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Thank you for your quick answers! @Yasser. I am sorry, but with this new version, it is the same. The underlying image is the ouptut of native SPM5 segmentation (spm_segment), which as far as I am correct, is also used by ibaspm, right? No, the input is not skullstripped. @Marko > "an additional "cleanup" procedure that may be too aggressive on your data" > Yes, that is what I was looking for! I tried with different HMRF values (0, 0.3, 0.45), but this does not change a lot. @Steve The normalisation is perfect, i.e. it matches exactly the one from native SPM. I am sure that it must be something very simple I have so far overlooked, but what? ;-) Thank you so much for your help! Markus 2009/1/30 Yasser Aleman <[log in to unmask]> > Dear Markus: > > Here I am sending to you our last version. I am preparing a new web page to > put it as soon as possible. I am also preparing a quick guide for users. > > I was checking your image and I can see lot of skull tissue in your gray > matter segmentation. Can you please tell me if your native image have skull > stripped or not? > > Best regards > Yasser > 2009/1/30 Marko Wilke <[log in to unmask]> > Maybe the answer's in the title of the Bookstein paper ;-) >> > > ... but if the T1 seems perfectly registered ... ??? If, as I assume, the > wT1 are the result of the same segmentation procedure, this argues against > normalization having gone awry. Is there (I do not know IBASPM well enough) > an additional "cleanup" procedure that may be too aggressive on your data? > > Best, > Marko > > -- > ===================================================================== > Marko Wilke (Dr.med./M.D.) > [log in to unmask] > > Universitäts-Kinderklinik University Children's Hospital > Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology) > Hoppe-Seyler-Str. 1, D - 72076 Tübingen > Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473 > ===================================================================== > -- Dr. med. Markus Gschwind, M.D. Laboratory for Neurology and Imaging of Cognition Dept of Neurosciences University Medical Center (CMU) 1 Michel-Servet - 1211 GENEVA - CH Tel 0041 (0) 22 379 5324 Fax 0041 (0) 22 379 5402 email: [log in to unmask] http://labnic.unige.ch