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

► We present a surface-based processing pipeline that allows accurate vertice-wise statistical comparisons of brain modifications, such as cortical thickness (CTE). ► The brain is first segmented into the three main brain tissue types: white matter (WM), gray matter (GM) and cerebrospinal fluid (CSF). ► A topology corrected mesh is generated. ► Partial inflation of surfaces is performed. ► Non rigid registration to a common space using shape context is eventually applied. ► The methods were incorporated in the plugins MILXCTE and MILXCTESurface as part of our downloadable software platform MILXView® available at http://aehrc.com/research/biomedical-imaging/medical-image-analysis/milxview.