Cortical Reconstruction and Analysis Software

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The goal of this proposal is to develop largely automated and user-friendly software tools for finding and mathematically representing the cerebral cortex in volumetric magnetic resonance (MR) images. These software tools will be made publicly and freely available and will be useful in studies involving 1) the development of a description of normal versus diseased cortical geometry, 2) landmark generation for deformable atlas registration, 3) statistical analyses of structure/function relationships, and 4) characterization of morphological changes in aging and disease. The algorithms that will form the basis for the developed software tools stem from our own research work on cortical reconstruction and analysis. We propose five specific aims: 1) incorporate the core volumetric processing algorithms into MIPAV, a commercial-quality but freely available software package developed at NIH; 2) implement a dedicatedGUI- based software package for performing a full reconstruction of the cerebral cortex from MR images; 3) implement surface-based processing and analysis tools within our dedicated software package that will allow definition of regions of interest on the cortex, cortical unfolding, surface editing, and sulcal labeling; 4) perform two phases of testing of the software package followed by a general public release; and 5) implement enhanced scripting and client/server-based versions of the software that will allow customization of the overall processing methodology and offload computationally intensive algorithms to a networked server. These aims will be achieved by 1) porting existing in-house software into the Java programming language using the MIPAV application programming interface, 2) developing graphical user interfaces for visualization and validation, and 3) making refinements based on tester feedback. Source code to all developed software will be made publicly available.