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 = 1000 s/mm^2, maximum b-value 1200 s/mm^2 (some success up to 1500 s/mm^2)	Basser et al. [BMLeBihan94b]
DTI (RESTORE)	Yes	Yes	Yes	Typical b-value = 1000 s/mm^2, maximum b-value 1200 s/mm^2 (some success up to 1500 s/mm^2)	Chang et al. [CJP05], Chung et al. [CLH06], Yendiki et al. [YKK+14]
FwDTI	No	Yes	No	DTI-style acquisition, multiple b=0, all shells should be within maximum b-value of 1000 s/mm^2 (or 32 directions evenly distributed 500 s/mm^2 and 1500 s/mm^2 per Neto Henriques et al. [NetoHenriquesRG+17])	Pasternak et al. [PSG+09], Neto Henriques et al. [NetoHenriquesRG+17]
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	Jensen et al. [JHR+05]
DKI+ Constraints	No	Yes	No	None	Dela Haije et al. [DelaHaijeOzarslanF20]
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 et al. [FJH11], Tabesh et al. [TJAH11]
Mean Signal DKI	No	Yes	No	b-values in increments of 500 from 0 to 2000 s/mm^2, 30 directions	Neto Henriques [NetoHenriques18]
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 et al. [ALS+10]
Westins CSA	Yes	No	No
IVIM	No	Yes	No	low b-values are needed	Le Bihan et al. [LeBihanBL+88]
IVIM Variable Projection	No	Yes	No		Fadnavis et al. [FRF+19]
SDT	Yes	No	No	QBI-style acquisition (60-64 directions, b-value 1000 s/mm^2)	Descoteaux et al. [DDKnoscheA09]
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, 3000 s/mm^2)	Wedeen et al. [WWS+08], Sotiropoulos et al. [SJX+13]
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 = 4000 s/mm^2	Canales-Rodríguez et al. [CRodriguezIMAlemanGomezMGarcia10]
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 et al. [YWT10]
SFM	Yes	Yes	No	At least 40 directions, b-value above 1000 s/mm^2	Rokem et al. [RYP+15]
Q-Ball (OPDT)	Yes	No	No	At least 64 directions, maximum b-values 3000-4000 s/mm^2, multi-shell, isotropic voxel size	Tuch [Tuc04], Descoteaux et al. [DAFD07], Tristán-Vega et al. [TristanVAFernandezW09]
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 and Deriche [MD13], Özarslan et al. [OzarslanKB08], Özarslan et al. [OzarslanKS+09]
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 et al. [OAM19] for candidate sub-sampling schemes)	Özarslan et al. [OzarslanKS+13], Olson et al. [OAM19]
MAP+ Constraints	No	Yes	No		Dela Haije et al. [DelaHaijeOzarslanF20]
MAPL	No	Yes	No	Multi-shell similar to WU-Minn HCP, with minimum of 60 samples from 2 shells b-value 1000 and 3000 s/mm^2	Fick et al. [FWCD16]
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 = 3000 s/mm^2 or multi-shell	Tournier et al. [TCGC04], Tournier et al. [TCC07], Descoteaux et al. [DAFD07]
SMS/MT CSD	No	Yes	No	5 b=0, 50 directions at 3 non-zero b-shells: b=1000, 2000, 3000 s/mm^2	Jeurissen et al. [JTD+14]
FORECAST	No	Yes	No	Multi-shell 64 direction b-values of 1000, 2000 s/mm^2 as in Alexander et al. [AEA+17]. Original model used 1480 s/mm^2 with 92 directions and 36 b=0	Anderson [And05], Alexander et al. [AEA+17]
RUMBA-SD	Yes	Yes	Yes	HARDI data with 64 directions at b = 2500 s/mm^2, 3 b=0 images (full original acquisition: 256 directions on a sphere at b = 2500 s/mm^2, 36 b=0 volumes)	Canales-Rodríguez et al. [CRodriguezDS+15]
QTI	No	Yes	No	Evenly distributed geometric sampling scheme of 216 measurements, 5 b-values (50, 250, 50, 1000, 200 s/mm^2), measurement tensors of four shapes: stick, prolate, sphere, and plane	Westin et al. [WKP+16]
QTI+	No	Yes	No	At least one b=0, minimum of 39 acquisitions with spherical and linear encoding; optimal 120 (see Morez et al. [MSdenDekker+23]), ideal 217 see Table 1 in Herberthson et al. [HBH+21]	Herberthson et al. [HBH+21], Morez et al. [MSdenDekker+23]
Ball & Stick	Yes	Yes	No	Three b=0, 60 evenly distributed directions per Jones et al. [JHS99] at b-value 1000 s/mm^2	Behrens et al. [BWMJ+03]
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 et al. [FPS+18]
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)	Dell'Acqua et al. [DellAcquaLCS14]
SMT / SMT2	No	Yes	No	72 directions at each of 5 evenly spaced b-values from 0.5 to 2.5 ms/μm^2, 5 b-values from 3 to 5 ms/μm^2, 5 b-values from 5.5 to 7.5 ms/μm^2, and 3 b-values from 8 to 9 ms/μm^2 / 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)	Kaden et al. [KKC+16], Neto Henriques et al. [NetoHenriquesJS19]
CTI	No	Yes	No		Neto Henriques et al. [NetoHenriquesJS20], Neto Henriques et al. [NetoHenriquesJS21], Novello et al. [NNetoHenriquesI+22]