Automated brain extraction for canine magnetic resonance images.
Authors
Affiliations (8)
Affiliations (8)
- DOS Software-Systeme GmbH, Wolfsburg, Germany.
- Peter L. Reichertz Institute for Medical Informatics, TU Braunschweig and Hannover Medical School, Braunschweig, Germany.
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hannover, Hanover, Germany.
- Centre for Systems Neuroscience, University of Veterinary Medicine Hannover, Hanover, Germany.
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, Davis, California, USA.
- Department of Clinical Science and Services, Royal Veterinary College, London, UK.
- Small Animal Hospital, School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hannover, Hanover, Germany. [email protected].
Abstract
Brain extraction is a common preprocessing step when working with intracranial medical imaging data. While several tools exist to automate the preprocessing of magnetic resonance imaging (MRI) of the human brain, none are available for canine MRIs. We present a pipeline mapping separate 2D scans to a 3D image, and a neural network for canine brain extraction. The training dataset consisted of T1-weighted and contrast-enhanced images from 68 dogs of different breeds, all cranial conformations (mesaticephalic, dolichocephalic, brachycephalic), with several pathological conditions, taken at three institutions. Testing was performed on a similarly diverse group of 10 dogs with images from a 4th institution. The model achieved excellent results in terms of Dice ([Formula: see text]) and Jaccard ([Formula: see text]) metrics and generalised well across different MRI scanners, the three aforementioned skull types, and variations in head size and breed. The pipeline was effective for a combination of one to three acquisition planes (i.e., transversal, dorsal, and sagittal). Aside from the T1 weighted imaging training datasets, the model also performed well on other MRI sequences with Jaccardian indices and median Dice scores ranging from 0.86 to 0.89 and 0.92 to 0.94, respectively. Our approach was robust for automated brain extraction. Variations in canine anatomy and performance degradation in multi-scanner data can largely be mitigated through normalisation and augmentation techniques. Brain extraction, as a preprocessing step, can improve the accuracy of an algorithm for abnormality classification in MRI image slices.