Open-source skull reconstruction with MONAI

SoftwareX, vol. 23, pp. 101432

Abstract

We present a deep learning model based on an autoencoder for the reconstruction of cranial and facial defects using the Medical Open Network for Artificial Intelligence (MONAI) framework, which has been pre-trained on the MUG500+ and SkullFix dataset. The implementation follows the MONAI contribution guidelines, hence, it can be easily tried out and used, and extended by MONAI users. The primary goal of this paper lies in the investigation of open-sourcing codes and pre-trained deep learning models under the MONAI framework. The pre-trained models generated in this work deliver reasonable results on the cranial and facial reconstruction task and provide an ideal starting-point for other researchers interested in further investigating the topic. We released the codes and the pre-trained model at the official MONAI ‘research contributions' GitHub repository: https://github.com/Project-MONAI/research-contributions/tree/master/SkullRec. This contribution has two novelties: 1. Pre-training an autoencoder on the MUG500+ and SkullFix dataset for cranial and facial reconstruction using MONAI, and open-sourcing the codes and weights for other MONAI users; 2. Demonstrating that existing MONAI tutorials can be easily adapted to new use cases, such as skull (cranial and facial) reconstruction.

Authors 9

1. Jianning Li corresponding

   Graz University of Technology · Computer Algorithms for Medicine · Essen University Hospital

   Affiliation as printed

   Computer Algorithms for Medicine Laboratory (Cafe), Graz, Austria

   Institute for Artificial Intelligence in Medicine (IKIM), Essen University Hospital (AöR), Girardetstraße 2, 45131 Essen, Germany

   Institute of Computer Graphics and Vision (ICG), Graz University of Technology, Inffeldgasse 16c, 8010 Graz, Austria

2. Behrus Puladi Aachen Department of Oral and Maxillofacial Surgery Institute of Medical Informatics

   Universitätsklinikum Aachen · RWTH Aachen University

   Affiliation as printed

   Department of Oral and Maxillofacial Surgery, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany

   Institute of Medical Informatics, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany

3. Victor Alves

   University of Minho

   Affiliation as printed

   ALGORITMI Research Centre/LASI, University of Minho, Braga, Portugal

4. Michael Kamp

   Stiftung Universitätsmedizin Essen · Monash University · Ruhr University Bochum

   Affiliation as printed

   Cancer Research Center Cologne Essen (CCCE), University Medicine Essen (AöR), Hufelandstraße 55, 45147 Essen, Germany

   Data Science and AI Department, Monash University, Melbourne, Australia

   Institute for Neuroinformatics, Ruhr University Bochum, Germany

5. Moon Kim

   Essen University Hospital · Stiftung Universitätsmedizin Essen

   Affiliation as printed

   Cancer Research Center Cologne Essen (CCCE), University Medicine Essen (AöR), Hufelandstraße 55, 45147 Essen, Germany

   Institute for Artificial Intelligence in Medicine (IKIM), Essen University Hospital (AöR), Girardetstraße 2, 45131 Essen, Germany

   Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen (AöR), Essen, Germany

6. Felix Nensa

   Essen University Hospital

   Affiliation as printed

   Institute for Artificial Intelligence in Medicine (IKIM), Essen University Hospital (AöR), Girardetstraße 2, 45131 Essen, Germany

   Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen (AöR), Essen, Germany

7. Jens Kleesiek

   Essen University Hospital · Deutsches Konsortium für Translationale Krebsforschung · Stiftung Universitätsmedizin Essen

   Affiliation as printed

   Cancer Research Center Cologne Essen (CCCE), University Medicine Essen (AöR), Hufelandstraße 55, 45147 Essen, Germany

   German Cancer Consortium (DKTK), Partner Site Essen, Hufelandstraße 55, 45147 Essen, Germany

   Institute for Artificial Intelligence in Medicine (IKIM), Essen University Hospital (AöR), Girardetstraße 2, 45131 Essen, Germany

8. Seyed‐Ahmad Ahmadi
   Affiliation as printed

   NVIDIA GmbH, Bavaria Towers - Blue Tower, Einsteinstrasse 172, 81677 Munich, Germany

9. Jan Egger corresponding

   Graz University of Technology · Computer Algorithms for Medicine · Essen University Hospital · Stiftung Universitätsmedizin Essen

   Affiliation as printed

   Cancer Research Center Cologne Essen (CCCE), University Medicine Essen (AöR), Hufelandstraße 55, 45147 Essen, Germany

   Computer Algorithms for Medicine Laboratory (Cafe), Graz, Austria

   Institute for Artificial Intelligence in Medicine (IKIM), Essen University Hospital (AöR), Girardetstraße 2, 45131 Essen, Germany

   Institute of Computer Graphics and Vision (ICG), Graz University of Technology, Inffeldgasse 16c, 8010 Graz, Austria