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) ✔ ✘ ✘ ✘ ✘

Preprocessing

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 ✔ ✔ ✔ ✔ ✔

Reconstruction

QSIPrep Tractoflow PreQual MRtrix3_connectome
MRTrix3 MSMT CSD ✔ ✘ ✘ ✔
CSD MRtrix3 DIPY ✘ MRtrix3
Single Shell 3-Tissue CSD ✔ ✘ ✘ ✘
DTI Metrics ✔ ✔ ✔ ✔
DSI Studio GQI ✔ ✘ ✘ ✘
MAPMRI ✔ ✘ ✘ ✘
3dSHORE ✔ ✘ ✘ ✘

Tractography

QSIPrep Tractoflow PreQual MRtrix3_connectome
DIPY Particle Filtering ✘ ✔ ✘ ✘
MRtrix3 iFOD2 ✔ ✘ ✘ ✔
Anatomically constrained Tractography ✔ ✔ ✘ ✔
DSI Studio QA-Enhanced Tractography ✔ ✘ ✘ ✘
Across-Software tractography ✔ ✘ ✘ ✘
SIFT weighting ✔ ✘ ✘ ✔

QC

QSIPrep Tractoflow PreQual MRtrix3_connectome
Automated methods boilerplate ✔ ✘ ✘ ✘
HTML Preprocessing Report NiWorkflows-based ✘ Custom EddyQuad
HTML Reconstruction Report NiWorkflows-based ✘ Custom ✘