Could you please suggest what may cause this and advise how I can run DARTEL on the raw space image and avoid running it on the aligned image? Thanks again.The coreg.png is from the same subject after linearly aligned to MNI space, and the coreg-gmpm.png is the GM probability map of the aligned image, which is much more reasonable.The raw.png is my raw space T1 image, and the raw-gmpm.png is the native space GM probability map given by 'Spatial'->'Segment' module in batch editor.Thank you for your detailed reply, John. I tried SPM12, but I'm afraid the segmentation is still not satisfactory. Probably the raw space T1 image is far from well aligned with MNI space.The attached images are a quick demonstration of what I was referring to, all performed in SPM12.Shengwei