Documentation 1.6.0. > Examples

Examples

Quick Start

Preprocessing

Gradients & Spheres

Brain Extraction

Basic SNR estimation

Reslice & Motion Correction

Denoising

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 - low b-values are needed LeBihan 1984
IVIM Variable Projection No Yes No 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 No 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

Fiber Orientation Estimated using Continuous Axially Symmetric Tensors

Simple Harmonic Oscillator based Reconstruction and Estimation

Mean Apparent Propagator (MAP)-MRI

Studying diffusion time-dependence using qt-dMRI

Diffusion Tensor Imaging

Free-water Diffusion Tensor Imaging

Diffusion Kurtosis Imaging

White Matter Tract Integrity Model

Q-Ball Constant Solid Angle

Diffusion Spectrum Imaging

Generalized Q-Sampling Imaging

DSI with Deconvolution

Sparse Fascicle Model

Intravoxel incoherent motion (IVIM)

Statistical evaluation

Intra-Voxel Signal Reconstruction

Q-space Trajectory Imaging

Q-space Trajectory Imaging with positivity constraints

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

Contextual enhancement

Fiber tracking

Streamline analysis and connectivity

Registration

Image-based Registration

Streamline-based Registration

Segmentation

Streamline Clustering

Brain Segmentation

Tissue Classification

Bundle Extraction

Simulations

Multiprocessing

File Formats

Visualization

Workflows