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An Introduction to Computational Diffusion MRI: the Diffusion Tensor and Beyond

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Book cover Visualization and Processing of Tensor Fields

Part of the book series: Mathematics and Visualization ((MATHVISUAL))

Abstract

This chapter gives an introduction to the principles of diffusion magnetic resonance imaging (MRI) with emphasis on the computational aspects. It introduces the philosophies underlying the technique and shows how to sensitize MRI measurements to the motion of particles within a sample material. The main body of the chapter is a technical review of diffusion MRI reconstruction algorithms, which determine features of the material microstructure from diffusion MRI measurements. The focus is on techniques developed for biomedical diffusion MRI, but most of the methods discussed are applicable beyond this domain. The review begins by showing how the standard reconstruction algorithms in biomedical diffusion MRI, diffusion-tensor MRI and diffusion spectrum imaging, arise from the principles of the measurement process. The discussion highlights the weaknesses of the standard approaches to motivate the development of a new generation of reconstruction algorithms and reviews the current state-of-the-art. The chapter concludes with a brief discussion of diffusion MRI applications, in particular fibre tracking, followed by a summary and a glimpse into the future of diffusion MRI acquisition and reconstruction.

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References

  1. Pierpaoli C, Jezzard P, Basser P J, Barnett A and Di Chiro G 1996 Diffusion tensor MR imaging of the human brain Radiology 201 637–48

    Google Scholar 

  2. Blinkov S and Glezer I 1968 The human brain in figures and tables New York, USA: Plenum Press

    Google Scholar 

  3. Highley J R, Esiri M M, McDonald B, Cortina-Borja M, Herron B M and Crow T J 1999 The size and fibre composition of the corpus callosum with respect to gender and schizophrenia: a post-mortem study Brain 122 99–110

    Article  Google Scholar 

  4. Stejskal E O and Tanner T E 1965 Spin diffusion measurements: spin echoes in the presence of a time-dependent field gradient The Journal of Chemical Physics 42 288–92

    Article  Google Scholar 

  5. Callaghan P T 1991 Principles of Magnetic Resonance Microscopy Oxford, UK: Oxford Science Publications

    Google Scholar 

  6. Merboldt K D, Hanicke W and Frahm J 1985 Self-diffusion NMR imaging using stimulated echoes Journal of Magnetic Resonance 64 479–486

    Google Scholar 

  7. LeBihan D and Breton E 1985 Imagerie de diffusion in-vivo par resonance magnetique nucleaire C. R. Acad. Sci. (Paris) 301 1109–1112

    Google Scholar 

  8. Lori N F, Conturo T E and Le Bihan D 2003 Definition of displacement probability and diffusion time in q-space magnetic resonance measurements that use finite-duration diffusion-encoding gradients Journal of Magnetic Resonance 165 185–195

    Article  Google Scholar 

  9. Mitra P P and Halperin B I 1995 Effects of finite gradient-pulse widths in pulsed-field-gradient diffusion measurements Journal of Magnetic Resonance 113 94–101

    Google Scholar 

  10. Liu C, Bammer R, Acar B and Moseley M E 2004 Characterizing Non-Gaussian Diffusion by Using Generalized Diffusion Tensors Magnetic Resonance in Medicine 51 924–937

    Article  Google Scholar 

  11. Brihuega-Moreno O, Heese F P, Tejos C and Hall L D 2004 Effects of, and corrections for, cross-term interactions in q-space MRI Magnetic Resonance in Medicine 51 1048–1054

    Article  Google Scholar 

  12. Sijbers J, den Dekker A J, Van Audekerke J, Verhoye M, Van Dyck D 1998 Estimation of the noise in magnitude MR images Magnetic Resonance Imaging 16 87–90.

    Article  Google Scholar 

  13. Inglis B A, Bossart E L, Buckley D L, Wirth E D, Mareci T H 2001 Visualization of neural tissue water compartments using biexponential diffusion tensor MRI Magnetic Resonance in Medicine 45 580–587.

    Article  Google Scholar 

  14. Basser P J, Matiello J and Le Bihan D 1994 MR diffusion tensor spectroscopy and imaging Biophysical Journal 66 259–67

    Article  Google Scholar 

  15. Wang Z, Vemuri B C, Chen Y and Mareci T 2003 A constrained variational principle for direct estimation and smoothing of the diffusion tensor field from DWI Proc. of 18th International Conference on Information Processing in Medical Imaging (Ambleside) (Springer: LNCS 2732) 660–671

    Google Scholar 

  16. Basser P J and Pierpaoli C 1996 Microstructural and physiological features of tissues elucidated by quantitative diffusion tensor MRI Journal of Magnetic Resonance Series B 111 209–19

    Article  Google Scholar 

  17. Pajevic S and Pierpaoli C 1999 Color schemes to represent the orientation of anisotropic tissues from diffusion tensor data: application to white matter fibre tract mapping in the human brain Magnetic Resonance in Medicine 42 526–540

    Article  Google Scholar 

  18. Jones D K, Horsfield M A and Simmons A 1999 Optimal strategies for measuring diffusion in anisotropic systems by magnetic resonance imaging Magnetic Resonance in Medicine 42 515–525

    Article  Google Scholar 

  19. Jones D K 2004 The effect of gradient sampling schemes on measures derived from diffusion tensor MRI: a Monte Carlo study Magnetic Resonance in Medicine 51 807–815

    Article  Google Scholar 

  20. Parker G J M and Alexander D C 2003 Probabilistic Monte Carlo Based Mapping of Cerebral Connections Utilising Whole-Brain Crossing Fibre Information Proc. of 18th International Conference on Information Processing in Medical Imaging (Ambleside) (Springer: LNCS 2732) 684–695

    Google Scholar 

  21. Frank L R 2002 Characterization of anisotropy in high angular resolution diffusion-weighted MRI Magnetic Resonance in Medicine 47 1083–99

    Article  Google Scholar 

  22. Alexander D C, Barker G J and Arridge S R 2002 Detection and modeling of non-Gaussian apparent diffusion coefficient profiles in human brain data Magnetic Resonance in Medicine 48 331–40

    Article  Google Scholar 

  23. Armitage P and Berry G 1971 Statistical methods in medical research Oxford, UK: Blackwell Scientific Publications

    Google Scholar 

  24. Ozarslan E and Mareci T H 2003 Generalized diffusion tensor imaging and analytical relationships between diffusion tensor imaging and high angular resolution diffusion imaging Magnetic Resonance in Medicine 50 955–965

    Article  Google Scholar 

  25. Press W H, Teukolsky S A, Vettering W T and Flannery B P 1988 Numerical Recipes in C New York, USA: Press Syndicate of the University of Cambridge

    MATH  Google Scholar 

  26. Parker G J M, Luzzi S, Alexander D C, Wheeler-Kingshott C A M, Ciccarelli O and Lambon-Ralph M A 2004 Non-invasive structural mapping of two auditory-language pathways in the human brain Neuroimage In press

    Google Scholar 

  27. Blyth R, Cook P A and Alexander D C 2003 Tractography with multiple fibre directions Proc. 11th Annual Meeting of the ISMRM (Toronto) (Berkeley, USA: ISMRM) 240

    Google Scholar 

  28. Tuch D S, Reese T G, Wiegell M R, Makris N, Belliveau J W and Wedeen V J 2002 High angular resolution diffusion imaging reveals intravoxel white matter fiber heterogeneity Magnetic Resonance in Medicine 48 577–582

    Article  Google Scholar 

  29. Chen Y, Guo W, Zeng Q, He G, Vemuri B and Liu Y 2004 Recovery of intravoxel structure from HARD DWI Proc. IEEE International Symposium on Biomedical Imaging (Arlington) (IEEE)

    Google Scholar 

  30. Behrens T E J, Woolrich M W, Jenkinson M, Johansen-Berg H, Nunes R G, Clare S, Matthews P M, Brady J M and Smith S M 2003 Characterization and propagation of uncertainty in diffusion-weighted MR imaging Magnetic Resonance in Medicine 50 1077–1088

    Article  Google Scholar 

  31. Assaf Y, Freidlin R Z, Rohde G K and Basser P J 2004 New modelling and experimental framework to characterize hindered and restricted water diffusion in brain white matter Magnetic Resonance in Medicine 52 965–978

    Article  Google Scholar 

  32. Neuman C H 1974 Spin echo of spins diffusing in a bounded medium Journal of Chemical Physics 60 4508–4511

    Article  Google Scholar 

  33. Wedeen V J, Reese T G, Tuch D S, Dou J-G, Weiskoff R M and Chessler D 1999 Mapping fiber orientation spectra in cerebral white matter with Fourier-transform diffusion MRI Proc. 7th Annual Meeting of the ISMRM (Philadelphia) (Berkeley, USA: ISMRM) 321

    Google Scholar 

  34. Tuch D S 2002 Diffusion MRI of Complex Tissue Structure Doctor of Philosophy in Biomedical Imaging at the Massachusetts Institute of Technology

    Google Scholar 

  35. Tuch D S, Reese T G, Wiegell M R and Wedeen V J 2003 Diffusion MRI of complex neural architecture Neuron 40 885–895

    Article  Google Scholar 

  36. S Helgason 1999 The Radon Transform Birkhäuser

    Google Scholar 

  37. Lin C P, Tseng W Y I, Kuo L, Wedeen V J and Chen J H 2003 Mapping orientation distribution function with spherical encoding Proc. 11th Annual Meeting of the ISMRM (Toronto) (Berkeley, USA: ISMRM) 2120

    Google Scholar 

  38. Ozarslan E, Vemuri B C and Mareci T H 2004 Fiber orientation mapping using generalized diffusion tensor imaging Proc. IEEE International Symposium on Biomedical Imaging (Arlington) (IEEE)

    Google Scholar 

  39. Anderson A and Ding Z 2002 Sub-voxel measurement of fiber orientation using high angular resolution diffusion tensor imaging Proc. 10th Annual Meeting of the ISMRM (Honolulu) (Berkeley, USA: ISMRM) 440

    Google Scholar 

  40. Tournier J-D, Calamante F, Gadian D G and Connelly A 2004 Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution NeuroImage 23 1176–1185

    Article  Google Scholar 

  41. Jansons K M and Alexander D C 2003 Persistent Angular Structure: new insights from diffusion MRI data Inverse Problems 19 1031–1046

    Article  MathSciNet  MATH  Google Scholar 

  42. Alexander D C 2004 A comparison of q-ball and PASMRI on sparse diffusion MRI data Proc. 12th Annual Meeting of the ISMRM (Kyoto) (Berkeley, USA: ISMRM) 90

    Google Scholar 

  43. Dong Q, Welsh R C, Chenevert T L, Carlos R C, Maly-Sundgren P, Gomez-Hasan D M and Mukherji S K 2004 Clinical applications of diffusion tensor imaging Journal of Magnetic Resonance Imaging 19 6–18

    Article  Google Scholar 

  44. Dou J, Reese T G, Tseng W-Y I and Wedeen V J 2002 Cardiac diffusion MRI without motion effects Magnetic Resonance in Medicine 48 105–114

    Article  Google Scholar 

  45. Hsu E W and Setton L A 1999 Diffusion tensor microscopy of the intervertebral disc annulus fibrosus Magnetic Resonance in Medicine 41 992–999

    Article  Google Scholar 

  46. Li T-Q 1997 Porous structure of cellulose fibers studied by Q-Space NMR Imaging Langmuir 13 3570–3574

    Article  Google Scholar 

  47. Mansfield P and Issa B 1994 Studies of fluid transport in porous rocks by echoplanar MRI Magnetic Resonance Imaging 12 275–278

    Article  Google Scholar 

  48. Mori S and van Zijl P C M 2002 Fiber tracking: principles and strategies — a technical review NMR in Biomedicine 15 468–480

    Article  Google Scholar 

  49. Lori N F, Akbudak E, Shimony J S, Cull T S, Snyder A Z, Guillory R K and Conturo T E 2002 Diffusion tensor fiber tracking of human brain connectivity: acquisition methods, reliability analysis and biological results NMR in Biomedicine 15 494–515

    Article  Google Scholar 

  50. Cook P A, Alexander D C and Parker G J M 2004 Modelling noise-induced fibre-orientation error in diffusion-tensor MRI Proc. IEEE International Symposium on Biomedical Imaging (Arlington) (IEEE)

    Google Scholar 

  51. Parker G J M and Alexander D C 2005 Probabilistic anatomic connectivity derived from the microscopic persistent angular structure of cerebral tissue. Philosophical Transactions of the Royal Society In press

    Google Scholar 

  52. Clark C A, Barrick T R, Murphy M M, Bell B A 2003 White matter fiber tracking in patients with space-occupying lesions of the brain: a new technique for neurosurgical planning? NeuroImage 20 1601–1608

    Article  Google Scholar 

  53. Mori S, Frederiksen K, van Zijl P C M, Steiltjes B, Kraut M A, Solaiyappan M and Pomper M G 2002 Brain white matter anatomy of tumor patients evaluated with diffusion tensor imaging Annals of Neurology 51 377–380

    Article  Google Scholar 

  54. Behrens T E J, Johansen-Berg H, Woolrich M W, Smith S M, Wheeler-Kingshott C A M, Boulby P A, Barker G J, Sillery E L, Sheehan K, Ciccarelli O, Thompson A J, Brady J M and Matthews P M 2003 Non-invasive mapping of connections between human thalamus and cortex using diffusion imaging Nature Neuroscience 7 750–757

    Article  Google Scholar 

  55. Ciccarelli O, Toosey A T, Parker G J M, Wheeler-Kingshott C A M, Barker G J, Miller D H and Thompson A J 2003 Diffusion tractography based group mapping of major white-matter pathways in the human brain NeuroImage 19 1545–1555

    Article  Google Scholar 

  56. Barrick T R, Lawes I N and Clark C A 2004 Automatic segmentation of white matter pathways by application of a region growing algorithm Proc. 12th Annual Meeting of the ISMRM (Kyoto) (Berkeley, USA: ISMRM) 619

    Google Scholar 

  57. Behrens T E J, Johansen-Berg H, Drobnjak I, Brady J M, Matthews P M, Smith S M and Higham D J 2004 Delineation of functional subunits in the human cortex from diffusion based connectivity matrices Proc. 12th Annual Meeting of the ISMRM (Kyoto) (Berkeley, USA: ISMRM) 621

    Google Scholar 

  58. Mori S, Itoh R, Zhang J Y, Kaufmann W E, van Zijl P C M, Solaiyappan M and Yarowsky P 2001 Diffusion tensor imaging of the developing mouse brain Magnetic Resonance in Medicine 46 18–23

    Article  Google Scholar 

  59. Ulug A M 2002 Monitoring brain development with quantitative diffusion tensor imaging Developmental Science 5 286–292

    Article  Google Scholar 

  60. Jones D K 2003 Determining and visualizing uncertainty in estimates of fiber orientation from diffusion tensor MRI Magnetic Resonance in Medicine 49 7–12

    Article  Google Scholar 

  61. Alexander D C 2005 Multiple-fibre reconstruction algorithms in diffusion MRI Annals of the New York Academy of Sciences In Press

    Google Scholar 

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© 2006 Springer-Verlag Berlin Heidelberg

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Alexander, D.C. (2006). An Introduction to Computational Diffusion MRI: the Diffusion Tensor and Beyond. In: Weickert, J., Hagen, H. (eds) Visualization and Processing of Tensor Fields. Mathematics and Visualization. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-31272-2_5

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