[Freesurfer] Subcutaneous fat and intensity normalisation

Dear FreeSurfers, I have a question concerning pctsurfcon and subcutaneous fat. The first step in the Freesurfer processing pipeline is intensity normalisation, which assumes that high intensity signal is due to white matter and uses this as a reference point. However this happens prior to

Re: [Freesurfer] Subcutaneous fat and intensity normalisation

Hi Nenad we actually do the intensity normalization mutliple times, the final one on the skull stripped images. We do try to distinguish even if the skull is in the image using connectivity constraints. cheers Bruce On Fri, 11 Apr 2014, N. Medic wrote: Dear FreeSurfers, I have a question