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Diffusion MRI
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Diffusion MRI
Theory, Methods, and Applications
Edited by
Derek K. Jones, PhD
Director of MRI
Cardiff University Brain Research Imaging Centre (CUBRIC)
School of Psychology, Cardiff University
Cardiff, Wales
United Kingdom
1 2011
1
Oxford University Press, Inc., publishes works that further
Oxford University’s objective of excellence
in research, scholarship, and education.
With offices in
Argentina Austria Brazil Chile Czech Republic France Greece
Guatemala Hungary Italy Japan Poland Portugal Singapore
South Korea Switzerland Thailand Turkey Ukraine Vietnam
135798642
Printed in the United States of America
on acid-free paper
This book is dedicated to Claire, Sam, and Millie—the most wonderful,
loving, and supportive family a man could ever wish for.
D.K.J.
This page intentionally left blank
Foreword
It is a great privilege to introduce this book devoted to diffusion white matter fiber structure. DTI (and variants such as HARDI
MRI and it cannot arrive at a better time, as we will celebrate in or DSI) can now produce gorgeous three-dimensional color
2010 the 25th anniversary of diffusion MRI, as we know it. images of the circuitry of the brain which will be used to map,
This very powerful method and concept was, indeed, intro- for the first time, the human brain “connectome”, opening up new
duced in 1985, as well as its potential for brain imaging. Of lines of inquiry for human neuroscience and for treating brain
course, earlier works had demonstrated that molecular diffusion disorders, such as autism, schizophrenia or neurodegenerative
could be measured with NMR with the pioneering work of Hahn, diseases. More recently, diffusion MRI has also been proposed
Carr and Purcell, and most importantly Stejskal and Tanner in the as an approach to obtain images of brain function. One should
1960s. However, the possibility to localize those measurements not overlook also applications of diffusion MRI to the body,
under the form of maps of the diffusion coefficients of water especially for the screening of primary or secondary malignant
in tissues, especially in vivo and in the human brain, had never tumors, an approach which is fast becoming a standard.
been shown before. This might look a simple achievement, but The editor of this volume, Dr. Derek Jones is internationally
the localization of molecular diffusion (a microscopic process) known for his original contributions to the literature on white
through MRI (with a millimetric resolution) was certainly not a matter fiber tractography with diffusion MRI. I remember well
trivial challenge, and there are still many technical outstanding my first encounter with Derek at the workshop I had organized in
issues—as can be seen within the chapters of this book—as well 2002 in Saint-Malo on the “Biophysical issues of diffusion MRI:
as in the recollections from the minds of key players which are What can we measure?”. Although many aspects of this question
assembled at the end of the book. are yet unanswered (enough to keep researchers busy for life),
Since that time, diffusion MRI has been an extraordinarily tremendous progress has been made since then and the publica-
successful imaging technique (more than 130 000 entries in tion of the first book on diffusion MRI in 1995. I sincerely con-
Google Scholar for ‘diffusion MRI’ at the time of this writing). gratulate Derek and his contributing authors, all well-recognized
This is not a surprise as the power of diffusion MRI resides in experts, to have made this body of knowledge available to the
its potential to probe tissue structure and function at the cellu- community. This state-of-the-art book will be of immense help to
lar level without using contrast media or ionizing radiations. Its the scientists and clinicians, experts or in training, who want to
main clinical domain of application has been with neurological improve their skills in diffusion MRI.
disorders, especially for the management of acute stroke patients I wish Derek great success with this book which should
in the emergency room when treatment is still possible and thus definitely stimulate and inspire readers.
saving patients from permanent brain damage. It has also rap-
idly become a standard for investigating white matters disorders,
as Diffusion Tensor Imaging (DTI) can reveal abnormalities in Saclay, France Denis Le Bihan
vii
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Preface
In 1994, I was working as a Medical Physicist in Leicester Royal on the team; it is inevitable that I have not been able to include
Infirmary in the UK, on a national medical physics training all the star players in the field. However, you know who you are,
scheme in radiotherapy and nuclear medicine. There I met Mark and we know who you are, and I thank you for your understand-
Horsfield—the only MR physicist in the department, who said ing about this.
“Del—if you ever fancy doing a PhD, come and see me. There’s
this new thing that’s just been published called diffusion tensor
imaging.” At the time, Peter Basser and colleagues had just pub-
About the Contents
lished their first full papers on estimating and imaging the diffu- The book starts and ends with history. It opens with a historical
sion tensor (following the presentation at the ISMRM in Berlin in overview of the developments in the study of white matter—way
1992). I accepted Mark’s invitation (thanks Mark!), and set about before diffusion MRI—to put diffusion MRI into context. We
trying to understand diffusion MRI. cannot capture the thoughts of those that pioneered these early
As The Faces (or was it Rod Stewart?) sang, “I wish that I works, but we can capture the thoughts of those who have pio-
knew what I know now, when I was younger” (more specifically, neered important aspects of diffusion MRI. The book therefore
at the start of my PhD). What I wanted was a “Big Book” contain- closes with personal accounts from six scientists who champi-
ing a graduate course in diffusion MRI. Denis Le Bihan’s book oned the field into what it is today. I am absolutely thrilled to
Diffusion/Perfusion MRI (Raven Press, 1995) was very helpful, include personal accounts from Ed Stejskal and John Tanner, Paul
but it predated many important developments in the early days of Callaghan, Denis Le Bihan, Mike Moseley, and Peter Basser.
DT-MRI. Moreover, fifteen years have passed since Denis’ book In between, the book is broadly divided into two halves. The
was written and the field has changed a lot since then. It also first half details mainly theoretical and technical developments in
seems that there is increasing demand for a comprehensive trea- diffusion MRI, while the second half deals predominantly with
tise on diffusion MRI from the basic science and clinical imaging applications in vivo. In terms of selecting disease states, it would
community. be impossible to cover all diseases to which diffusion MRI has
So, the book you are holding in your hands is my humble been applied. My selection therefore aims to capture different
attempt to produce “The Big Book” that serves as a graduate challenges to the technique, or to highlight cases where diffu-
course in diffusion MRI. My hope is that the newcomer to the sion MRI has made a real difference in the clinical or clinical–
field will find at least half of the answers to his or her questions research domain.
between the pages of this book. I also hope that the level of detail Throughout the book, there is a strong bias toward imaging
provided will provide a sufficiently firm grounding as to enable of the white matter. I don’t apologize for this. I may be reflecting
and inspire entirely new avenues to be explored. At the very least, personal biases, but it occurs to me that the strongest motivator
there should be inspiration for a few dozen PhD projects here! pushing the technological envelope is gaining increased preci-
sion and accuracy of quantifying aspects of neural tissue in vivo.
Consequently, I am absolutely sure that I haven’t covered every-
About the Authors
thing that it is important to know about diffusion MRI. You may,
When Oxford University Press invited me to take on this project, of course, consider there to be some striking omissions, but you
I was first asked to submit a proposal for the book, which was can’t please all of the people all of the time.
to be sent out for review. I sat with a blank piece of paper, and
sketched out a long list of topics that I felt should be included
Expression of Thanks
(see the index at the back of the book). I am a great believer in the
saying “Every man to his own trade.” In other words, I thought I would like to conclude this preface with some words of thanks:
that a book like this should not be written by a single author but The Authors: First and foremost, I would like to thank the
that each topic should be covered by an expert—a person who had authors who have contributed to this book. I feel extremely privi-
pioneered, developed, or led the field. So, I sat about sketching leged to have worked with this dream team, to have chatted with
out a hypothetical “dream team” of star players (from which the them at conferences, and to call many of them a friend. These
Editor excludes himself) as the authors. I was clearly delighted folks have been extremely patient with me when I sent back a
when I got 100% acceptance from all the invitations, and so, you chapter for the fourth or fifth revision. This gang of 50 or more
hold the product of the efforts of a substantial dream team. Of authors has battled through some personal challenges in order for
course, like any dream team, there can only be so many players the book to see fruition. Over the course of the book’s preparation,
ix
x Preface
I have shared in news of the arrivals of babies, family deaths, The Purchasers of this Book: Unless someone buys the book
serious personal assaults, surgery, floods, changes of jobs, and and reads it, the whole exercise would have been pointless. I hope
other equally challenging situations (you know who you are, and that you, the reader, find the book useful. If you do, and you bump
an extra personal thanks to you for still delivering the chapters). into one of the authors at a conference, then please tell them—
Moreover, I thank the authors for caving in to my cajoling in the and thank them. I’m sure that they would appreciate it!
first place. I think I owe about 20 gallons of beer and 15 magnums My Family: If you read this book, and get something useful
of champagne in bribes, which I will pay if you ask me (but who out of it, please consider gratitude to Claire, Sam, and Millie
reads the Preface anyway?) Jones—my wonderful family who have put up with so much. At
Oxford University Press: My thanks go to O.U.P. for the some point in the last year, I’ve read over 1900 pages of manu-
wonderful opportunity to produce this book, and especially to script (not including references, legends, and figures), each an
David D’Addona and Craig Panner for their continued support average of 5 times, not to mention over 1700 e-mail exchanges
and assistance from initial contact to production of the book. I am about the book, which takes a lot of “after-hours” time. So, my
also hugely indebted to Jerri Hurlbutt, copy editor extraordinaire, biggest thanks go to Claire, Sam, and Millie who have put up
who painstakingly read each and every word and improved the with their husband and dad working late, working at weekends,
readability of the book immeasurably. Thank you Jerri! and not being able to play “at the front.” Without their support,
The Staff of Cardiff University Brain Research Imaging patience, and understanding, this book would never have made it
Centre (CUBRIC): Thanks go to everyone in CUBRIC for their to fruition. Thank you!
support, especially in the period leading up to the deadline when I Derek K. Jones
“disappeared” to complete the manuscript. Diolch yn fawr! October 1, 2009
Contents
Section I What Are We Studying and Why? 11. Hardware Considerations for Diffusion MRI 171
Nirbhay N. Yadav, Tim Stait-Gardner, and William S. Price
1. The Functional Anatomy of White Matter: From Postmortem
Dissections to In Vivo Virtual Tractography 5 12. EPI-Based Pulse Sequences for Diffusion Tensor MRI 182
Marco Catani Stefan T. Skare and Roland Bammer
2. Neurobiology of White Matter Disorders 19 13. Non-EPI Pulse Sequences for Diffusion MRI 203
Christopher M. Filley James G. Pipe
3. Invasive Methods for Tracing White Matter Architecture 31 14. Phase Errors in Diffusion-Weighted Imaging 218
Hubertus Axer Roland Bammer, Samantha J. Holdsworth, Murat Aksoy,
and Stefan T. Skare
Section II The Basics of Diffusion MRI
15. Optimal Approaches to Diffusion MRI Acquisition 250
4. Physics of Diffusion 45 Derek K. Jones
Paul T. Callaghan
16. Least Squares Approaches to Diffusion
5. Magnetic Resonance Diffusion Imaging: Tensor Estimation 272
Introduction and Concepts 57 Cheng Guan Koay
Denis Le Bihan
17. Image Distortion and Its Correction in Diffusion MRI 285
6. Anisotropic Diffusion: From the Apparent Diffusion Jesper L.R. Andersson and Stefan Skare
Coefficient to the Apparent Diffusion Tensor 79
Peter J. Basser and Evren Özarslan 18. Artifacts in Diffusion MRI 303
Carlo Pierpaoli
7. What Makes Diffusion Anisotropic in the
Nervous System? 92 19. Quality Assurance for Diffusion MRI 319
Christian Beaulieu Nicholas G. Dowell and Paul S. Tofts
8. Biophysics of Diffusion in Cells 110 20. Statistical Issues in Diffusion Tensor MRI 331
Joseph J.H. Ackerman and Jeffrey J. Neil Sinisa Pajevic
9. Extracting Geometric Properties of White Matter with 21. Visualization of Diffusion MRI Data 354
q-Space Diffusion MRI (QSI) 125 Alexander Leemans
Yoram Cohen and Yaniv Assaf
Section IV Fiber Tracking
10. The Cumulant Expansion: An Overarching Mathematical
Framework For Understanding Diffusion NMR 152 22. Deterministic White Matter Tractography 383
Valerij G. Kiselev Andrew L. Alexander
xi
xii Contents
23. Probabilistic Fiber Tracking 396 37. Diffusion MRI in Psychiatric Disorders 608
Geoff J.M. Parker Tonya White and Kelvin O. Lim
24. Connectivity-Based Parcellation of Gray Matter 409 38. Diffusion Tensor Imaging in Aging and Age-Related
Timothy Behrens, Johannes C. Klein, Saad Jbabdi, Neurodegenerative Disorders 624
and Heidi Johansen-Berg Edith V. Sullivan and Adolf Pfefferbaum
27. Mathematics of Crossing Fibers 451 41. Diffusion Imaging in Muscle 672
Daniel C. Alexander and Kiran K. Seunarine Gustav J. Strijkers, Maarten R. Drost, and Klaas Nicolay
28. The Biophysics of Crossing Fibers 465 42. Insights into Diffusion Tensor Imaging from Animal
Jacques-Donald Tournier Models of White Matter Pathology 690
Matthew D. Budde and Sheng-Kwei Song
Section VI Diffusion MRI of Brain Disorders
Section VIII How It All Started—Personal
29. Strategies for Patient–Control Comparison of Perspectives from the Pioneers
Diffusion MR Data 485
Mara Cercignani 43. Reminiscences about the Development of Pulsed Field
Gradient Spin Echo NMR (PFGSE-NMR) 705
30. Diffusion Tensor MRI in Brain Development 500 E. O. Stejskal and J. E. Tanner
Petra Hüppi
44. Diffusion, Diffraction, and Microimaging 708
31. Diffusion in Acute Stroke 518 Paul T. Callaghan
Ona Wu, Lauren Nentwich, Aurauma Chutinet,
and Ahmad Bayrlee 45. Diffusion MRI: Conception, Birth, and Adolescence 711
Denis Le Bihan
32. Diffusion in Chronic Stroke and Small
Vessel Disease 529 46. DWI in Cerebral Ischemia: The Early Days 719
Michael O’Sullivan Michael E. Moseley
33. Diffusion Imaging in Brain Tumors 547 47. Invention and Development of Diffusion Tensor MRI
Aaron S. Field (DT-MRI or DTI) at the NIH 730
Peter J. Basser
34. Diffusion Tensor MRI in Multiple Sclerosis 564
Massimo Filippi and Maria A. Rocca Author Index 741
xiii
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