Deformable Organisms Skullstripping

Overview - Deformable Organisms Skullstripping

Pipeline will skull-strip an magnetic resonance (MR) image of the brain using a deformable organisms framework.

Problem addressed by this workflow

Segment or delineate the brain in whole head MR images. Creates a mask of the brain, separating it from skull, skin, eyes, neck, and cerebro-spinal fluid (CSF).

Detailed Workflow Usage & Specifications

The module takes ANALYZE or NIFTI magnetic resonance images of the head as input and will output a compressed NIFTI binary mask delineating a segmentation of the brain. Our method registers the subject image into a common space and performs deformable organisms segmentation. It then applies the inverse transform to the binary mask image back into native space to complete the segmentation.

Details of the method may be found in

G. Prasad, A.J. Joshi, P.M. Thompson, A.W. Toga, D.W. Shattuck, D. Terzopoulos, “Skull-stripping With Deformable Organisms,” IEEE International Symposium on Biomedical Imaging (ISBI), 2011.

http://www.loni.ucla.edu/twiki/bin/view/CCB/DoSkullstripping

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