Skull segmentation from MR scans using a higher-order shape model based on convolutional restricted Boltzmann machines

Oula Puonti, Koen Van Leemput, Jesper Duemose Nielsen, Christian Bauer, Hartwig Roman Siebner, Kristoffer Hougaard Madsen, Axel Thielscher

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

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Transcranial brain stimulation (TBS) techniques such as transcranial magnetic stimulation (TMS), transcranial direct current stimulation (tDCS) and others have seen a strong increase as tools in therapy and research within the last 20 years. In order to precisely target the stimulation, it is important to accurately model the individual head anatomy of a subject. Of particular importance is accurate reconstruction of the skull, as it has the strongest impact on the current pathways due to its low conductivity. Thus providing automated tools, which can reliably reconstruct the anatomy of the human head from magnetic resonance (MR) scans would be highly valuable for the application of transcranial stimulation methods. These head models can also be used to inform source localization methods such as EEG and MEG.Automated segmentation of the skull from MR images is, however, challenging as the skull emits very little signal in MR. In order to avoid topological defects, such as holes in the segmentations, a strong model of the skull shape is needed. In this paper we propose a new shape model for skull segmentation based on the so-called convolutional restricted Boltzmann machines (cRBMs). Compared to traditionally used lower-order shape models, such as pair-wise Markov random fields (MRFs), the cRBMs model local shapes in larger spatial neighborhoods while still allowing for efficient inference. We compare the skull segmentation accuracy of our approach to two previously published methods and show significant improvement.
Original languageEnglish
Title of host publicationMedical Imaging 2018: Image Processing
EditorsElsa D. Angelini , Bennett A. Landman
Number of pages8
PublisherSPIE - International Society for Optical Engineering
Publication date2018
Publication statusPublished - 2018
EventSPIE Medical Imaging 2018 - Marriott Marquis Houston, Houston, United States
Duration: 10 Feb 201815 Feb 2018


ConferenceSPIE Medical Imaging 2018
LocationMarriott Marquis Houston
Country/TerritoryUnited States
Internet address
SeriesProceedings of SPIE - The International Society for Optical Engineering


  • Skull segmentation
  • MRI
  • Shape modeling
  • Transcranial brain stimulation
  • Head modeling


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