter Tract Integrity Model ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - :ref:`example_reconst_dki_micro` 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_tracking_introduction_eudx` - :ref:`example_tracking_deterministic` - :ref:`example_tracking_probabilistic` - :ref:`example_tracking_bootstrap_peaks` - :ref:`example_tracking_stopping_criterion` - :ref:`example_tracking_pft` - :ref:`example_tracking_sfm` ------------------------- 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` - :ref:`example_afq_tract_profiles` ------------ Registration ------------ Image-based Registration ~~~~~~~~~~~~~~~~~~~~~~~~ - :ref:`example_affine_registration_3d` - :ref:`example_syn_registration_2d` - :ref:`example_syn_registration_3d` - :ref:`example_register_binary_fuzzy` Streamline-based Registration ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - :ref:`example_bundle_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 ~~~~~~~~~~~~~~~~~~ - :ref:`example_brain_extraction_dwi` Tissue Classification ~~~~~~~~~~~~~~~~~~~~~ - :ref:`example_tissue_classification` Bundle Extraction ~~~~~~~~~~~~~~~~~ - :ref:`example_bundle_extraction` ----------- Simulations ----------- - :ref:`example_simulate_multi_tensor` - :ref:`example_reconst_dsid` - :ref:`example_simulate_dki` --------------- Multiprocessing --------------- - :ref:`example_reconst_csd_parallel` - :ref:`example_reconst_csa_parallel` ------------ File Formats ------------ - :ref:`example_streamline_formats` ------------- Visualization ------------- - :ref:`example_viz_advanced` - :ref:`example_viz_slice` - :ref:`example_viz_bundles` - :ref:`example_viz_roi_contour` --------- Workflows --------- - :ref:`example_workflow_creation` - :ref:`example_combined_workflow_creation`