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Philipp, Thank you for helping me! Yes, I have compared the smwc*.img files with the templates in the tmp folder. When segmenting though, I use 1x1x1 mm3 voxel size setting, with the distributed templates, can this cause a problem? I followed yor suggestions and checked the unsmoothed images, to me they seem to be aligned. I attach the CheckReg picture containing (from left to right, top to bottom): 1. The Grey template from the tpm folder. 2-8. 8 unsmoothed images selected at random. 9-13. The Beta images. 14. The Con image. 15. The Mask image. Can you find anything weird? Best regards, Carl Johan