7 Tesla MRI of the ex vivo human brain at 100 micron resolution

We present an ultra-high resolution MRI dataset of an ex vivo human brain specimen. The brain specimen was donated by a 58-year-old woman who had no history of neurological disease and died of non-neurological causes. After fixation in 10% formalin, the specimen was imaged on a 7 Tesla MRI scanner at 100 μm isotropic resolution using a custom-built 31-channel receive array coil. Single-echo multi-flip Fast Low-Angle SHot (FLASH) data were acquired over 100 hours of scan time (25 hours per flip angle), allowing derivation of a T1 parameter map and synthesized FLASH volumes. This dataset provides an unprecedented view of the three-dimensional neuroanatomy of the human brain. To optimize the utility of this resource, we warped the dataset into standard stereotactic space. We now distribute the dataset in both native space and stereotactic space to the academic community via multiple platforms. We envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance understanding of human brain anatomy in health and disease.

[1]  Geert Jan Biessels,et al.  Microbleed and microinfarct detection in amyloid angiopathy: a high-resolution MRI-histopathology study. , 2016, Brain : a journal of neurology.

[2]  Siobhan Ewert,et al.  Toward defining deep brain stimulation targets in MNI space: A subcortical atlas based on multimodal MRI, histology and structural connectivity , 2016, NeuroImage.

[3]  Robert Turner,et al.  Myelin and iron concentration in the human brain: A quantitative study of MRI contrast , 2014, NeuroImage.

[4]  M. Tovi,et al.  Measurements of T1 and T2 over time in formalin-fixed human whole-brain specimens. , 1992, Acta radiologica.

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

[6]  Peter Kellman,et al.  Image reconstruction in SNR units: A general method for SNR measurement † , 2005, Magnetic resonance in medicine.

[7]  T. Peters,et al.  High‐resolution T1 and T2 mapping of the brain in a clinically acceptable time with DESPOT1 and DESPOT2 , 2005, Magnetic resonance in medicine.

[8]  Cheuk Y. Tang,et al.  Multimodal Characterization of the Late Effects of Traumatic Brain Injury: A Methodological Overview of the Late Effects of Traumatic Brain Injury Project. , 2018, Journal of neurotrauma.

[9]  Ann C. McKee,et al.  Quantitative validation of a nonlinear histology-MRI coregistration method using generalized Q-sampling imaging in complex human cortical white matter , 2017, NeuroImage.

[10]  Jeremy D. Schmahmann,et al.  Detection of postmortem human cerebellar cortex and white matter pathways using high angular resolution diffusion tractography: A feasibility study , 2013, NeuroImage.

[11]  Vasily L Yarnykh,et al.  Actual flip‐angle imaging in the pulsed steady state: A method for rapid three‐dimensional mapping of the transmitted radiofrequency field , 2007, Magnetic resonance in medicine.

[12]  Siobhan Ewert,et al.  Lead-DBS v2: Towards a comprehensive pipeline for deep brain stimulation imaging , 2018, NeuroImage.

[13]  C. Almli,et al.  Unbiased nonlinear average age-appropriate brain templates from birth to adulthood , 2009, NeuroImage.

[14]  Julien Cohen-Adad,et al.  The Human Connectome Project and beyond: Initial applications of 300mT/m gradients , 2013, NeuroImage.

[15]  Jiangyang Zhang,et al.  Feasibility of creating a high-resolution 3D diffusion tensor imaging based atlas of the human brainstem: A case study at 11.7T , 2013, NeuroImage.

[16]  Horn Andreas.  PCA MNI 2009b NLIN template , 2017 .

[17]  Markus Axer,et al.  Teaching NeuroImages: In vivo visualization of Edinger comb and Wilson pencils , 2019, Neurology.

[18]  Steven G. Johnson,et al.  The Design and Implementation of FFTW3 , 2005, Proceedings of the IEEE.

[19]  Karla L Miller,et al.  Ex vivo diffusion MRI of the human brain: Technical challenges and recent advances , 2018, NMR in biomedicine.

[20]  G. Dai,et al.  Neuroanatomic Connectivity of the Human Ascending Arousal System Critical to Consciousness and Its Disorders , 2012, Journal of neuropathology and experimental neurology.

[21]  Brian B. Avants,et al.  Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain , 2008, Medical Image Anal..

[22]  Daniel D. Dilks,et al.  Size‐optimized 32‐channel brain arrays for 3 T pediatric imaging , 2011, Magnetic resonance in medicine.

[23]  Bruce Fischl,et al.  Medial temporal cortices in ex vivo magnetic resonance imaging , 2013, The Journal of comparative neurology.

[24]  Rainer Goebel,et al.  High resolution anatomical and quantitative MRI of the entire human occipital lobe ex vivo at 9.4 T , 2017, NeuroImage.

[25]  A. Schleicher,et al.  High‐resolution MRI reflects myeloarchitecture and cytoarchitecture of human cerebral cortex , 2005, Human brain mapping.

[26]  Loren Daniel Bridgers.  Design and manufacture of an ultra-high field ex vivo coil assembly , 2012 .

[27]  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.

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

[29]  Oliver Speck,et al.  Erratum: T1-weighted in vivo human whole brain MRI dataset with an ultrahigh isotropic resolution of 250 μm , 2017, Scientific Data.