7 Tesla MRI followed by histological 3D reconstructions in whole-brain specimens

Poster No:


Submission Type:

Abstract Submission 


Anneke Alkemade1, Kerrin Pine2, Evgeniya Kirilina3, Pierre-Louis Bazin4, Max Keuken5, Martijn Mulder5, Rawien Balesar5, Josephine Groot6, Robert Trampel2, Nikolaus Weiskopf7, Andreas Herrler8, Harald Möller9, Birte Forstmann1


1University of Amsterdam, Amsterdam, Netherlands, 2Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany, 3Max Planck Institute for Human Cognitive and Brain Sceinces, Leipzig, Germany, 4Universiteit van Amsterdam, Amsterdam, Netherlands, 5Integrative Model-Based Neuroscience Research Unit, University of Amsterdam, Amsterdam, Netherlands, 6UiT - The Arctic University of Tromsø & University of Amsterdam, Amsterdam, Netherlands, 7Department of Neurophysics Max Plank Institute for HUman Cognitiveand Brain Sceinces, Leipzig, Germany, 8Department of Anatomy and Embryology, Maastricht University, Maastricht, Netherlands, 9NMR Methods & Development Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany



Post mortem magnetic resonance imaging (MRI) studies on the human brain are of great interest for the validation of in vivo MRI, and facilitate linking between functional and anatomical information available from MRI in vivo and neuroanatomical knowledge available from histology [Forstmann et al., 2017]. Formalin fixation alters the physical properties of brain tissue, and MRI approaches need to be adjusted accordingly. In addition, 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.


We developed a pipeline for whole-heads, mitigating these challenges and extending our previous work (Weiss et al., 2014; Fig. 1) . Using a MAGNETOM 7T whole-body system (Siemens Healthineers, Erlangen, Germany), and a total acquisition time of 7:04h, we acquired multi-parametric mapping MRI [Weiskopf et al., 2013] in situ, with an isotropic resolution of (0.40 mm)³(scanning parameters: 3D multi-echo GRE with (T1, PD, MT) weighting, FA = (38,7,7) degrees, (8,8,6) echoes with TE in [3.4ms, 21.6ms], TR=31.8 ms). Maps of the RF magnetic field were acquired for B1+ correction [Lutti et al., 2012]. After offline image reconstruction with SENSE, quantitative maps of longitudinal relaxation rate, proton density, magnetization transfer and effective transversal relaxation time were calculated (Weiskopf et al., 2014; Fig. 2), Autopsy was performed and the tissue was cryoprotected in sucrose, frozen, and cut in serial coronal 200 m sections using a cryomacrotome, while performing optimized blockface imaging and collection of each individual section. This allowed three-dimensional reconstructions, and subsequent histology/immunocytochemistry (Fig. 2).


MRI image acquisition of four in situ specimens allowed clear identification of small subcortical structures, including substructures within, e.g., the thalamus (Fig. 2). Images have a very high signal-to-noise ratio as a result of the averaging of 4 scan repetitions, and the absence of movement artifacts. The acquired scans could be overlaid directly without registration since no movement occurred. Distortions resulting from tissue-air interfaces at the level of the oral and nasal cavities were absent, since these cavities were filled with susceptibility-matched phosphate-buffered saline. Small air bubbles were however present in the brain and ventricular system in all tested specimens. Removal of the brain from the skull did not resolve the air bubbles, and caused tissue deformation. Blockface images were restacked without additional registration (Fig. 2). Over 850 individual sections were collected for further histological/immunocytochemical processing.
Supporting Image: Fig1caption.jpg
Supporting Image: Fig2caption.jpg


The anatomical detail that can be obtained post mortem remains unmatched by today's in vivo approaches and post mortem MRI and microscopy allow histological validation of MRI studies, which cannot be performed in vivo [Alkemade et al., 2018]. The pipeline presented here allows bridging between and thereby comparisons across modalities, allowing MRI scanning with minimal tissue deformation inside the skull, as well as detailed reconstructions of the 3D microscopic structure of the human brain. The development of novel post mortem approaches will continue to provide an invaluable addition to different fields including neuroanatomy as well as the cognitive/computational and clinical neurosciences.

Imaging Methods:

Anatomical MRI 1
Imaging Methods Other 2


Anatomy and Functional Systems
Subcortical Structures
Neuroanatomy Other


Basal Ganglia
Other - post mortem

1|2Indicates the priority used for review

My abstract is being submitted as a Software Demonstration.


Please indicate below if your study was a "resting state" or "task-activation” study.


Healthy subjects only or patients (note that patient studies may also involve healthy subjects):

Healthy subjects

Was any human subjects research approved by the relevant Institutional Review Board or ethics panel? NOTE: Any human subjects studies without IRB approval will be automatically rejected.


Was any animal research approved by the relevant IACUC or other animal research panel? NOTE: Any animal studies without IACUC approval will be automatically rejected.

Not applicable

Please indicate which methods were used in your research:

Structural MRI
Postmortem anatomy

For human MRI, what field strength scanner do you use?


Which processing packages did you use for your study?

Other, Please list  -   hMRI Toolbox, MIPAV, Nighres

Provide references using author date format

Alkemade A, Groot JM, Forstmann BU (2018): Do We Need a Human post mortem Whole-Brain Anatomical Ground Truth in in vivo Magnetic Resonance Imaging? Front Neuroanat 12:110. https://www.frontiersin.org/article/10.3389/fnana.2018.00110/full.
Forstmann BU, de Hollander G, van Maanen L, Alkemade A, Keuken MC (2017): Towards a mechanistic understanding of the human subcortex. Nat Rev Neurosci 18:57–65. http://www.nature.com/doifinder/10.1038/nrn.2016.163.
Lutti A, Stadler J, Josephs O, Windischberger C, Speck O, Bernarding J, Hutton C, Weiskopf N (2012): Robust and Fast Whole Brain Mapping of the RF Transmit Field B1 at 7T. Ed. Wang Zhan. PLoS One 7:e32379. http://dx.plos.org/10.1371/journal.pone.0032379.
Weiskopf N, Callaghan MF, Josephs O, Lutti A, Mohammadi S (2014): Estimating the apparent transverse relaxation time (R2*) from images with different contrasts (ESTATICS) reduces motion artifacts. Front Neurosci 8:278. http://journal.frontiersin.org/article/10.3389/fnins.2014.00278/abstract.
Weiskopf N, Suckling J, Williams G, Correia MM, Inkster B, Tait R, Ooi C, Bullmore ET, Lutti A (2013): Quantitative multi-parameter mapping of R1, PD*, MT, and R2* at 3T: a multi-center validation. Front Neurosci 7:95. http://journal.frontiersin.org/article/10.3389/fnins.2013.00095/abstract.
Weiss M, Alkemade A, Keuken MC, Muller-Axt C, Geyer S, Turner R, Forstmann BU (2014): Spatial normalization of ultrahigh resolution 7 T magnetic resonance imaging data of the postmortem human subthalamic nucleus: a multistage approach. Brain Struct Funct. http://www.ncbi.nlm.nih.gov/pubmed/24663802.