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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
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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