Examples

Examples

Quick Start

  • example_quick_start

  • example_tracking_introduction_eudx

Preprocessing

Gradients & Spheres

  • example_gradients_spheres

Brain Extraction

  • example_brain_extraction_dwi

Basic SNR estimation

  • example_snr_in_cc

Reslice & Motion Correction

  • example_reslice_datasets

  • example_motion_correction

Denoising

  • example_denoise_patch2self

  • example_denoise_nlmeans

  • example_denoise_localpca

  • example_denoise_mppca

  • example_denoise_gibbs

Reconstruction

Below, an overview of all reconstruction models available on DIPY.

Note: Some reconstruction models do not have a tutorial yet

Method Single Shell Multi Shell Cartesian Ideal Data Requirements References
DTI (SLS, WLS, NNLS) Yes Yes Yes - All shells should be < 1000 Basser 1994
FwDTI No Yes No Pasternak 2009, Henriques et al., 2017
DKI - Standard No Yes No Jensen 2005
DKI - Micro (WMTI) No Yes No Fieremans 2011
Mean Signal DKI No Yes No Henriques, 2018
CSA Yes No No Aganj 2010
Westin's CSA Yes No No
IVIM No Yes No - 10 b-values less than b=1000 is needed.
- b-values range: 0-2000 ideally		 LeBihan 1984
IVIM Variable Projection No Yes No - 10 b-values less than b=1000 is needed. Fadnavis 2019
SDT Yes No No Descoteaux 2009
DSI No No Yes Wedeen 2008
DSID No No Yes Canales-Rodriguez 2010
GQI - GQI2 No Yes Yes Yeh 2010
SFM Yes Yes No Rokem 2015
Q-Ball (OPDT) Yes No No Tuch 2004, Descoteaux 2007, Tristan-Vega 2010
SHORE No Yes No Merlet 2013, Özarslan 2009, Özarslan 2008
MAP-MRI No Yes No Ozarslan 2013
MAPL No Yes No Fick 2016
CSD Yes No No Tournier 2017 Descoteaux 2008 Tournier 2007
SMS/MT CSD No Yes No Jeurissen 2014
ForeCast No Yes No Anderson 2005
RUMBA-SD Yes Yes Yes Canales-Rodríguez 2015
QTI No Yes No Westin 2016
QTI+ No Yes No Herberthson 2021
Ball & Stick Yes Yes No Behrens 2013
QTau-MRI No Yes No Fick 2017
Power Map Yes Yes No DellAcqua2014
SMT / SMT2 No Yes No NetoHe2019, Kaden2016b

Constrained Spherical Deconvolution

  • example_reconst_csd

  • example_reconst_mcsd

Fiber Orientation Estimated using Continuous Axially Symmetric Tensors

  • example_reconst_forecast

Simple Harmonic Oscillator based Reconstruction and Estimation

  • example_reconst_shore

  • example_reconst_shore_metrics

Mean Apparent Propagator (MAP)-MRI

  • example_reconst_mapmri

Studying diffusion time-dependence using qt-dMRI

  • example_reconst_qtdmri

Diffusion Tensor Imaging

  • example_reconst_dti

  • example_restore_dti

Free-water Diffusion Tensor Imaging

  • example_reconst_fwdti

Diffusion Kurtosis Imaging

  • example_reconst_dki

  • example_reconst_msdki

White Matter Tract Integrity Model

  • example_reconst_dki_micro

Q-Ball Constant Solid Angle

  • example_reconst_csa

Diffusion Spectrum Imaging

  • example_reconst_dsi

  • example_reconst_dsi_metrics

Generalized Q-Sampling Imaging

  • example_reconst_gqi

DSI with Deconvolution

  • example_reconst_dsid

Sparse Fascicle Model

  • example_reconst_sfm

Intravoxel incoherent motion (IVIM)

  • example_reconst_ivim

Statistical evaluation

  • example_kfold_xval

Intra-Voxel Signal Reconstruction

  • example_reconst_sh

Q-space Trajectory Imaging

  • example_reconst_qti

Q-space Trajectory Imaging with positivity constraints

  • example_reconst_qtiplus

Robust and Unbiased Model-BAsed Spherical Deconvolution (RUMBA-SD)

  • example_reconst_rumba

Contextual enhancement

  • example_contextual_enhancement

  • example_fiber_to_bundle_coherence

Fiber tracking

  • example_tracking_introduction_eudx

  • example_tracking_deterministic

  • example_tracking_probabilistic

  • example_tracking_bootstrap_peaks

  • example_tracking_stopping_criterion

  • example_tracking_pft

  • example_tracking_sfm

  • example_tracking_rumba

  • example_linear_fascicle_evaluation

  • example_surface_seed

Streamline analysis and connectivity

  • example_streamline_tools

  • example_streamline_length

  • example_cluster_confidence

  • example_path_length_map

  • example_afq_tract_profiles

  • example_bundle_assignment_maps

  • example_bundle_shape_similarity

Registration

Image-based Registration

  • example_affine_registration_3d

  • example_affine_registration_masks

  • example_syn_registration_2d

  • example_syn_registration_3d

  • example_register_binary_fuzzy

Streamline-based Registration

  • example_bundle_registration

  • example_bundle_group_registration

  • example_streamline_registration

  • example_bundlewarp_registration

Segmentation

Streamline Clustering

  • example_segment_quickbundles

  • example_segment_extending_clustering_framework

  • example_segment_clustering_features

  • example_segment_clustering_metrics

Brain Segmentation

  • example_brain_extraction_dwi

Tissue Classification

  • example_tissue_classification

Bundle Extraction

  • example_bundle_extraction

Simulations

  • example_simulate_multi_tensor

  • example_reconst_dsid

  • example_simulate_dki

Multiprocessing

  • example_reconst_csd_parallel

  • example_reconst_csa_parallel

File Formats

  • example_streamline_formats

Visualization

  • example_viz_advanced

  • example_viz_slice

  • example_viz_bundles

  • example_viz_roi_contour

Workflows

  • example_workflow_creation

  • example_combined_workflow_creation