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Hi, I am using FLIRT linear registration tool for generating T2map. I've got into several problems while I have been doing it. Besides complete registration failure, I have seen 'blank', somehow 'mirror images in each slice',or 'no matching with reference images'. One of examples is attached. Here is what I did for my analysis. flirt -ref xx -in xx -out xx -dof 6 -cost mutualinfo -omat xx.mat flirt -ref xx -in xxx -out xxxx -init xx.mat -applyxmf Is anybody who has seen something like this problem? Thank you for your time, Mi Jung