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Dear Luca, Further to the other sensible comments, you can benefit from extra anatomical information as advocated by John by using MAPER* & the Hammers_mith atlases** to directly segment the substantia nigra with good accuracy (leave-one-out Jaccard 0.555 = Dice 0.714; see 2010 ref. below). The approach has for example been used in Keihaninejad S et al. 2012. Happy to help if you want to give it a try. All the best, Alexander *(Heckemann RA et al. Neuroimage 2006, 2010) **(Hammers A, Allom R et al. 2003 …. Wild et al. 2017; available via www.brain-development.org<http://www.brain-development.org>) ----------------------------------------- Alexander Hammers, MD PhD Professor (Honorary Consultant) of Imaging and Neuroscience Head of PET Imaging Centre Interim Head of Division (with Prof Rene Botnar) Division of Imaging Sciences and Biomedical Engineering King's College London St Thomas' Hospital, London SE1 7EH Email [log in to unmask]<mailto:[log in to unmask]> PET Centre & academic matters: Telephone +44-(0)20 7188 8364 (PA Laura Zappulla) Email [log in to unmask]<mailto:[log in to unmask]> Divisional matters: Telephone +44-(0)20 7188 5440 (EA Anne Williams) Email [log in to unmask]<mailto:[log in to unmask]>