Introduction to Diffusion MRI

This note provides details on the basic principles and key aspects of analysis in diffusion MRI

General references

Author	Journal	Year	Title
Tromp	(Blog)	2009	A blog/tutorial on diffusion MRI
Mori et al.	Neuron	2006	Principles of Diffusion Tensor Imaging and Its Applications to Basic Neuroscience Research
Jbabdi et al.	Nature Neuroscience	2015	Measuring macroscopic brain connections in vivo
Johansen-Berg et al.	Annu Rev Neurosci	2009	Using diffusion imaging to study human connectional anatomy
Tournier et al.	Magn Reson Med	2011	Diffusion tensor imaging and beyond
Le Bihan et al.	NeuroImage	2012	Diffusion MRI at 25: exploring brain tissue structure and function
Dell'Acqua et al.	NMR Biomed	2019	Modelling white matter with spherical deconvolution: How and why?
Jeurisson et al.	NMR Biomed	2019	Diffusion MRI fiber tractography of the brain
Alexander et al.	NMR Biomed	2019	Imaging brain microstructure with diffusion MRI: practicality and applications
Tax et al.	NeuroImage	2022	What’s new and what’s next in diffusion MRI preprocessing

Limitations of dMRI and tractography

Author	Journal	Year	Title
Jones et al.	NeuroImage	2013	White matter integrity, fiber count, and other fallacies: The do's and don'ts of diffusion MRI
Thomas et al.	PNAS	2014	Anatomical accuracy of brain connections derived from diffusion MRI tractography is inherently limited
Calabrese et al.	Cereb Cortex	2015	A Diffusion MRI Tractography Connectome of the Mouse Brain and Comparison with Neuronal Tracer Data
Reveley et al.	PNAS	2015	Superficial white matter fiber systems impede detection of long-range cortical connections in diffusion MR tractography

Artifacts in dMRI

Author	Journal	Year	Title
Yendiki et al.	NeuroImage	2014	Spurious group differences due to head motion in a diffusion MRI study

Various processing tips

Author	Journal	Year	Title
Smith et al.	NeuroImage	2012	Anatomically-constrained tractography: Improved diffusion MRI streamlines tractography through effective use of anatomical information
Smith et al.	NeuroImage	2013	SIFT: Spherical-deconvolution informed filtering of tractograms
Smith et al.	NeuroImage	2015	SIFT2: Enabling dense quantitative assessment of brain white matter connectivity using streamlines tractography
Cieslak et al.	Nature Methods	2021	QSIPrep: Preprocessing and analysis of q-space images
Laamouni et al.	NMR Biomed	2025	A taxonomic guide to diffusion MRI tractography visualization tools
Oldham et al.	NeuroImage	2025