Smooth Brain Masks

This algorithm smooths a brain mask, usually obtained after skull-stripping a 3D MR volume. E.g. it could be used to smooth the brain mask obtained from SPECTRE. The resultant mask has the same topology of a sphere.

Input Types

You should be able to apply this algorithm to any brain mask of a 3D MRI image.

Parameters

Original Volume

The raw MR volume with skull.

Brain Mask

Brain mask binary volume, 0 is background and 1 is foreground.

Level set value

Max Curvature

Controls the smoothness of the mask, increasing this parameter will decrease the smoothness.

Translation


Example Usage

Example JIST layout

 Example JIST layout

Example input image with skull.

 Input volume

Example input brainmask.

 input brain mask

Output stripped volume.

 Output stripped volume

Output mask.

 Output brain mask

References [1] H. Hoppe, " Progressive meshes," SIGGRAPH, vol. 33, pp. 317-324, 1999.
[2] M. Desbrun, M. Meyer, P. Schröder and A. H. Barr, " Implicit fairing of irregular meshes using diffusion and curvature flow," SIGGRAPH, pp. 99-108, 1996.
[3] P. L. Bazin and D. L. Pham, " Topology correction using fast marching methods and its application to brain segmentation," MICCAI, pp. 484-491, 2005.