Microstructure
& Connectivity Lab

Publication collection

Reviews & Consensus

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2026
Brain Structure and FunctionReview

Did you know? State-of-the-art preprocessing diffusion MRI data can improve tractography

Kurt G. Schilling et al. · Last author: Jelle Veraart

This review explains how modern diffusion MRI preprocessing improves the anatomical fidelity and repeatability of tractography. It brings together evidence for denoising and correction of motion, eddy currents, susceptibility distortion, and Gibbs ringing. Practical acquisition advice and integrated pipelines help researchers apply these methods consistently.

Image ProcessingTractographyReviews & Consensus
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Effects of individual diffusion MRI preprocessing steps on fiber orientations and tractography.
2026
Brain Structure and FunctionReview

Diffusion tractography outside the brain: the road less travelled

Kurt G. Schilling et al. · Last author: Alexander Leemans

Tractography can probe organized tissue far beyond cerebral white matter. This review surveys applications in the spinal cord, heart, peripheral nerves, brachial plexus, kidney, skeletal muscle, and prostate. It explains the acquisition and modeling adaptations each region requires, together with the anatomical opportunities and unresolved interpretation challenges.

TractographySpinal CordReviews & Consensus
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Ex vivo mouse heart tractography shows the changing orientation of cardiomyocytes through the ventricular wall.
2025
Brain Structure and FunctionCommentary

Atlas-based templates vs. subject-specific tractography: resolving the debate

Kurt G. Schilling, Fan Zhang, J-Donald Tournier, Francesco Vergani, Stamatios N. Sotiropoulos, Ariel Rokem, Lauren J. O’Donnell

Atlas templates and subject-specific tractography answer overlapping but different anatomical questions. This debate article explains the strengths of standardized population references and individual pathway reconstruction. It outlines why methodological choices should follow the research question, especially when individual variation and pathway geometry are central to an analysis.

TractographyReviews & Consensus
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Comparison of atlas propagation and subject-specific tractography workflows.
2025
Brain Structure and FunctionCommentary

Short association fiber tractography: key insights and surprising facts

Kurt Schilling, Fan Zhang, Claudio Román, Lauren J. O’Donnell, Pamela Guevara

Short association fibers are numerous but challenging to reconstruct because of their small size, variable anatomy, and partial volume effects. This communication summarizes key anatomical and methodological insights. It describes how better images, adapted processing, and suitable tracking parameters are opening the superficial white matter to investigation.

TractographyReviews & Consensus
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Short association fibers reconstructed in superficial white matter using high-resolution diffusion MRI.
2025
Brain Structure and FunctionCommentary

Animal models are useful in studying human neuroanatomy with tractography

Alard Roebroeck, Suzanne Haber, Elena Borra, Simona Schiavi, Stephanie J. Forkel, Kathleen Rockland, Tim B. Dyrby, Kurt Schilling

This short communication examines how animal models inform human tractography, drawing on a debate at the 2024 Tract-Anat Retreat. It highlights histological validation, high-resolution imaging, disease research, and comparative anatomy. The discussion also addresses species differences and the care required when translating findings to humans.

TractographyReviews & Consensus
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Title and author block of the commentary Animal models are useful in studying human neuroanatomy with tractography.
2025
Magnetic Resonance in MedicineReview

Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI : Part 2—Ex vivo imaging: Added value and acquisition

Kurt G. Schilling et al. · Last author: Ileana O. Jelescu

The second ISMRM preclinical diffusion MRI paper examines the value of ex vivo imaging and how to acquire reliable data. It covers specimen selection, fixation, preparation, and scanning. The recommendations explain both the opportunities for detailed tissue characterization and the experimental differences that complicate comparison with living tissue.

Reviews & ConsensusMicrostructure
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High-resolution ex vivo human imaging supports detailed tissue maps and tractography.
2025
Magnetic Resonance in MedicineReview

Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI : Part 1: In vivo small-animal imaging

Ileana O. Jelescu et al. · Last author: Kurt G. Schilling

The first paper in the ISMRM preclinical diffusion MRI series presents community recommendations for imaging living small animals. It covers model selection, preparation, acquisition, processing, and interpretation, with an emphasis on reproducibility. The authors also identify open methodological questions and resources for sharing data and software.

Reviews & ConsensusMicrostructureTractography
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Diffusion MRI across small-animal models illustrates differences in brain size, geometry, and tissue organization.
2025
Magnetic Resonance in MedicineReview

Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI : Part 3—Ex vivo imaging: Data processing, comparisons with microscopy, and tractography

Kurt G. Schilling et al. · Last author: Ileana O. Jelescu

The third ISMRM preclinical diffusion MRI paper addresses ex vivo image processing, comparisons with microscopy, and tractography. It explains how fixed-tissue experiments require choices that differ from in vivo workflows. Community recommendations and unresolved questions guide the design and interpretation of rigorous, reproducible validation studies.

Reviews & ConsensusImage ProcessingTractography
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Examples of artifacts addressed by preprocessing ex vivo diffusion MRI data.
2025
Handbook of Diffusion MR TractographyBook chapter

Tractography validation Part 1: Foundations, numerical simulations, and phantom models

Tim B. Dyrby, Els Fieremans, Francois Rheault, Adam W. Anderson, Marco Palombo, Silvio Sarubbo, Peter Neher, Kurt G. Schilling

This handbook chapter introduces the foundations of tractography validation and the roles of numerical simulations and physical phantoms. It explains how controlled reference systems can test reconstruction methods at different anatomical scales. The discussion helps researchers choose validation strategies and understand the limits of their conclusions.

TractographyReviews & Consensus
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The tractography validation process spans acquisition, local orientation estimation, tracking, and anatomical interpretation.
2025
Handbook of Diffusion MR TractographyBook chapter

Tractography validation Part 2: The use of anatomical model systems and measures for validation

Tim B. Dyrby et al. · Last author: Kurt G. Schilling

The second tractography-validation chapter reviews anatomical reference systems, empirical validation when ground truth is unavailable, and ways to quantify agreement. It connects validation in real tissue with the practical interpretation of reconstructed pathways.

TractographyReviews & Consensus
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Microdissection and ex vivo diffusion tractography compared for association pathways in the same monkey brain.
2025
Handbook of Diffusion MR TractographyBook chapter

Tractography validation part 3: Lessons learned through validation studies

Kurt G. Schilling, Francois Rheault, Tim B. Dyrby

This handbook chapter synthesizes what validation studies have taught us about tractography. Evidence from simulations, phantoms, histology, and anatomical comparisons reveals both reliable capabilities and persistent limitations. The chapter connects complex tissue anatomy and reconstruction assumptions to the practical interpretation and continued development of diffusion MRI tractography.

TractographyReviews & Consensus
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Differences in anatomical definitions and dissection protocols alter reconstructed pathway size, shape, and connections.
2020
Journal of Neuroscience MethodsReview

Challenges for biophysical modeling of microstructure

Ileana O. Jelescu, Marco Palombo, Francesca Bagnato, Kurt G. Schilling

This review follows diffusion MRI biophysical models from design to clinical application. It explains how model assumptions, acquisition choices, parameter estimation, and validation determine what can be inferred about tissue, and why interpreting model parameters becomes especially difficult in disease.

MicrostructureReviews & Consensus
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A roadmap for developing, estimating, and validating diffusion MRI models of tissue microstructure.
2019
Magnetic Resonance ImagingReview

Challenges in diffusion MRI tractography – Lessons learned from international benchmark competitions

Kurt G. Schilling et al. · Last author: Maxime Descoteaux

This review synthesizes a decade of tractography benchmark competitions. Physical phantoms, simulated data, and anatomical references reveal recurring tradeoffs between finding true pathways and avoiding false connections, while showing how acquisition, reconstruction, seeding, and evaluation choices shape apparent performance.

TractographyReviews & Consensus
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Overview of benchmark datasets and anatomical references used in tractography challenges.