cortical_myelin_segmentation
Description
The Matlab routines allow to segment heavily and sparsely myelinated cortical layers from high-resolution (0.8 mm isotropic and higher) MP2rage images.. In short, the intensities of the MP2rage sequence outputs images are re-scaled and a UNI/T1map ratio image (RATIO) and INV1/INV2 (INVC) image calculated. The cortical rim and adjacent CSF and white matter are isolated and k-means clustering used to identify 6 intensity clusters corresponding to a white matter and csf cluster, two partial volume clusters and a sparsely and highly myelinated rim clusters. Please see Word document for detailed step-by-step instructions. Contact of author Susanne Mueller M.D. Center for Imaging of Neurodegenerative Diseases VAMC San Francisco 4150 Clement Street San Francisco, CA, 94121 USA USA e-mail: susanne.mueller@ucsf.edu You need to have Matlab with the Image Processing, Statistics, Curve Fitting, and Optimization toolboxes and spm12 (https://www.fil.ion.ucl.ac.uk/spm/) Make sure you have the cortex_2_layer directory in your Matlab search path. The Matlab routines are not for commercial use. Disclaimer: Use of the Matlab routines at your own risk.