Brain labels reported after topology correction

Topology correction of brain surfaces


2009-2012. CSIRO Brisbane, Australia (Olivier Salvado)


Brain surfaces provide a reliable representation for cortical mapping. The construction of correct surfaces from magnetic resonance images (MRI) segmentation is a challenging task, especially when genus zero surfaces are required for further processing such as parameterization, partial inflation and registration. The generation of such surfaces has been approached either by correcting a binary image as part of the segmentation pipeline or by modifying the mesh representing the surface. During this task, the preservation of the structure may be compromised because of the convoluted nature of the brain and noisy/imperfect segmentations. In this paper, we propose a combined, voxel and surface based, topology correction method which preserves the structure of the brain while yielding genus zero surfaces. The topology of the binary segmentation is first corrected using a set of topology preserving operators applied sequentially. This results in a white matter/gray matter binary set with correct sulci delineation, homotopic to a filled sphere. Using the corrected segmentation, a marching cubes mesh is then generated and the tunnels and handles resulting from the meshing are finally removed with an algorithm based on the detection of nonseparating loops. Topology correction of brain surfaces

The approach was validated using 20 young individuals MRI from the OASIS database, acquired at two different timepoints. Reproducibility and robustness were evaluated using global and local criteria such as surface area, curvature and point to point distance. Results demonstrated the method capability to produce genus zero meshes while preserving geometry, two fundamental properties for reliable and accurate cortical mapping and further clinical studies.


. Cortical surface mapping using topology correction‚ partial flattening and 3D shape context-based non-rigid registration for use in quantifying atrophy in Alzheimer’s disease. In Journal of Neuroscience Methods, 205:96-109, 2012.


. A combined voxel and surface based method for topology correction of brain surfaces. SPIE Medical Imaging, 2010.

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