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.

Method	Single Shell	Multi Shell	Cartesian	Paper Data Descriptions	References
DTI (SLS, WLS, NNLS)	Yes	Yes	Yes	Typical b-value = 1000s/mm^2, maximum b-value 1200s/mm^2 (some success up to 1500s/mm^2)	Basser 1994
DTI (RESTORE)	Yes	Yes	Yes	Typical b-value = 1000s/mm^2, maximum b-value 1200s/mm^2 (some success up to 1500s/mm^2)	Yendiki2013, Chang2005, Chung2006
FwDTI	No	Yes	No	DTI-style acquistion, multiple b=0, all shells should be within maximum b-value of 1000 (or 32 directions evenly distributed 500mm/s^2 and 1500mm/s^2 per Henriques 2017)	Pasternak 2009, Henriques et al., 2017
DKI - Standard	No	Yes	No	Dual spin echo diffusion-weighted 2D EPI images were acquired with b values of 0, 500, 1000, 1500, 2000, and 2500 s/mm^2 (max b value of 2000 suggested as sufficient in brain tissue); at least 15 directions	Jensen2005
DKI+ Constraints	No	Yes	No	None	Tom Dela Haije 2020
DKI - Micro (WMTI)	No	Yes	No	DKI-style acquisition: at least two non-zero b shells (max b value 2000), minimum of 15 directions; typically b-values in increments of 500 from 0 to 2000, 30 directions	Fieremans 2011, Tabesh 2010
Mean Signal DKI	No	Yes	No	b-values in increments of 500 from 0 to 2000, 30 directions	Henriques, 2018
CSA	Yes	No	No	HARDI data (preferably 7T) with at least 200 diffusion images at b=3000 s/mm^2, or multi-shell data with high angular resolution	Aganj 2010
Westins 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	QBI-style acquisition (60-64 directions, b-value 1000mm/s^2)	Descoteaux 2009
DSI	No	No	Yes	515 diffusion encodings, b-values from 12,000 to 18,000 s/mm^2. Acceleration in subsequent studies with ~100 diffusion encoding directions in half sphere of the q-space with b-values = 1000, 2000, 3000s/mm2)	Wedeen 2008, Sotiropoulos 2013
DSID	No	No	Yes	203 diffusion encodings (isotropic 3D grid points in the q-space contained within a sphere with radius 3.6), maximum b-value=4000mm/s^2	Canales-Rodriguez 2010
GQI - GQI2	No	Yes	Yes	Fits any sampling scheme with at least one non-zero b-shell, benefits from more directions. Recommended 23 b-shells ranging from 0 to 4000 in a 258 direction grid-sampling scheme	Yeh 2010
SFM	Yes	Yes	No	At least 40 directions, b-value above 1000mm/s^2	Rokem 2015
Q-Ball (OPDT)	Yes	No	No	At least 64 directions, maximum b-values 3000-4000mm/s^2, multi-shell, isotropic voxel size	Tuch 2004, Descoteaux 2007, Tristan-Vega 2010
SHORE	No	Yes	No	Multi-shell HARDI data (500, 1000, and 2000 s/mm^2; minimum 2 non-zero b-shells) or DSI (514 images in a cube of five lattice-units, one b=0)	Merlet 2013, Özarslan 2009, Özarslan 2008
MAP-MRI	No	Yes	No	Six unit sphere shells with b = 1000, 2000, 3000, 4000, 5000, 6000 s/mm^2 along 19, 32, 56, 87, 125, and 170 directions (see Olson 2019 for candidate sub-sampling schemes)	Ozarslan 2013, Olson 2019
MAP+ Constraints	No	Yes	No		`Tom Dela Haije < https://doi.org/10.1016/j.neuroimage.2019.116405>`__
MAPL	No	Yes	No	Multi-shell similar to WU-Minn HCP, with minimum of 60 samples from 2 shells b-value 1000 and 3000s/mm^2	Fick 2016
CSD	Yes	No	No	Minimum: 20 gradient directions and a b-value of 1000 s/mm^2; benefits additionally from 60 direction HARDI data with b-value = 3000s/mm^2 or multi-shell	Tournier 2017, Descoteaux 2008, Tournier 2007
SMS/MT CSD	No	Yes	No	5 b=0, 50 directions at 3 non-zero b-shells: b=1000, b=2000, b=3000	Jeurissen 2014
ForeCast	No	Yes	No	Multi-shell 64 direction b-values of 1000, 2000s/mm^2 as in Alexander 2017. Original model used 1480 s/mm^2 with 92 directions and 36 b=0	Anderson 2005, Alexander 2017
RUMBA-SD	Yes	Yes	Yes	HARDI data with 64 directions at b = 2500s/mm^2, 3 b=0 images (full original acquisition: 256 directions on a sphere at b = 2500s/mm^2, 36 b=0 volumes)	Canales-Rodríguez 2015
QTI	No	Yes	No	Evenly distributed geometric sampling scheme of 216 measurements, 5 b-values (50, 250, 50, 1000, 200mm/s^2), measurement tensors of four shapes: stick, prolate, sphere, and plane	Westin 2016
QTI+	No	Yes	No	At least one b=0, minimum of 39 acquisitions with spherical and linear encoding; optimal 120 (see Morez 2023), ideal 217 see Herberthson 2021 Table 1	Herberthson 2021, Morez 2023
Ball & Stick	Yes	Yes	No	Three b=0, 60 evenly distributed directions per Jones 1999 at b-value 1000mm/s^2	Behrens 2003
QTau-MRI	No	Yes	No	Minimum 200 volumes of multi-spherical dMRI (multi-shell, multi-diffusion time; varying gradient directions, gradient strengths, and diffusion times)	Fick 2017
Power Map	Yes	Yes	No	HARDI data with 60 directions at b-value = 3000 s/mm^2, 7 b=0 (Minimum: HARDI data with at least 30 directions)	DellAcqua2014
SMT / SMT2	No	Yes	No	72 directions at each of 5 evenly spaced b-values from 0.5 to 2.5 ms/μm2, 5 b-values from 3 to 5 ms/μm2, 5 b-values from 5.5 to 7.5 ms/μm2, and 3 b-values from 8 to 9 ms/μm2 / b=0 ms/μm^-2, and along 33 directions at b-values from 0.2–3 ms/μm^-2 in steps of 0.2 ms/μm^−2 (24 point spherical design and 9 directions identified for rapid kurtosis estimation)	NetoHe2019, Kaden2016b
CTI	No	Yes	No		NetoHe2020, NovelloL2022, NetHe2021