Journal of Neurology

, Volume 266, Supplement 1, pp 52–61 | Cite as

A probabilistic atlas of the human inner ear’s bony labyrinth enables reliable atlas-based segmentation of the total fluid space

  • Valerie KirschEmail author
  • F. Nejatbakhshesfahani
  • S.-A. Ahmadi
  • M. Dieterich
  • B. Ertl-Wagner
Original Communication


Intravenous contrast agent-enhanced magnetic resonance imaging of the endolymphatic space (ELS) of the inner ear permits direct, in-vivo, non-invasive visualization of labyrinthine structures and thus verification of endolymphatic hydrops (ELH). However, current volumetric assessment approaches lack normalization. The aim of this study was to develop a probabilistic atlas of the inner ear’s bony labyrinth as a first step towards an automated and reproducible volume-based quantification of the ELS. The study included three different datasets: a source dataset (D1) to build the probabilistic atlas and two testing sets (D2, D3). D1 included 24 right-handed patients (12 females; mean age 51.5 ± 3.9 years) and D2 5 patients (3 female; mean age 48.8 ± 5.01 years) with vestibular migraine without ELH or any measurable vestibular deficits. D3 consisted of five patients (one female; mean age 46 ± 5.2 years) suffering from unilateral Menière’s disease and ELH. Data processing comprised three steps: preprocessing using an affine and deformable fusion registration pipeline, computation of an atlas for the left and right inner ear using a label-assisted approach, and validation of the atlas based on localizing and segmenting previously unseen ears. The three-dimensional probabilistic atlas of the inner ear’s bony labyrinth consisted of the internal acoustic meatus and inner ears (including cochlea, otoliths, and semicircular canals) for both sides separately. The analyses showed a high level of agreement between the atlas-based segmentation and the manual gold standard with an overlap of 89% for the right ear and 86% for the left ear (measured by dice scores). This probabilistic in vivo atlas of the human inner ear’s bony labyrinth and thus of the inner ear’s total fluid space for both ears represents a necessary step towards a normalized, easily reproducible and reliable volumetric quantification of the perilymphatic and endolymphatic space in view of MR volumetric assessment of ELH. The proposed atlas lays the groundwork for state-of-the-art approaches (e.g., deep learning) and will be provided to the scientific community.


Total fluid space Endolymphatic space Endolymphatic hydrops Bony labyrinth Inner ear Deformable registration Probabilistic atlas Automatic segmentation 



Three dimensional


Constructive interference in steady state


Dice score


Endolymphatic hydrops


Endolymphatic space


Fluid-attenuated inversion recovery


Generalized auto-calibrating partially parallel acquisition


Magnetic resonance






Gadolinium-enhanced high-resolution magnetic resonance imaging of the inner ear


Intratympanal applied iMRI


Intravenous applied delayed iMRI




Menière’s disease


Magnetic resonance imaging




Right handed


Root-mean-square error


Standard deviation


Subjective visual vertical


Total number of voxels


Total volume


Videooculography during head impulse test


Vestibular migraine



Partially funded by the Society for the Advancement of Science and Research at the Medical Faculty of the Ludwig Maximilians University Munich (Verein zur Förderung von Wissenschaft und Forschung an der Medizinischen Fakultät der Ludwig-Maximilians-Universität München), the Friedrich-Baur-Stiftung (FBS), the Graduate School of Systemic Neurosciences (GSN), and the German Federal Ministry of Education and Research (German Center for Vertigo and Balance Disorders-IFBLMU, Grant code 01EO140). This is part of the dissertation of F. Nejatbakhshesfahani. We thank Gregory C. Sharp for his help in choosing the right applications in 3D Slicer, Gary E Christensen and his group for sending us a CT-template of the inner ear, and Albert Berman for introducing this project.

Compliance with ethical standards

Conflicts of interest

The authors declare they have no competing financial interests.

Ethical standard

All the procedures conducted with the participants of this study were carried out according to the Declaration of Helsinki. The protocol of the study was approved by the Institutional Review Board approval was obtained prior to the initiation of the study (No 641-15).

Informed consent

Each patient provided informed consent.


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Neurology, University HospitalLudwig-Maximilians-Universität MünchenMunichGermany
  2. 2.Graduate School of Systemic Neuroscience (GSN)Ludwig-Maximilians-UniversitätMunichGermany
  3. 3.German Center for Vertigo and Balance Disorders- IFB, University HospitalLudwig-Maximilians-UniversitätMunichGermany
  4. 4.Department of Radiology, University HospitalLudwig-Maximilians-UniversitätMunichGermany
  5. 5.Munich Cluster for Systems Neurology (SyNergy)MunichGermany
  6. 6.Department of Radiology, The Hospital for Sick ChildrenUniversity of TorontoTorontoCanada

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