April 2020
Intermediate to advanced
438 pages
12h 2m
English
Content preview from Python Image Processing Cookbook
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Segmentation with GMM-EM
Run the following steps to segment an MR T1 brain image using GMM–EM, this time using scikit-learn library functions:
- First, download the atlas image from atlas_slicez90.nii.gz (this is a high-quality image, obtained by registering and averaging interpatient T1 brain images) from https://github.com/curiale/Medical-Image-Analysis-IPython-Tutorials/tree/master/tutorial_3/data. Read the brain slice image with the following code snippet:
max_int_val = 512;image = sitk.ReadImage("images/atlas_slicez90.nii.gz", sitk.sitkFloat32)image = sitk.RescaleIntensity(image,0.0,max_int_val)image_data = sitk.GetArrayFromImage(image)
- Compute the parameters for the Gaussian mixture model:
g = GaussianMixture(n_components=4, covariance_type='diag', ...
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