Comparisons to other pipelines
Other pipelines for preprocessing DWI data are currently being developed. Below are tables comparing
their current feature sets. These other
dMRIPrep exclusively performs preprocessing and is therefore omitted from the reconstruction and tractography sections.
Supported Sampling Schemes
QSIPrep
Tractoflow
PreQual
MRtrix3_connectome
dMRIPrep
Single Shell
✔
✔
✔
✔
✔
Multi Shell
✔
✔
✔
✔
✔
Cartesian
✔
✘
✘
✘
✘
Random (Compressed Sensing)
✔
✘
✘
✘
✘
QSIPrep
Tractoflow
PreQual
MRtrix3_connectome
dMRIPrep
BIDS App
✔
✔
✘
✔
✔
Gradient direction sanity check
Q-form matching
✘
dwigradcheck
✘
✘
Workflow management
NiPyPe
NextFlow
Custom
Custom
NiPyPe
MP-PCA denoising
✔
✔
✔
✔
✘
Patch2self denoising
✔
✘
✘
✘
✘
Gibbs unringing
mrdegibbs
mrdegibbs
(disabled)
mrdegibbs
(disabled)
mrdegibbs
✘
B1 bias field correction
N4
N4
N4
N4
✘
Automatic distortion group concatenation
✔
✘
✘
✔
✘
T1w brain extraction
ANTs
ANTs
✘
✘
ANTs
Intensity normalization
scaled by b =0 means
b =0 mean set to 1000
✘
mtnormalize
✘
b=0 to T1w coregistration
ANTs linear registration
ANTs Non-Linear SyN
✘
mrregister
FSL BBR
Head Motion Correction (shelled schemes)
eddy
eddy
eddy
eddy
✘
Head Motion Correction (Cartesian / Random Schemes)
SHORELine
✘
✘
✘
✘
PEPOLAR EPI distortion correction
TOPUP
TOPUP
TOPUP
TOPUP
TOPUP
GRE Fieldmap EPI distortion correction
✔
✘
✘
✘
✔
Fieldmapless Distortion Correction
PE-Direction SyN
✘
Non-Linear registration
SyN b0-DISCO
PE-Direction SyN
T1w-based Normalization
ANTs (SyN)
✘
✘
✘
ANTs (SyN)
HTML Report
✔
✘
✔
✘
✔
Containerized
✔
✔
✔
✔
✔
QSIPrep
Tractoflow
PreQual
MRtrix3_connectome
MRTrix3 MSMT CSD
✔
✘
✘
✔
CSD
MRtrix3
DIPY
✘
MRtrix3
Single Shell 3-Tissue CSD
✔
✘
✘
✘
DTI Metrics
✔
✔
✔
✔
DSI Studio GQI
✔
✘
✘
✘
MAPMRI
✔
✘
✘
✘
3dSHORE
✔
✘
✘
✘
QSIPrep
Tractoflow
PreQual
MRtrix3_connectome
DIPY Particle Filtering
✘
✔
✘
✘
MRtrix3 iFOD2
✔
✘
✘
✔
Anatomically constrained Tractography
✔
✔
✘
✔
DSI Studio QA-Enhanced Tractography
✔
✘
✘
✘
Across-Software tractography
✔
✘
✘
✘
SIFT weighting
✔
✘
✘
✔
QSIPrep
Tractoflow
PreQual
MRtrix3_connectome
Automated methods boilerplate
✔
✘
✘
✘
HTML Preprocessing Report
NiWorkflows-based
✘
Custom
EddyQuad
HTML Reconstruction Report
NiWorkflows-based
✘
Custom
✘