Gist 51ee3c0f179008ff4a15

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Gist 51ee3c0f179008ff4a15

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Last edited Aug 26, 2014

Created on Aug 26, 2014

This visualization demonstrates white-stripe normalization of a T1-weighted brain MRI, overlaying a colored white-stripe mask on the normalized anatomical image. The notebook imports nipy’s `plot_map` for rendering, and uses scikit-image’s `threshold_otsu` to mask background voxels. It processes a control subject’s N4-corrected, rigidly aligned image via an R script (WhiteStripe package) called through rpy2, then visualizes the mask at the stripe’s centroid coordinates derived from the affine transform. The rendering uses a HSV colormap for the stripe overlay.

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