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7 Tesla MRI Followed by Histological 3D Reconstructions in Whole-Brain Specimens

  • Alkemade, Anneke1
  • Pine, Kerrin2
  • Kirilina, Evgeniya2, 3
  • Keuken, Max C.1
  • Mulder, Martijn J.1, 4
  • Balesar, Rawien1, 5
  • Groot, Josephine M.1
  • Bleys, Ronald L. A. W.6
  • Trampel, Robert2
  • Weiskopf, Nikolaus2
  • Herrler, Andreas7
  • Möller, Harald E.8
  • Bazin, Pierre-Louis1, 2, 9
  • Forstmann, Birte U.1
  • 1 Integrative Model-Based Neuroscience Research Unit, University of Amsterdam, Amsterdam , (Netherlands)
  • 2 Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig , (Germany)
  • 3 Neurocomputation and Neuroimaging Unit, Department of Psychology and Educational Science, Free University Berlin, Berlin , (Germany)
  • 4 Department of Experimental Psychology, Utrecht University, Utrecht , (Netherlands)
  • 5 The Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam , (Netherlands)
  • 6 Department of Anatomy, University Medical Center Utrecht, Utrecht University, Utrecht , (Netherlands)
  • 7 Department of Anatomy and Embryology, Maastricht University, Maastricht , (Netherlands)
  • 8 NMR Methods & Development Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig , (Germany)
  • 9 Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig , (Germany)
Published Article
Frontiers in Neuroanatomy
Frontiers Media SA
Publication Date
Oct 06, 2020
DOI: 10.3389/fnana.2020.536838
PMID: 33117133
PMCID: PMC7574789
PubMed Central


Post mortem magnetic resonance imaging (MRI) studies on the human brain are of great interest for the validation of in vivo MRI. It facilitates a link between functional and anatomical information available from MRI in vivo and neuroanatomical knowledge available from histology/immunocytochemistry. However, linking in vivo and post mortem MRI to microscopy techniques poses substantial challenges. Fixation artifacts and tissue deformation of extracted brains, as well as co registration of 2D histology to 3D MRI volumes complicate direct comparison between modalities. Moreover, post mortem brain tissue does not have the same physical properties as in vivo tissue, and therefore MRI approaches need to be adjusted accordingly. Here, we present a pipeline in which whole-brain human post mortem in situ MRI is combined with subsequent tissue processing of the whole human brain, providing a 3-dimensional reconstruction via blockface imaging. To this end, we adapted tissue processing procedures to allow both post mortem MRI and subsequent histological and immunocytochemical processing. For MRI, tissue was packed in a susceptibility matched solution, tailored to fit the dimensions of the MRI coil. Additionally, MRI sequence parameters were adjusted to accommodate T1 and T2∗ shortening, and scan time was extended, thereby benefiting the signal-to-noise-ratio that can be achieved using extensive averaging without motion artifacts. After MRI, the brain was extracted from the skull and subsequently cut while performing optimized blockface imaging, thereby allowing three-dimensional reconstructions. Tissues were processed for Nissl and silver staining, and co-registered with the blockface images. The combination of these techniques allows direct comparisons across modalities.

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