Reconstruction#

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

Note

Some reconstruction models do not have a tutorial yet

Reconstruction methods available in DIPY#
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]