Comparisons to other pipelines

Other pipelines for preprocessing DWI data are currently being developed. Below are tables comparing their current feature sets. These other

• Tractoflow

• PreQual

• MRtrix3_connectome

• dMRIPrep

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	✔	✔	✔	✔	✔

QC

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