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Hi Hidayath, I have met similar troubles to yours. It could be caused by low contrast of your T1 images where GM and WM were hardly separable, or by bad orientation. For the latter case, you may reoriente you T1 images using SPM. Below is what SPM manual tells: " Segmentation can sometimes fail if the source (structural) image is not close in orientation to the MNI templates. It is generally advisable to manually orient the structural to match the template (ie MNI space) as close as possible by using the "Display" button, adjusting x/y/z/pitch/roll/yaw, and then pressing the "Reorient" button. " Hope it help. Best, Zhenhao ----- Zhenhao SHI Culture and Social Cognitive Neuroscience Lab Department of Psychology Peking University 5 Yiheyuan Road Beijing 100871, P.R.China On 23 November 2011 08:19, Hidayath Ansari <[log in to unmask]> wrote: > Hi > > I'm trying to perform routine segmentation on some MRI images. For most of > the images I have it works fine, but for some of them it ends up with a > bizarre-looking image, like it's been excessively smoothed or sheared, or > *something*. I'm not changing any parameters between the segmentations > that turn out fine and the ones that look weird. I'm attaching an image of > a slice that illustrates what I'm referring to. If anyone knows what issue > I might be running into, I would really appreciate a reply! > > Thank you, > > Mohammed Ansari > Graduate Student > Dept. of Computer Sciences > University of Wisconsin-Madison >