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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
