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Hello group, I have no luck to register a high resolution T1-weighted (1.5T) volume (stored at http://www.uku.fi/~kavec/reference_brain.tar.gz ) and T1-weighted (0.12T) volume (stored at http://www.uku.fi/~kavec/input_brain_bias.tar.gz ). Problematic is, I believe, the input volume. (1) It was masked by the manufacturer of the MR system with an ellipsoid mask to hide artefacts due to B0 inhomogeneities. The mask introduces false boundaries in the image, which confuses registration. (2) Additionally, the images were acquired with a large diameter surface coil producing large intensity variations, which I did my best to correct using FAST. To address (1), I am created a brain mask (stored at http://www.uku.fi/~kavec/input_brain_mask.tar.gz ) using BET and I use this as an input weighting volume. I would expect that normalize mutual information should be able to register the imaged using DOF=6-9, but after failing in this I tried virtually every combination of DOF<6 and cost function, but as I mentioned without any good results. I would appreciate any input as to what am I doing wrong. Many thanks in advance. Martin