Abstract
Diffusion magnetic resonance imaging (dMRI) can be used to probe the connectivity and microstructure of human brain tissue non-invasively in vivo. The diffusion-weighted MR signal has sensitivity to micrometer-scale tissue properties averaged over the imaging voxel size, for example, intra-cellular and extra-cellular volumes and the 3D orientations of axonal bundles. It derives its contrast from sensitivity to the bulk displacement of water through what is known as thermal motion, Brownian motion, or passive (self-)diffusion. In the brain, cell membranes, organelles, and myelin sheaths create barriers and form biological compartments that constrain the displacement of water molecules, modifying the statistical behavior of bulk diffusion over time. This review therefore focuses on the use of dMRI for estimates of the local orientations and estimates of microstructure of fiber tracts, and on an understanding of dMRI signal mechanisms and appropriate signal processing and modeling for this purpose. It first discusses basic diffusion MRI acquisition principles and diffusion contrast and the constraints the acquisition places on the modeling of diffusion. It then sets out the diffusion tensor model, the most used model in dMRI that underlies diffusion tensor imaging, in a way which prepares a discussion of its limitations. The next sections set out advances in dMRI beyond DTI as focusing on tractography and connectomics, with a need to accurately model spatially complex fiber configurations and on diffusion microstructure, with a need to accurately model restricted diffusion and compartmentalization. Throughout, the emphasis is on a thorough understanding of basic principles and assumptions underlying techniques, as well as their possibilities and limitations for inference of brain connectivity, with a minimum of technical detail and mathematics. This review ends with an outlook on future developments emanating from current trends.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
Notes
- 1.
Diffusion gradients have a well-defined direction, with polarity, whereas the symmetry of the diffusion weighting mechanism makes dMRI only sensitive to the orientation, without polarity, of anisotropic structures. This is why this review refers to the direction of diffusion gradients and orientation of anisotropic structures such as white matter fibers.
- 2.
This review uses the conventional terminology of referring to the virtual entities created by tractography (a processing and modeling of dMRI data) as “tracks,” and to the actual neuroanatomical bundles of axons or fibers as “tracts.”
References
Aboitiz, F., A. B. Scheibel, R. S. Fisher, and E. Zaidel. 1992. 'Fiber composition of the human corpus callosum', Brain Res, 598: 143-53.
Alexander, D. C., G. J. Barker, and S. R. Arridge. 2002. 'Detection and modeling of non-Gaussian apparent diffusion coefficient profiles in human brain data', Magn Reson Med, 48: 331-40.
Alexander, D. C., T. B. Dyrby, M. Nilsson, and H. Zhang. 2017. ‘Imaging brain microstructure with diffusion MRI: practicality and applications’, Nmr in Biomedicine.
Alexander, D. C., P. L. Hubbard, M. G. Hall, E. A. Moore, M. Ptito, G. J. Parker, and T. B. Dyrby. 2010. 'Orientationally invariant indices of axon diameter and density from diffusion MRI', Neuroimage, 52: 1374-89.
Assaf, Y., D. C. Alexander, D. K. Jones, A. Bizzi, T. E. Behrens, C. A. Clark, Y. Cohen, T. B. Dyrby, P. S. Huppi, T. R. Knoesche, D. Lebihan, G. J. Parker, C. Poupon, Connect consortium, D. Anaby, A. Anwander, L. Bar, D. Barazany, T. Blumenfeld-Katzir, S. De-Santis, D. Duclap, M. Figini, E. Fischi, P. Guevara, P. Hubbard, S. Hofstetter, S. Jbabdi, N. Kunz, F. Lazeyras, A. Lebois, M. G. Liptrot, H. Lundell, J. F. Mangin, D. M. Dominguez, D. Morozov, J. Schreiber, K. Seunarine, S. Nava, C. Poupon, T. Riffert, E. Sasson, B. Schmitt, N. Shemesh, S. N. Sotiropoulos, I. Tavor, H. G. Zhang, and F. L. Zhou. 2013. 'The CONNECT project: Combining macro- and micro-structure', Neuroimage, 80: 273-82.
Assaf, Y., and P. J. Basser. 2005. 'Composite hindered and restricted model of diffusion (CHARMED) MR imaging of the human brain', Neuroimage, 27: 48-58.
Assaf, Y., T. Blumenfeld-Katzir, Y. Yovel, and P. J. Basser. 2008. 'AxCaliber: a method for measuring axon diameter distribution from diffusion MRI', Magn Reson Med, 59: 1347-54.
Assaf, Y., R. Z. Freidlin, G. K. Rohde, and P. J. Basser. 2004. 'New modeling and experimental framework to characterize hindered and restricted water diffusion in brain white matter', Magn Reson Med, 52: 965-78.
Assaf, Y., and O. Pasternak. 2008. 'Diffusion tensor imaging (DTI)-based white matter map** in brain research: a review', J Mol Neurosci, 34: 51-61.
Basser, P. J., J. Mattiello, and D. LeBihan. 1994. 'MR diffusion tensor spectroscopy and imaging', Biophys J, 66: 259-67.
Basser, P. J., S. Pajevic, C. Pierpaoli, J. Duda, and A. Aldroubi. 2000. 'In vivo fiber tractography using DT-MRI data', Magn Reson Med, 44: 625-32.
Basser, P. J., and C. Pierpaoli. 1996. 'Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI', J Magn Reson B, 111: 209-19.
Bassett, D. S., J. A. Brown, V. Deshpande, J. M. Carlson, and S. T. Grafton. 2011. 'Conserved and variable architecture of human white matter connectivity', Neuroimage, 54: 1262-79.
Bastiani, M., M. Cottaar, K. Dikranian, A. Ghosh, H. Zhang, D. C. Alexander, T. E. Behrens, S. Jbabdi, and S. N. Sotiropoulos. 2017. 'Improved tractography using asymmetric fibre orientation distributions', Neuroimage, 158: 205-18.
Bastiani, M., N. J. Shah, R. Goebel, and A. Roebroeck. 2012. 'Human cortical connectome reconstruction from diffusion weighted MRI: the effect of tractography algorithm', Neuroimage, 62: 1732-49.
Beaulieu, C. 2002. 'The basis of anisotropic water diffusion in the nervous system – a technical review', Nmr in Biomedicine, 15: 435-55.
Behrens, T. E., H. J. Berg, S. Jbabdi, M. F. Rushworth, and M. W. Woolrich. 2007. 'Probabilistic diffusion tractography with multiple fibre orientations: What can we gain?', Neuroimage, 34: 144-55.
Behrens, T. E., H. Johansen-Berg, M. W. Woolrich, S. M. Smith, C. A. Wheeler-Kingshott, P. A. Boulby, G. J. Barker, E. L. Sillery, K. Sheehan, O. Ciccarelli, A. J. Thompson, J. M. Brady, and P. M. Matthews. 2003a. 'Non-invasive map** of connections between human thalamus and cortex using diffusion imaging', Nat Neurosci, 6: 750-7.
Behrens, T. E., M. W. Woolrich, M. Jenkinson, H. Johansen-Berg, R. G. Nunes, S. Clare, P. M. Matthews, J. M. Brady, and S. M. Smith. 2003b. 'Characterization and propagation of uncertainty in diffusion-weighted MR imaging', Magn Reson Med, 50: 1077-88.
Benitez, A., E. Fieremans, J. H. Jensen, M. F. Falangola, A. Tabesh, S. H. Ferris, and J. A. Helpern. 2014. 'White matter tract integrity metrics reflect the vulnerability of late-myelinating tracts in Alzheimer’s disease', Neuroimage Clin, 4: 64-71.
Bergers, E., J. C. Bot, C. J. De Groot, C. H. Polman, G. J. Lycklama, A Nijeholt, J. A. Castelijns, P. van der Valk, and F. Barkhof. 2002. 'Axonal damage in the spinal cord of MS patients occurs largely independent of T2 MRI lesions', Neurology, 59: 1766-71.
Budde, M. D., and J. Annese. 2013. 'Quantification of anisotropy and fiber orientation in human brain histological sections', Front Integr Neurosci, 7: 3.
Budde, M. D., and J. A. Frank. 2012. 'Examining brain microstructure using structure tensor analysis of histological sections', Neuroimage, 63: 1-10.
Buxton, R. B. 1993. 'The diffusion sensitivity of fast steady-state free precession imaging', Magn Reson Med, 29: 235-43.
Campbell, J. S., P. MomayyezSiahkal, P. Savadjiev, I. R. Leppert, K. Siddiqi, and G. B. Pike. 2014. 'Beyond crossing fibers: bootstrap probabilistic tractography using complex subvoxel fiber geometries', Front Neurol, 5: 216.
Catani, M., F. Dell'acqua, F. Vergani, F. Malik, H. Hodge, P. Roy, R. Valabregue, and M. Thiebaut de Schotten. 2012. 'Short frontal lobe connections of the human brain', Cortex, 48: 273-91.
Catani, M., R. J. Howard, S. Pajevic, and D. K. Jones. 2002. 'Virtual in vivo interactive dissection of white matter fasciculi in the human brain', Neuroimage, 17: 77-94.
Catani, M., and M. Thiebaut de Schotten. 2008. 'A diffusion tensor imaging tractography atlas for virtual in vivo dissections', Cortex, 44: 1105-32.
Cheng, H., Y. Wang, J. Sheng, O. Sporns, W. G. Kronenberger, V. P. Mathews, T. A. Hummer, and A. J. Saykin. 2011. 'Optimization of seed density in DTI tractography for structural networks', J Neurosci Methods.
Conturo, T. E., N. F. Lori, T. S. Cull, E. Akbudak, A. Z. Snyder, J. S. Shimony, R. C. McKinstry, H. Burton, and M. E. Raichle. 1999. 'Tracking neuronal fiber pathways in the living human brain', Proc Natl Acad Sci U S A, 96: 10422-7.
Cote, M. A., G. Girard, A. Bore, E. Garyfallidis, J. C. Houde, and M. Descoteaux. 2013. 'Tractometer: towards validation of tractography pipelines', Med Image Anal, 17: 844-57.
De Santis, S., M. Drakesmith, S. Bells, Y. Assaf, and D. K. Jones. 2014. 'Why diffusion tensor MRI does well only some of the time: variance and covariance of white matter tissue microstructure attributes in the living human brain', Neuroimage, 89: 35-44.
De Santis, S., D. K. Jones, and A. Roebroeck. 2016. 'Including diffusion time dependence in the extra-axonal space improves in vivo estimates of axonal diameter and density in human white matter', Neuroimage, 130: 91-103.
Dell’Acqua, F., and J. D. Tournier. 2018. 'Modelling white matter with spherical deconvolution: How and why?', Nmr in Biomedicine: e3945.
Dong, Q., R. C. Welsh, T. L. Chenevert, R. C. Carlos, P. Maly-Sundgren, D. M. Gomez-Hassan, and S. K. Mukherji. 2004. 'Clinical applications of diffusion tensor imaging', J Magn Reson Imaging, 19: 6-18.
Fieremans, E., A. Benitez, J. H. Jensen, M. F. Falangola, A. Tabesh, R. L. Deardorff, M. V. Spampinato, J. S. Babb, D. S. Novikov, S. H. Ferris, and J. A. Helpern. 2013. 'Novel white matter tract integrity metrics sensitive to Alzheimer disease progression', AJNR Am J Neuroradiol, 34: 2105-12.
Fieremans, E., Y. De Deene, S. Delputte, M. S. Ozdemir, Y. D'Asseler, J. Vlassenbroeck, K. Deblaere, E. Achten, and I. Lemahieu. 2008. 'Simulation and experimental verification of the diffusion in an anisotropic fiber phantom', J Magn Reson, 190: 189-99.
Frank, L. R. 2001. 'Anisotropy in high angular resolution diffusion-weighted MRI', Magn Reson Med, 45: 935-9.
Frank, L. R. 2002. 'Characterization of anisotropy in high angular resolution diffusion-weighted MRI', Magn Reson Med, 47: 1083-99.
Goulas, A., M. Bastiani, G. Bezgin, H. B. Uylings, A. Roebroeck, and P. Stiers. 2014. 'Comparative analysis of the macroscale structural connectivity in the macaque and human brain', PLoS Comput Biol, 10: e1003529.
Hagmann, P., L. Cammoun, X. Gigandet, R. Meuli, C. J. Honey, V. J. Wedeen, and O. Sporns. 2008. 'Map** the structural core of human cerebral cortex', PLoS Biol, 6: e159.
Hagmann, P., M. Kurant, X. Gigandet, P. Thiran, V. J. Wedeen, R. Meuli, and J. P. Thiran. 2007. 'Map** human whole-brain structural networks with diffusion MRI', PLoS One, 2: e597.
Harms, R. L., F. J. Fritz, A. Tobisch, R. Goebel, and A. Roebroeck. 2017. 'Robust and fast nonlinear optimization of diffusion MRI microstructure models', Neuroimage, 155: 82-96.
Harms, R. L., and A. Roebroeck. 2018. 'Robust and Fast Markov Chain Monte Carlo Sampling of Diffusion MRI Microstructure Models', Front Neuroinform, 12: 97.
Heidemann, R. M., D. A. Porter, A. Anwander, T. Feiweier, K. Heberlein, T. R. Knosche, and R. Turner. 2010. 'Diffusion imaging in humans at 7T using readout-segmented EPI and GRAPPA', Magn Reson Med, 64: 9-14.
Horsfield, M. A., and D. K. Jones. 2002. 'Applications of diffusion-weighted and diffusion tensor MRI to white matter diseases – a review', Nmr in Biomedicine, 15: 570-7.
Iturria-Medina, Y., E. J. Canales-Rodriguez, L. Melie-Garcia, P. A. Valdes-Hernandez, E. Martinez-Montes, Y. Aleman-Gomez, and J. M. Sanchez-Bornot. 2007. 'Characterizing brain anatomical connections using diffusion weighted MRI and graph theory', Neuroimage, 36: 645-60.
Jansons, K. M., and D. C. Alexander. 2003. 'Persistent Angular Structure: new insights from diffusion MRI data. Dummy version', Inf Process Med Imaging, 18: 672-83.
Jbabdi, S., and H. Johansen-Berg. 2011. 'Tractography: where do we go from here?', Brain Connect, 1: 169-83.
Jbabdi, S., J. F. Lehman, S. N. Haber, and T. E. Behrens. 2013. 'Human and monkey ventral prefrontal fibers use the same organizational principles to reach their targets: tracing versus tractography', J Neurosci, 33: 3190-201.
Jbabdi, S., M. W. Woolrich, J. L. Andersson, and T. E. Behrens. 2007. 'A Bayesian framework for global tractography', Neuroimage, 37: 116-29.
Jelescu, I. O., J. Veraart, V. Adisetiyo, S. S. Milla, D. S. Novikov, and E. Fieremans. 2015. 'One diffusion acquisition and different white matter models: How does microstructure change in human early development based on WMTI and NODDI?', Neuroimage, 107: 242-56.
Jensen, J. H., and J. A. Helpern. 2010. 'MRI quantification of non-Gaussian water diffusion by kurtosis analysis', Nmr in Biomedicine, 23: 698-710.
Jensen, J. H., J. A. Helpern, A. Ramani, H. Lu, and K. Kaczynski. 2005. 'Diffusional kurtosis imaging: the quantification of non-gaussian water diffusion by means of magnetic resonance imaging', Magn Reson Med, 53: 1432-40.
Jeurissen, B., M. Descoteaux, S. Mori, and A. Leemans. 2017. ‘Diffusion MRI fiber tractography of the brain’, Nmr in Biomedicine.
Jeurissen, B., A. Leemans, J. D. Tournier, D. K. Jones, and J. Sijbers. 2013. 'Investigating the prevalence of complex fiber configurations in white matter tissue with diffusion magnetic resonance imaging', Hum Brain Mapp, 34: 2747-66.
Jeurissen, B., J. D. Tournier, T. Dhollander, A. Connelly, and J. Sijbers. 2014. 'Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data', Neuroimage, 103: 411-26.
Jones, D. K. 2003. 'Determining and visualizing uncertainty in estimates of fiber orientation from diffusion tensor MRI', Magn Reson Med, 49: 7-12.
Jones, D. K., D. C. Alexander, R. Bowtell, M. Cercignani, F. Dell'Acqua, D. J. McHugh, K. L. Miller, M. Palombo, G. J. M. Parker, U. S. Rudrapatna, and C. M. W. Tax. 2018. 'Microstructural imaging of the human brain with a 'super-scanner': 10 key advantages of ultra-strong gradients for diffusion MRI', Neuroimage, 182: 8-38.
Jones, D. K., T. R. Knosche, and R. Turner. 2013. 'White matter integrity, fiber count, and other fallacies: the do's and don'ts of diffusion MRI', Neuroimage, 73: 239-54.
Jones, Derek K. 2010. 'Challenges and limitations of quantifying brain connectivity in vivo with diffusion MRI', Imaging in Medicine, 2: 341-55.
Kamagata, K., T. Hatano, A. Okuzumi, Y. Motoi, O. Abe, K. Shimoji, K. Kamiya, M. Suzuki, M. Hori, K. K. Kumamaru, N. Hattori, and S. Aoki. 2016. 'Neurite orientation dispersion and density imaging in the substantia nigra in idiopathic Parkinson disease', Eur Radiol, 26: 2567-77.
Khayal, I. S., S. R. Vandenberg, K. J. Smith, C. P. Cloyd, S. M. Chang, S. Cha, S. J. Nelson, and T. R. McKnight. 2011. 'MRI apparent diffusion coefficient reflects histopathologic subtype, axonal disruption, and tumor fraction in diffuse-type grade II gliomas', Neuro Oncol, 13: 1192-201.
Kreher, B. W., I. Mader, and V. G. Kiselev. 2008. 'Gibbs tracking: a novel approach for the reconstruction of neuronal pathways', Magn Reson Med, 60: 953-63.
Kunz, N., H. Zhang, L. Vasung, K. R. O'Brien, Y. Assaf, F. Lazeyras, D. C. Alexander, and P. S. Huppi. 2014. 'Assessing white matter microstructure of the newborn with multi-shell diffusion MRI and biophysical compartment models', Neuroimage, 96: 288-99.
LaMantia, A. S., and P. Rakic. 1990. 'Cytological and quantitative characteristics of four cerebral commissures in the rhesus monkey', J Comp Neurol, 291: 520-37.
Lebel, C., S. Caverhill-Godkewitsch, and C. Beaulieu. 2010. 'Age-related regional variations of the corpus callosum identified by diffusion tensor tractography', Neuroimage, 52: 20-31.
Li, L., J. K. Rilling, T. M. Preuss, M. F. Glasser, and X. Hu. 2011. ‘The effects of connection reconstruction method on the interregional connectivity of brain networks via diffusion tractography’, Hum Brain Mapp.
Lundell, H., D. C. Alexander, and T. B. Dyrby. 2014. 'High angular resolution diffusion imaging with stimulated echoes: compensation and correction in experiment design and analysis', Nmr in Biomedicine, 27: 918-25.
McKinstry, R. C., A. Mathur, J. H. Miller, A. Ozcan, A. Z. Snyder, G. L. Schefft, C. R. Almli, S. I. Shiran, T. E. Conturo, and J. J. Neil. 2002. 'Radial organization of develo** preterm human cerebral cortex revealed by non-invasive water diffusion anisotropy MRI', Cereb Cortex, 12: 1237-43.
McNab, J. A., S. Jbabdi, S. C. Deoni, G. Douaud, T. E. Behrens, and K. L. Miller. 2009. 'High resolution diffusion-weighted imaging in fixed human brain using diffusion-weighted steady state free precession', Neuroimage, 46: 775-85.
Mcnab, J. A., and K. L. Miller. 2010. 'Steady-state diffusion-weighted imaging: theory, acquisition and analysis', Nmr in Biomedicine, 23: 781-93.
Merboldt, K. D., H. Bruhn, J. Frahm, M. L. Gyngell, W. Hanicke, and M. Deimling. 1989. 'MRI of "diffusion" in the human brain: new results using a modified CE-FAST sequence', Magn Reson Med, 9: 423-9.
Merboldt, K. D., W. Hanicke, and J. Frahm. 1991. 'Diffusion imaging using stimulated echoes', Magn Reson Med, 19: 233-9.
Modo, M., T. K. Hitchens, J. R. Liu, and R. M. Richardson. 2016. 'Detection of Aberrant Hippocampal Mossy Fiber Connections: Ex Vivo Mesoscale Diffusion MRI and Microtractography With Histological Validation in a Patient With Uncontrolled Temporal Lobe Epilepsy', Hum Brain Mapp, 37: 780-95.
Mollink, J., K. M. van Baarsen, P. J. Dederen, S. Foxley, K. L. Miller, S. Jbabdi, C. H. Slump, J. A. Grotenhuis, M. Kleinnijenhuis, and A. M. van Cappellen van Walsum. 2015. 'Dentatorubrothalamic tract localization with postmortem MR diffusion tractography compared to histological 3D reconstruction', Brain Struct Funct.
Mori, S., B. J. Crain, V. P. Chacko, and P. C. van Zijl. 1999. 'Three-dimensional tracking of axonal projections in the brain by magnetic resonance imaging', Ann Neurol, 45: 265-9.
Mori, S., and P. C. van Zijl. 2002. 'Fiber tracking: principles and strategies – a technical review', Nmr in Biomedicine, 15: 468-80.
Neher, P. F., M. Descoteaux, J. C. Houde, B. Stieltjes, and K. H. Maier-Hein. 2015. 'Strengths and weaknesses of state of the art fiber tractography pipelines--A comprehensive in-vivo and phantom evaluation study using Tractometer', Med Image Anal, 26: 287-305.
Neil, J., J. Miller, P. Mukherjee, and P. S. Huppi. 2002. 'Diffusion tensor imaging of normal and injured develo** human brain – a technical review', Nmr in Biomedicine, 15: 543-52.
Nilsson, Markus, Danielle van Westen, Freddy Ståhlberg, Pia C. Sundgren, and Jimmy Lätt. 2013. 'The role of tissue microstructure and water exchange in biophysical modelling of diffusion in white matter', Magnetic Resonance Materials in Physics, Biology and Medicine, 26: 345-70.
Novikov, D. S., E. Fieremans, S. N. Jespersen, and V. G. Kiselev. 2018a. 'Quantifying brain microstructure with diffusion MRI: Theory and parameter estimation', Nmr in Biomedicine: e3998.
Novikov, D. S., J. Veraart, I. O. Jelescu, and E. Fieremans. 2018b. 'Rotationally-invariant map** of scalar and orientational metrics of neuronal microstructure with diffusion MRI', Neuroimage, 174: 518-38.
Ozarslan, E., T. M. Shepherd, B. C. Vemuri, S. J. Blackband, and T. H. Mareci. 2006. 'Resolution of complex tissue microarchitecture using the diffusion orientation transform (DOT)', Neuroimage, 31: 1086-103.
Panagiotaki, E., T. Schneider, B. Siow, M. G. Hall, M. F. Lythgoe, and D. C. Alexander. 2012. 'Compartment models of the diffusion MR signal in brain white matter: a taxonomy and comparison', Neuroimage, 59: 2241-54.
Parker, G. J., and D. C. Alexander. 2005. 'Probabilistic anatomical connectivity derived from the microscopic persistent angular structure of cerebral tissue', Philos Trans R Soc Lond B Biol Sci, 360: 893-902.
Parker, G. J., H. A. Haroon, and C. A. Wheeler-Kingshott. 2003. 'A framework for a streamline-based probabilistic index of connectivity (PICo) using a structural interpretation of MRI diffusion measurements', J Magn Reson Imaging, 18: 242-54.
Pestilli, F., J. D. Yeatman, A. Rokem, K. N. Kay, and B. A. Wandell. 2014. 'Evaluation and statistical inference for human connectomes', Nat Methods, 11: 1058-63.
Pfefferbaum, A., E. V. Sullivan, M. Hedehus, K. O. Lim, E. Adalsteinsson, and M. Moseley. 2000. 'Age-related decline in brain white matter anisotropy measured with spatially corrected echo-planar diffusion tensor imaging', Magn Reson Med, 44: 259-68.
Plantinga, B. R., A. Roebroeck, V. G. Kemper, K. Uludag, M. Melse, J. Mai, M. L. Kuijf, A. Herrler, A. Jahanshahi, B. M. Ter Haar Romeny, and Y. Temel. 2016. 'Ultra-High Field MRI Post Mortem Structural Connectivity of the Human Subthalamic Nucleus, Substantia Nigra, and Globus Pallidus', Frontiers in Neuroanatomy, 10: 66.
Pullens, P., A. Roebroeck, and R. Goebel. 2010. 'Ground Truth Hardware Phantoms for Validation of Diffusion-Weighted MRI Applications', Journal of Magnetic Resonance Imaging, 32: 482-88.
Reeves, C., M. Tachrount, D. Thomas, Z. Michalak, J. Liu, M. Ellis, B. Diehl, A. Miserocchi, A. W. McEvoy, S. Eriksson, T. Yousry, and M. Thom. 2016. 'Combined Ex Vivo 9.4T MRI and Quantitative Histopathological Study in Normal and Pathological Neocortical Resections in Focal Epilepsy', Brain Pathol, 26: 319-33.
Reisert, M., E. Kellner, and V. G. Kiselev. 2012. 'About the geometry of asymmetric fiber orientation distributions', IEEE Trans Med Imaging, 31: 1240-9.
Reisert, M., and V. G. Kiselev. 2011. 'Fiber continuity: an anisotropic prior for ODF estimation', IEEE Trans Med Imaging, 30: 1274-83.
Reisert, M., I. Mader, C. Anastasopoulos, M. Weigel, S. Schnell, and V. Kiselev. 2011. 'Global fiber reconstruction becomes practical', Neuroimage, 54: 955-62.
Reveley, C., A. K. Seth, C. Pierpaoli, A. C. Silva, D. Yu, R. C. Saunders, D. A. Leopold, and F. Q. Ye. 2015. 'Superficial white matter fiber systems impede detection of long-range cortical connections in diffusion MR tractography', Proc Natl Acad Sci U S A, 112: E2820-8.
Roebroeck, A., R. Galuske, E. Formisano, O. Chiry, H. Bratzke, I. Ronen, D. S. Kim, and R. Goebel. 2008. 'High-resolution diffusion tensor imaging and tractography of the human optic chiasm at 9.4 T', Neuroimage, 39: 157-68.
Rubinov, M., and O. Sporns. 2010. 'Complex network measures of brain connectivity: uses and interpretations', Neuroimage, 52: 1059-69.
Santis, S., Y. Assaf, C. J. Evans, and D. K. Jones. 2014. 'Improved precision in CHARMED assessment of white matter through sampling scheme optimization and model parsimony testing', Magn Reson Med, 71: 661-71.
Savadjiev, P., J. S. Campbell, M. Descoteaux, R. Deriche, G. B. Pike, and K. Siddiqi. 2008. 'Labeling of ambiguous subvoxel fibre bundle configurations in high angular resolution diffusion MRI', Neuroimage, 41: 58-68.
Savadjiev, P., J. S. Campbell, G. B. Pike, and K. Siddiqi. 2006. '3D curve inference for diffusion MRI regularization and fibre tractography', Med Image Anal, 10: 799-813.
Seehaus, A. K., A. Roebroeck, O. Chiry, D. S. Kim, I. Ronen, H. Bratzke, R. Goebel, and R. A. Galuske. 2013. 'Histological validation of DW-MRI tractography in human postmortem tissue', Cereb Cortex, 23: 442-50.
Seehaus, A., A. Roebroeck, M. Bastiani, L. Fonseca, H. Bratzke, N. Lori, A. Vilanova, R. Goebel, and R. Galuske. 2015. 'Histological validation of high-resolution DTI in human post mortem tissue', Frontiers in Neuroanatomy, 9.
Setsompop, K., R. Kimmlingen, E. Eberlein, T. Witzel, J. Cohen-Adad, J. A. McNab, B. Keil, M. D. Tisdall, P. Hoecht, P. Dietz, S. F. Cauley, V. Tountcheva, V. Matschl, V. H. Lenz, K. Heberlein, A. Potthast, H. Thein, J. Van Horn, A. Toga, F. Schmitt, D. Lehne, B. R. Rosen, V. Wedeen, and L. L. Wald. 2013. 'Pushing the limits of in vivo diffusion MRI for the Human Connectome Project', Neuroimage, 80: 220-33.
Sherbondy, A. J., R. F. Dougherty, R. Ananthanarayanan, D. S. Modha, and B. A. Wandell. 2009. 'Think global, act local; projectome estimation with BlueMatter', Med Image Comput Comput Assist Interv, 12: 861-8.
Sherbondy, A. J., R. F. Dougherty, M. Ben-Shachar, S. Napel, and B. A. Wandell. 2008. 'ConTrack: finding the most likely pathways between brain regions using diffusion tractography', J Vis, 8: 15 1-16.
Sherbondy, A. J., M. C. Rowe, and D. C. Alexander. 2010. 'MicroTrack: an algorithm for concurrent projectome and microstructure estimation', Med Image Comput Comput Assist Interv, 13: 183-90.
Smith, R. E., J. D. Tournier, F. Calamante, and A. Connelly. 2013. 'SIFT: Spherical-deconvolution informed filtering of tractograms', Neuroimage, 67: 298-312.
Sotak, C. H. 2002. 'The role of diffusion tensor imaging in the evaluation of ischemic brain injury – a review', Nmr in Biomedicine, 15: 561-9.
Sotiropoulos, S. N., L. Bai, P. S. Morgan, C. S. Constantinescu, and C. R. Tench. 2010. 'Brain tractography using Q-ball imaging and graph theory: Improved connectivities through fibre crossings via a model-based approach', Neuroimage, 49: 2444-56.
Sotiropoulos, S. N., and A. Zalesky. 2017. 'Building connectomes using diffusion MRI: why, how and but', Nmr in Biomedicine.
Sporns, O., G. Tononi, and R. Kotter. 2005. 'The human connectome: A structural description of the human brain', PLoS Comput Biol, 1: e42.
Stanisz, G. J., A. Szafer, G. A. Wright, and R. M. Henkelman. 1997. 'An analytical model of restricted diffusion in bovine optic nerve', Magn Reson Med, 37: 103-11.
Stejskal, E.O., and J.E. Tanner. 1965. 'Spin Diffusion Measurements: Spin Echoes in the Presence of a Time-Dependent Field Gradient', Journal of Chemical Physics, 42.
Stikov, N., J. Campbell, M. Boudreau, S. Narayanan, T. Stroh, S. Nuara, J. Novek, S. Frey, Ming-Kay Ho, B. Bedell, and B. Pike. 2014. "In vivo histology of the myelin g-ratio." In Proceedings of the 2014 Organization for Human Brain Map** annual meeting, 2249. Hamburg, Germany.
Sundgren, P. C., Q. Dong, D. Gomez-Hassan, S. K. Mukherji, P. Maly, and R. Welsh. 2004. 'Diffusion tensor imaging of the brain: review of clinical applications', Neuroradiology, 46: 339-50.
Tariq, M., T. Schneider, D. C. Alexander, C. A. Gandini Wheeler-Kingshott, and H. Zhang. 2016. 'Bingham-NODDI: Map** anisotropic orientation dispersion of neurites using diffusion MRI', Neuroimage, 133: 207-23.
Tasaki, I., F. Ishii, and H. Ito. 1943. 'On the relation between the conduction rate and fiber diameter and the internodal distance of the medullated nerve fiber', Japanese Journal of Medical Sciences, 9: 189-99.
Thomas, C., F. Q. Ye, M. O. Irfanoglu, P. Modi, K. S. Saleem, D. A. Leopold, and C. Pierpaoli. 2014. 'Anatomical accuracy of brain connections derived from diffusion MRI tractography is inherently limited', Proc Natl Acad Sci U S A, 111: 16574-9.
Timmers, I., H. Zhang, M. Bastiani, B. M. Jansma, A. Roebroeck, and M. E. Rubio-Gozalbo. 2015. 'White matter microstructure pathology in classic galactosemia revealed by neurite orientation dispersion and density imaging', J Inherit Metab Dis, 38: 295-304.
Tournier, J. D., F. Calamante, and A. Connelly. 2007. 'Robust determination of the fibre orientation distribution in diffusion MRI: non-negativity constrained super-resolved spherical deconvolution', Neuroimage, 35: 1459-72.
Tournier, J. D., F. Calamante, D. G. Gadian, and A. Connelly. 2004. 'Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution', Neuroimage, 23: 1176-85.
Tuch, D. S. 2004. 'Q-ball imaging', Magn Reson Med, 52: 1358-72.
Tuch, D. S., T. G. Reese, M. R. Wiegell, N. Makris, J. W. Belliveau, and V. J. Wedeen. 2002. 'High angular resolution diffusion imaging reveals intravoxel white matter fiber heterogeneity', Magn Reson Med, 48: 577-82.
Ugurbil, K., J. Xu, E. J. Auerbach, S. Moeller, A. T. Vu, J. M. Duarte-Carvajalino, C. Lenglet, X. Wu, S. Schmitter, P. F. Van de Moortele, J. Strupp, G. Sapiro, F. De Martino, D. Wang, N. Harel, M. Garwood, L. Chen, D. A. Feinberg, S. M. Smith, K. L. Miller, S. N. Sotiropoulos, S. Jbabdi, J. L. Andersson, T. E. Behrens, M. F. Glasser, D. C. Van Essen, E. Yacoub, and W. U-Minn HCP Consortium. 2013. 'Pushing spatial and temporal resolution for functional and diffusion MRI in the Human Connectome Project', Neuroimage, 80: 80-104.
van den Heuvel, M. P., R. C. Mandl, C. J. Stam, R. S. Kahn, and H. E. Hulshoff Pol. 2010. 'Aberrant frontal and temporal complex network structure in schizophrenia: a graph theoretical analysis', J Neurosci, 30: 15915-26.
van den Heuvel, M. P., and O. Sporns. 2011. 'Rich-club organization of the human connectome', J Neurosci, 31: 15775-86.
Van Essen, D., S. Jbabdi, S. N. Sotiropoulos, C. Chen, K. Dikranian, T. Coalson, J. Harwell, T. E. Behrens, and M. F. Glasser. 2014. 'MAPPING CONNECTIONS IN HUMANS AND NON-HUMAN PRIMATES: ASPIRATIONS AND CHALLENGES FOR DIFFUSION IMAGING.' in, Diffusion MRI.
Vu, A. T., E. Auerbach, C. Lenglet, S. Moeller, S. N. Sotiropoulos, S. Jbabdi, J. Andersson, E. Yacoub, and K. Ugurbil. 2015. 'High resolution whole brain diffusion imaging at 7T for the Human Connectome Project', Neuroimage, 122: 318-31.
Wakana, S., H. Jiang, L. M. Nagae-Poetscher, P. C. van Zijl, and S. Mori. 2004. 'Fiber tract-based atlas of human white matter anatomy', Radiology, 230: 77-87.
Wedeen, V. J., P. Hagmann, W. Y. Tseng, T. G. Reese, and R. M. Weisskoff. 2005. 'Map** complex tissue architecture with diffusion spectrum magnetic resonance imaging', Magn Reson Med, 54: 1377-86.
Wedeen, V. J., R. P. Wang, J. D. Schmahmann, T. Benner, W. Y. Tseng, G. Dai, D. N. Pandya, P. Hagmann, H. D'Arceuil, and A. J. de Crespigny. 2008. 'Diffusion spectrum magnetic resonance imaging (DSI) tractography of crossing fibers', Neuroimage, 41: 1267-77.
Wen, Q., D. A. Kelley, S. Banerjee, J. M. Lupo, S. M. Chang, D. Xu, C. P. Hess, and S. J. Nelson. 2015. 'Clinically feasible NODDI characterization of glioma using multiband EPI at 7 T', Neuroimage Clin, 9: 291-9.
Werring, D. J., C. A. Clark, G. J. Barker, A. J. Thompson, and D. H. Miller. 1999. 'Diffusion tensor imaging of lesions and normal-appearing white matter in multiple sclerosis', Neurology, 52: 1626-32.
Yeh, F. C., V. J. Wedeen, and W. Y. Tseng. 2010. 'Generalized q-sampling imaging', IEEE Trans Med Imaging, 29: 1626-35.
Zalesky, A., and A. Fornito. 2009. 'A DTI-derived measure of cortico-cortical connectivity', IEEE Trans Med Imaging, 28: 1023-36.
Zalesky, A., A. Fornito, I. H. Harding, L. Cocchi, M. Yucel, C. Pantelis, and E. T. Bullmore. 2010. 'Whole-brain anatomical networks: does the choice of nodes matter?', Neuroimage, 50: 970-83.
Zatorre, R. J., R. D. Fields, and H. Johansen-Berg. 2012. 'Plasticity in gray and white: neuroimaging changes in brain structure during learning', Nat Neurosci, 15: 528-36.
Zhang, H., P. L. Hubbard, G. J. Parker, and D. C. Alexander. 2011. 'Axon diameter map** in the presence of orientation dispersion with diffusion MRI', Neuroimage, 56: 1301-15.
Zhang, H., T. Schneider, C. A. Wheeler-Kingshott, and D. C. Alexander. 2012. 'NODDI: practical in vivo neurite orientation dispersion and density imaging of the human brain', Neuroimage, 61: 1000-16.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Roebroeck, A. (2021). dMRI: Diffusion Magnetic Resonance Imaging as a Window onto Structural Brain Networks and White Matter Microstructure. In: Diwadkar, V.A., B. Eickhoff, S. (eds) Brain Network Dysfunction in Neuropsychiatric Illness. Springer, Cham. https://doi.org/10.1007/978-3-030-59797-9_6
Download citation
DOI: https://doi.org/10.1007/978-3-030-59797-9_6
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-59796-2
Online ISBN: 978-3-030-59797-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)