Development and Implementation of a Corriedale Ovine Brain Atlas for Use in Atlas-Based Segmentation.
Segmentation is the process of partitioning an image into subdivisions and can be applied to medical images to isolate anatomical or pathological areas for further analysis. This process can be done manually or automated by the use of image processing computer packages. Atlas-based segmentation automates this process by the use of a pre-labelled template and a registration algorithm. We developed an ovine brain atlas that can be used as a model for neurological conditions such as Parkinson's disease and focal epilepsy. 17 female Corriedale ovine brains were imaged in-vivo in a 1.5T (low-resolution) MRI scanner. 13 of the low-resolution images were combined using a template construction algorithm to form a low-resolution template. The template was labelled to form an atlas and tested by comparing manual with atlas-based segmentations against the remaining four low-resolution images. The comparisons were in the form of similarity metrics used in previous segmentation research. Dice Similarity Coefficients were utilised to determine the degree of overlap between eight independent, manual and atlas-based segmentations, with values ranging from 0 (no overlap) to 1 (complete overlap). For 7 of these 8 segmented areas, we achieved a Dice Similarity Coefficient of 0.5-0.8. The amygdala was difficult to segment due to its variable location and similar intensity to surrounding tissues resulting in Dice Coefficients of 0.0-0.2. We developed a low resolution ovine brain atlas with eight clinically relevant areas labelled. This brain atlas performed comparably to prior human atlases described in the literature and to intra-observer error providing an atlas that can be used to guide further research using ovine brains as a model and is hosted online for public access.
Vascular Bionics Laboratory, Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia.|Department of Radiology, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia.
Kishan Andre
http://orcid.org/0000-0003-2153-2228
KA
Liyanage
Department of Radiology, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia.
Christopher
C
Steward
Department of Radiology, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia.|Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Victoria, Australia.
Bradford Armstrong
BA
Moffat
Vascular Bionics Laboratory, Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia.|The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia.
Nicholas Lachlan
NL
Opie
Vascular Bionics Laboratory, Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia.|The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia.
Gil Simon
GS
Rind
Vascular Bionics Laboratory, Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia.|The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia.|NeuroEngineering Laboratory, Department of Electrical & Electronic Engineering, The University of Melbourne and Centre for Neural Engineering, Parkville, Victoria, Australia.
Sam Emmanuel
SE
John
Vascular Bionics Laboratory, Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia.|The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia.
Stephen
S
Ronayne
Vascular Bionics Laboratory, Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia.|The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia.
Clive Newton
CN
May
Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia.
Terence John
TJ
O'Brien
Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Werribee, Victoria, Australia.
Marjorie Eileen
ME
Milne
Vascular Bionics Laboratory, Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia.|The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia.
Thomas James
TJ
Oxley
D000465:Algorithms; D000716:Anatomy, Artistic / Q000379:methods*; D019412:Anatomy, Cross-Sectional / Q000379:methods; D000719:Anatomy, Veterinary; D000818:Animals; D001271:Atlases as Topic; D001921:Brain / Q000033:anatomy & histology* / Q000000981:diagnostic imaging; D001931:Brain Mapping / Q000379:methods / Q000662:veterinary; D007090:Image Interpretation, Computer-Assisted; D007091:Image Processing, Computer-Assisted; D008279:Magnetic Resonance Imaging / Q000379:methods; D012756:Sheep / Q000033:anatomy & histology*