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Hi all, I have been using the clinical toolbox to normalize scans with lesions due to stroke to the MNI template. The normalization itself proceeds well, but the 3D normalized lesion mask no longer aligns with the 3D normalized anatomical after processing. I checked the header information and the origin is the same for both files. I assume that the same transformation parameters that are applied to the anatomical are used to transform the lesion mask (as output in the seg_sn file). Has anyone else run into this issue? I wasn't able to find any messages on the subject in the archives... Thanks! Michelle