MR Skull Stripping

This tool serves for extracting the brain part from anatomical MR images which need to be provided in HFS orientation. There are three processing variants available:

1. Mask (Normalization): This procedure is based on the Brain Normalization II method implemented in the fusion tool. Depending on the setting Template to MR or MR to Template + Inverse, the normalization between the MR and the MR MNI template is calculated, and then applied to transform the standard MNI brain mask to the MRI space.
2. Mask (Segmentation): The normalization between the MR and the MR MNI template is calculated based on the GREY + WHITE + CSF segmentation method. It is then applied to transform the standard MNI brain mask to the MRI space.
3. Sum of maps: The MRI images is segmented using the GREY + WHITE + CSF method. The mask is created by applying a threshold to the summed segments.

Finally, the mask is inverted and applied to the MR image for removing all non-brain pixels.