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I'm re-sending the message below with the links to the images. raw.png https://drive.google.com/file/d/0B1-hPZ22Vq1VSG1kTlBwbjVRSk0/view?usp=sharing raw-gmpm.png https://drive.google.com/file/d/0B1-hPZ22Vq1VRlo2Yjk0bjJOOG8/view?usp=sharing coreg.png https://drive.google.com/file/d/0B1-hPZ22Vq1VbUJTMHNLWXVFdW8/view?usp=sharing coreg-gmpm.png https://drive.google.com/file/d/0B1-hPZ22Vq1VUHh3UU5za01Cakk/view?usp=sharing Shengwei On Fri, Nov 7, 2014 at 11:39 AM, Shengwei Zhang <[log in to unmask]> wrote: > 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. > 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. > 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. > > 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. > > Shengwei > >