Software - Multiple Atlas Brain Extraction (ICC)
This is a multiple atlas skull stripping application that works on T1 images to remove the skull. A pre defined set of atlases is taken and each atlas is rigidly, then affinely registered to the image of interest. Then using diffeomorphic demons, non-rigid registration is performed to the target image. The resulting non-rigid transform is then used to warp the ICC mask defined on the atlas to the image of interest space. Finally using a procedure known as STAPLE (Simultaneous Truth And Performance Level Estimation), the most likely ICC segmentation is iteratively computed. The stripped brain is then "stamped" out using this ICC mask.
For minor cleanups we use a version of the slice viewer that displays the stripped brain overlaid in color on the whole head image. A brush of adjustable size can then either erase small areas that jut from the brain or restore small chunks that have been mistakenly removed during the skullstrip.
Figure Multi-Atlas Brain Extraction. Left: unstripped image. Right: stripped image after automated stage and minor user cleanup.
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