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Yes, there is an error in the dimension of the images, that happened while reorganizing the original GE images with medx. Thanks for catching that. I will let you know how it turns out. Stefano -----Original Message----- From: Stephen Smith [mailto:[log in to unmask]] Sent: Saturday, January 12, 2002 12:17 PM To: [log in to unmask] Subject: Re: [FSL] segmentation from 2 channels Hi Stefano. > I am attempting to do a segmentation starting from 2 channels, a proton > density weighted and a T2 weighted image, but I get too much grey matter in > places where white matter should be. Steve, I am now working from the same > images I sent you recently. I was able to extract the brain, and after noise > reduction the images look much better. Also, registration of either image to > a T1 weighted image acquired on a 3T scanner (rather than 1.5), does not > work well at all, when T1 weighted images from 1.5 register fine. Which > parameters should I play with in the advanced options for registration to > have this work? Any suggestions? Stefano Hi - when I tried registering the brain-extracted versions of the images that you sent (including the T2-weighted) to a high res that I have from the 3T here these work fine with the default FLIRT settings. You may be having problems due to the fact that I think your slice thickness is set too small in your images - it needs increasing by around a factor of 1.5? If you can't get this to work ok then feel free to email me the reference image you are working with. Thanks, Steve.