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Alternatively, maybe the initial affine registration isn't working so well. Try using "Check Reg" to see how well aligned your T1w image is to the MNI-space data released with SPM12. If the initial alignment isn't so good (more than about 4cm and 15 degrees) then there's a greater chance of a failure. I'm not sure which segmentation you are using. If you are using SPM8 or older, then maybe update to SPM12. If you are using CAT, then Christian might have other suggestions. Best regards, -John On Sat, 30 Mar 2019 at 17:37, Marko Wilke <[log in to unmask]> wrote: > Kathleen, > from the looks of the image you postd, I would guess that this is an issue > of insufficient inhomogeneity correction. I would suggest playing with the > respective parameters in the segmentation module and see if that changes > things. > > Cheers > Marko > > > -- > ____________________________________________________ > Prof. Dr. med. Marko Wilke > Facharzt für Kinder- und Jugendmedizin > Leiter, Experimentelle Pädiatrische Neurobildgebung > Oberarzt der Abteilung Neuropädiatrie > Universitäts-Kinderklinik > > Marko Wilke, MD, PhD > Pediatrician > Head, Experimental Pediatric Neuroimaging > Consultant in Pediatric Neurology > University Children's Hospital > > Hoppe-Seyler-Str. 1 > D - 72076 Tübingen, Germany > Tel. +49 7071 29-83416 > Fax +49 7071 29-5473 > [log in to unmask] > > http://www.medizin.uni-tuebingen.de/kinder/epn/ > ____________________________________________________ > > > >>> "Hupfeld,Kathleen E" <[log in to unmask]> 30.03.19 17.48 Uhr >>> > Dear SPM experts, > > > I am having an issue where, with a "normal-looking" T1 image, segmentation > is not appropriately identifying all of the gray matter (2 screenshots > below): > > [cid:018fd93b-5352-40a8-9e4a-590244590ae5] > [cid:c5554984-1ddc-4fee-a157-28caec0d2ba5] > > > Could anyone please provide insight into why this might be happening? Gray > matter segmentation for other subjects using the same parameters and T1s > collected with the same MPRAGE sequence have worked fine: > > [cid:8d07bcc3-7370-4340-a18c-fa57759375db] > > > Best, > Kathleen > > > > Kathleen Hupfeld > > PhD Candidate, Biobehavioral Science > Neuromotor Behavior Lab > Department of Applied Physiology & Kinesiology > University of Florida > -- Prof John Ashburner Professor of Imaging Science UCL Institute of Neurology Queen Square Wellcome Trust Centre for Neuroimaging University College London 12 Queen Square, London, WC1N 3BG E: [log in to unmask] T: +44 (0)20 3448 4365 http://www.fil.ion.ucl.ac.uk/