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Dear Stephen, this data set looks quite challenging and I am afraid that a reliable segmentation will be difficult or even impossible. The names GWM and CGM indicate the mixed GM classes at the border to WM (GWM) and CSF (CGM) and these mixed classes will be attributed to the 3 main tissues at the end of the segmentation. Tweaking the code to only use GM for spatial registration will probably not help because the anatomy of the data set is so deviating and segmentation quality seems to be not sufficient. Best, Christian On Sat, 17 Jun 2017 17:04:05 +0200, Stephen LARROQUE <[log in to unmask]> wrote: >Hello everyone, > >I am using CAT12 to segment a brain to do a VBM analysis. > >The brain is quite damaged, and some areas, particularly the frontal lobe, >suffer from inhomogenous intensity of the white matter. > >However, the CAT12 report indicates that the segmentation could separate >the white matter tissue in the "GWM" class (I guess meaning it cannot know >if it's grey matter or white matter?). I posted a picture of the report >here: > >http://imgur.com/a/leLOH > >I would like to know if it is possible to force CAT12 to only use the >tissue classes GM and CGM for the normalization, excluding the GWM class. > >Also, what does CGM stands for? Cerebrospinal-fluid mixed with Grey Matter? > >Thank you very much in advance, >Best regards, >Stephen L. >