MRI 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 Template 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. Select the T1 or the T2 MR template, depending on the type of input data.
   
2. Mask (Segmentation): The normalization between the MR and the MR MNI template is calculated based on the 3 Probability Maps segmentation method (Unified Segmentation, SPM8). It is then applied to transform the standard MNI brain mask to the MRI space.
   
   The Bias regularisation serves for compensating modulations of the image intensity across the field-of-view. Depending on the degree of the modulation, a corresponding setting can be selected from the list: None, Very Light, Light, Medium, Heavy, Very Heavy. The parameter to the right indicates the FWHM [mm] to be applied. The larger the FWHM, the smoother the variation that is assumed
3. Sum of maps: The MR image is segmented using the 3 Probability Maps method. The mask is created by applying a threshold at the Binarization level to the summed segments.
   

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