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 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 skull stripping and therefore slices contain subcutaneous fat, which also has a high signal intensity. When processing images from obese subjects might the large amount of subcutaneous fat affect intensity normalisation thereby affecting measures like pctsurfcon further down the line? Or does freesurfer distinguish between subcutaneous fat and white matter?

Thanks Nenad _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer