MRI Methods for In-Vivo Cortical Parcellation

The advent of whole-body MRI scanners at field strengths as high as 7 T has enabled a dramatic improvement of the spatial resolution of human brain images, in all three major attributes: structure, function and neural connectivity. Structural imaging of entire living human brains with an isotropic resolution of 300–400 μm is now feasible. Such images allow the discrimination of discrete cortical areas based largely on their distinctive myeloarchitecture. This chapter describes the challenges that have to be overcome in creating such images. Sources of contrast in structural MR brain images are summarized. Rationales are then provided for the currently preferred acquisition techniques, which give good signal-to-noise ratios, and relative freedom from the effects of the non-uniformity of the radiofrequency magnetic fields relating to spin excitation and MR signal reception.

[1]  P. Morosan,et al.  Observer-Independent Method for Microstructural Parcellation of Cerebral Cortex: A Quantitative Approach to Cytoarchitectonics , 1999, NeuroImage.

[2]  R. Turner,et al.  Anatomical imaging at 7 T using 2D GRASE – A Comparison with 2D TSE , 2009, NeuroImage.

[3]  Bing Wu,et al.  Quantitative susceptibility mapping of human brain reflects spatial variation in tissue composition , 2011, NeuroImage.

[4]  Kevin L. Briggman,et al.  Structural neurobiology: missing link to a mechanistic understanding of neural computation , 2012, Nature Reviews Neuroscience.

[5]  B. Mädler,et al.  Insights into brain microstructure from the T2 distribution. , 2006, Magnetic resonance imaging.

[6]  R M Henkelman,et al.  Relaxivity and magnetization transfer of white matter lipids at MR imaging: importance of cerebrosides and pH. , 1994, Radiology.

[7]  Katrin Amunts,et al.  In vivo imaging of the human brain at 1.5 T with 0.6-mm isotropic resolution. , 2010, Magnetic resonance imaging.

[8]  Burkhard Mädler,et al.  Myelin water imaging: Implementation and development at 3.0T and comparison to 1.5T measurements , 2009, Magnetic resonance in medicine.

[9]  Stephen M. Smith,et al.  Multiplexed Echo Planar Imaging for Sub-Second Whole Brain FMRI and Fast Diffusion Imaging , 2010, PloS one.

[10]  E. Hogan,et al.  Chromatographic resolution and quantitative assay of CNS tissue sphingoids and sphingolipids. , 2001, Journal of lipid research.

[11]  P. Lundberg,et al.  Novel whole brain segmentation and volume estimation using quantitative MRI , 2012, European Radiology.

[12]  Bruce Fischl,et al.  Mapping an intrinsic MR property of gray matter in auditory cortex of living humans: A possible marker for primary cortex and hemispheric differences , 2006, NeuroImage.

[13]  W. Maenhaut,et al.  Regional distribution of potassium, calcium, and six trace elements in normal human brain , 1989, Neurochemical Research.

[14]  Lawrence L. Wald,et al.  Accurate prediction of V1 location from cortical folds in a surface coordinate system , 2008, NeuroImage.

[15]  Maxim Zaitsev,et al.  Prospective motion correction for magnetic resonance spectroscopy using single camera retro‐grate reflector optical tracking , 2011, Journal of magnetic resonance imaging : JMRI.

[16]  I. Vavasour,et al.  A comparison between magnetization transfer ratios and myelin water percentages in normals and multiple sclerosis patients , 1998, Magnetic resonance in medicine.

[17]  Christopher L Lankford,et al.  On the inherent precision of mcDESPOT , 2013, Magnetic resonance in medicine.

[18]  E Courchesne,et al.  In vivo myeloarchitectonic analysis of human striate and extrastriate cortex using magnetic resonance imaging. , 1992, Cerebral cortex.

[19]  Steen Moeller,et al.  T 1 weighted brain images at 7 Tesla unbiased for Proton Density, T 2 ⁎ contrast and RF coil receive B 1 sensitivity with simultaneous vessel visualization , 2009, NeuroImage.

[20]  S. Francis,et al.  Correspondence of human visual areas identified using functional and anatomical MRI in vivo at 7 T , 2012, Journal of magnetic resonance imaging : JMRI.

[21]  N. J. Shah,et al.  Magnetic field dependence of the distribution of NMR relaxation times in the living human brain , 2008, Magnetic Resonance Materials in Physics, Biology and Medicine.

[22]  P. Dechent,et al.  Optimized high‐resolution mapping of magnetization transfer (MT) at 3 Tesla for direct visualization of substructures of the human thalamus in clinically feasible measurement time , 2009, Journal of magnetic resonance imaging : JMRI.

[23]  P. Molinoff,et al.  Basic Neurochemistry: Molecular, Cellular and Medical Aspects , 1989 .

[24]  Robert Turner,et al.  Optimizing T1-weighted imaging of cortical myelin content at 3.0T , 2013, NeuroImage.

[25]  Michael B. Smith,et al.  Exploring the limits of RF shimming for high‐field MRI of the human head , 2006, Magnetic resonance in medicine.

[26]  Tobias Kober,et al.  MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field , 2010, NeuroImage.

[27]  Derek K. Jones,et al.  Gleaning multicomponent T1 and T2 information from steady‐state imaging data , 2008, Magnetic resonance in medicine.

[28]  Sascha Krueger,et al.  Prospective real‐time correction for arbitrary head motion using active markers , 2009, Magnetic resonance in medicine.

[29]  Ameer Pasha Hosseinbor,et al.  Characterization of Cerebral White Matter Properties Using Quantitative Magnetic Resonance Imaging Stains , 2011, Brain Connect..

[30]  J Hennig,et al.  RARE imaging: A fast imaging method for clinical MR , 1986, Magnetic resonance in medicine.

[31]  D Matthaei,et al.  Rapid three-dimensional MR imaging using the FLASH technique. , 1986, Journal of computer assisted tomography.

[32]  Rolf Gruetter,et al.  On the origin of the MR image phase contrast: An in vivo MR microscopy study of the rat brain at 14.1 T , 2009, NeuroImage.

[33]  Maxim Zaitsev,et al.  An embedded optical tracking system for motion-corrected magnetic resonance imaging at 7T , 2012, Magnetic Resonance Materials in Physics, Biology and Medicine.

[34]  D Purves,et al.  Specialized vascularization of the primate visual cortex , 1991, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[35]  R. Deichmann,et al.  Fast structural brain imaging using an MDEFT sequence with a FLASH–EPI hybrid readout , 2006, NeuroImage.

[36]  D. Feinberg,et al.  GRASE (Gradient‐and Spin‐Echo) imaging: A novel fast MRI technique , 1991, Magnetic resonance in medicine.

[37]  P. Roemer,et al.  The NMR phased array , 1990, Magnetic resonance in medicine.

[38]  S J Riederer,et al.  Real‐time adaptive motion correction in functional MRI , 1996, Magnetic resonance in medicine.

[39]  Julien Cohen-Adad,et al.  T2* mapping and B0 orientation-dependence at 7T reveal cyto- and myeloarchitecture organization of the human cortex , 2012, NeuroImage.

[40]  Jozef H Duyn High-field MRI of brain iron. , 2011, Methods in molecular biology.

[41]  Alan C. Evans,et al.  Automated 3-D Extraction of Inner and Outer Surfaces of Cerebral Cortex from MRI , 2000, NeuroImage.

[42]  S. H. Koenig,et al.  Cholesterol of myelin is the determinant of gray‐white contrast in MRI of brain , 1991, Magnetic resonance in medicine.

[43]  R. Balaban,et al.  Magnetization transfer contrast (MTC) and tissue water proton relaxation in vivo , 1989, Magnetic resonance in medicine.

[44]  M. Fukunaga,et al.  Layer-specific variation of iron content in cerebral cortex as a source of MRI contrast , 2010, Proceedings of the National Academy of Sciences.

[45]  Robert Turner,et al.  High‐resolution fast spin echo imaging of the human brain at 4.7 T: Implementation and sequence characteristics , 2004, Magnetic resonance in medicine.

[46]  M. Mallar Chakravarty,et al.  Neurite density from magnetic resonance diffusion measurements at ultrahigh field: Comparison with light microscopy and electron microscopy , 2010, NeuroImage.

[47]  C. Cheong,et al.  One micrometer resolution NMR microscopy. , 2001, Journal of magnetic resonance.

[48]  P. Hof,et al.  Cytoarchitecture of the human cerebral cortex: MR microscopy of excised specimens at 9.4 Tesla. , 2002, AJNR. American journal of neuroradiology.

[49]  Peter Dechent,et al.  Modeling the influence of TR and excitation flip angle on the magnetization transfer ratio (MTR) in human brain obtained from 3D spoiled gradient echo MRI , 2010, Magnetic resonance in medicine.

[50]  David L. Thomas,et al.  Improving whole brain structural MRI at 4.7 Tesla using 4 irregularly shaped receiver coils , 2006, NeuroImage.

[51]  Robert Turner,et al.  3D MDEFT imaging of the human brain at 4.7 T with reduced sensitivity to radiofrequency inhomogeneity , 2005, Magnetic resonance in medicine.

[52]  Robert Turner,et al.  Do the congenitally blind have a stria of Gennari? First intracortical insights in vivo. , 2010, Cerebral cortex.

[53]  NMR microscopy--beginnings and new directions. , 1999 .

[54]  Cornelia Laule,et al.  Insight into in vivo magnetization exchange in human white matter regions , 2011, Magnetic resonance in medicine.

[55]  Nicholas A. Bock,et al.  Visualizing the entire cortical myelination pattern in marmosets with magnetic resonance imaging , 2009, Journal of Neuroscience Methods.

[56]  R. Turner,et al.  Optimised in vivo visualisation of cortical structures in the human brain at 3 T using IR-TSE. , 2008, Magnetic resonance imaging.

[57]  M. Jenkinson,et al.  In vivo identification of human cortical areas using high-resolution MRI: An approach to cerebral structure–function correlation , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[58]  Anders M. Dale,et al.  Sequence-independent segmentation of magnetic resonance images , 2004, NeuroImage.

[59]  Danielle Graveron-Demilly,et al.  Retrospective intra-scan motion correction. , 2003, Journal of magnetic resonance.

[60]  D. Salat,et al.  Detection of entorhinal layer II using Tesla magnetic resonance imaging , 2005 .

[61]  O. Speck,et al.  Prospective Real-Time Slice-by-Slice Motion Correction for fMRI in Freely Moving Subjects , 2006, Magnetic Resonance Materials in Physics, Biology and Medicine.

[62]  Karl J. Friston,et al.  Voxel-Based Morphometry—The Methods , 2000, NeuroImage.

[63]  P. Börnert,et al.  Transmit SENSE , 2003, Magnetic resonance in medicine.

[64]  J. Grafman,et al.  Imaging cortical anatomy by high‐resolution MR at 3.0T: Detection of the stripe of Gennari in visual area 17 , 2002, Magnetic resonance in medicine.

[65]  Ana-Maria Oros-Peusquens,et al.  Measuring the absolute water content of the brain using quantitative MRI. , 2011, Methods in molecular biology.

[66]  Oliver Speck,et al.  Prospective motion correction in brain imaging: A review , 2013, Magnetic resonance in medicine.

[67]  Dwight G. Nishimura,et al.  Principles of magnetic resonance imaging , 2010 .

[68]  D. V. van Essen,et al.  Mapping Human Cortical Areas In Vivo Based on Myelin Content as Revealed by T1- and T2-Weighted MRI , 2011, The Journal of Neuroscience.

[69]  Jeff H. Duyn,et al.  High-field MRI of brain cortical substructure based on signal phase , 2007, Proceedings of the National Academy of Sciences.

[70]  G A Johnson,et al.  MRI of brain iron. , 1986, AJR. American journal of roentgenology.

[71]  K Shmueli,et al.  High resolution MRI of the brain at 4.7 Tesla using fast spin echo imaging. , 2003, The British journal of radiology.

[72]  R. Turner,et al.  Microstructural Parcellation of the Human Cerebral Cortex – From Brodmann's Post-Mortem Map to in vivo Mapping with High-Field Magnetic Resonance Imaging , 2011, Front. Hum. Neurosci..

[73]  Robert Turner,et al.  Analysis of RF transmit performance for a 7T dual row multichannel MRI loop array , 2011, 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

[74]  R. Deichmann,et al.  Influence of RF spoiling on the stability and accuracy of T1 mapping based on spoiled FLASH with varying flip angles , 2009, Magnetic resonance in medicine.

[75]  Christoph Palm,et al.  A novel approach to the human connectome: Ultra-high resolution mapping of fiber tracts in the brain , 2011, NeuroImage.

[76]  Jeff H. Duyn,et al.  T2*-based fiber orientation mapping , 2011, NeuroImage.

[77]  M M Mesulam,et al.  Location of the central sulcus via cortical thickness of the precentral and postcentral gyri on MR. , 1996, AJNR. American journal of neuroradiology.

[78]  J. Mugler,et al.  Three‐dimensional magnetization‐prepared rapid gradient‐echo imaging (3D MP RAGE) , 1990, Magnetic resonance in medicine.

[79]  A. Mackay,et al.  In vivo measurement of T2 distributions and water contents in normal human brain , 1997, Magnetic resonance in medicine.

[80]  P. Matthews,et al.  Independent anatomical and functional measures of the V1/V2 boundary in human visual cortex. , 2005, Journal of vision.

[81]  J. Polimeni,et al.  96‐Channel receive‐only head coil for 3 Tesla: Design optimization and evaluation , 2009, Magnetic resonance in medicine.