MR Skull Stripping (PFUS option)

This tool serves for extracting the brain part from human 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 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.