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Hi, You can ignore this warning. It is only informing you that some coordinate information (stored in the sforms) will be lost in the registration, but in this situation that is absolutely fine, as you are resampling the image to move it to a different space, so it is OK to lose the coordinate information from the original space. All the best, Mark On 12 Feb 2014, at 08:30, Manuel Blesa Cábez <[log in to unmask]> wrote: > Dear all, > > I'm doing the TBSS linear and non linear registration, but when I use Flirt and Fnirt always appears a Warning like this: > > WARNING: Both reference and input images have an sform matrix set > > I can continue doing the process, but I don't know the importance of this warning. Somebody could help me and explain it to me? Thanks in advance. > > Best regards, > > Manuel Blesa