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Semi-automatic active contour-based segmentation to remove eyes, meninges, and skull from MRI



Brain imaging acquisition can present different issues, such as noisy images which can result in a problematic diagnosis. Image preparation such as skull stripping and region segmentation is a fundamental step in order to support a better medical diagnosis outcome. Therefore, this study presented a segmentation technique based on the active contour model to perform skull stripping.


The method is applied on the neuroimaging database available by the OASIS neuroimaging dataset. The method proposed here uses active contour model followed by k-means clustering technique in order to converge to a locally minimal energy value which can be equivalent to the brain tissue area aiming to avoid loss of image quality and brain structures. Statistical analysis was also performed in order to determine how image texture characteristics were affected.


The active contour method achieved results within the ones presented on the state-of-art values segmentation methods with 96.4% of sensitivity and 96% of specificity using only 4 k-means clusters. Image texture characteristics such as entropy and correlation presented values of 1.8804 and 0.96, respectively.


The high entropy value accentuated the gray-level contrast and highlighted anatomical structures for brain visualization. These high evaluation scores demonstrate that the semi-automatic contour-based segmentation algorithm is a powerful tool for segmentation and skull-stripping decreasing loss of image quality and brain structures.

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Authors would like to acknowledge OASIS Brains Project by the data provided (OASIS-3: Principal Investigators: T. Benzinger, D. Marcus, J. Morris; NIH P50AG00561, P30NS09857781, P01AG026276, P01AG003991, R01AG043434, UL1TR000448, R01EB009352. AV-45 doses were provided by Avid Radiopharmaceuticals, a wholly owned subsidiary of Eli Lilly), Federal University of Rio Grande do Norte (UFRN), Santos Dumont Institute (ISD) and Ministry of Education (MEC).

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Correspondence to José Micael Delgado Barbosa.

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José Micael Delgado Barbosa, Tassia Luiza Gonçalves Magalhães Nunes, Tâmara Luiza Gonçalves Magalhães Nunes, Abner Cardoso Rodrigues Neto, and Edgard Morya do not have any conflict of interest related to the present paper and data used to conduct the research.

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Barbosa, J.M.D., Nunes, T.L.G.M., Nunes, T.L.G.M. et al. Semi-automatic active contour-based segmentation to remove eyes, meninges, and skull from MRI. Res. Biomed. Eng. 36, 369–377 (2020).

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  • Brain imaging
  • Skull stripping
  • Active contour model
  • Clustering
  • Image texture