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An open, multi-vendor, multi-field-strength brain MR dataset and analysis of publicly available skull stripping methods agreement
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An open, multi-vendor, multi-field-strength brain MR dataset and analysis of publicly available skull stripping methods agreement
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Journal Article
An open, multi-vendor, multi-field-strength brain MR dataset and analysis of publicly available skull stripping methods agreement
2018
Overview
This paper presents an open, multi-vendor, multi-field strength magnetic resonance (MR) T1-weighted volumetric brain imaging dataset, named Calgary-Campinas-359 (CC-359). The dataset is composed of images of older healthy adults (29–80 years) acquired on scanners from three vendors (Siemens, Philips and General Electric) at both 1.5 T and 3 T. CC-359 is comprised of 359 datasets, approximately 60 subjects per vendor and magnetic field strength. The dataset is approximately age and gender balanced, subject to the constraints of the available images. It provides consensus brain extraction masks for all volumes generated using supervised classification. Manual segmentation results for twelve randomly selected subjects performed by an expert are also provided. The CC-359 dataset allows investigation of 1) the influences of both vendor and magnetic field strength on quantitative analysis of brain MR; 2) parameter optimization for automatic segmentation methods; and potentially 3) machine learning classifiers with big data, specifically those based on deep learning methods, as these approaches require a large amount of data. To illustrate the utility of this dataset, we compared to the results of a supervised classifier, the results of eight publicly available skull stripping methods and one publicly available consensus algorithm. A linear mixed effects model analysis indicated that vendor (p−value<0.001) and magnetic field strength (p−value<0.001) have statistically significant impacts on skull stripping results.
•A public multi-vendor, multi-field-strength brain MR dataset is proposed and it is now available for download at http://miclab.fee.unicamp.br/tools.•Consensus masks are used as “silver-standards” to assess agreement between different skull stripping methods.•Influences of scanner magnetic field strength and scanner vendor on skull stripping results are analyzed.
