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Hi, There is no scaling or modification of the intensities except for interpolation. Is it possible that what you are seeing are just interpolation effects? If the resolution of the PD is lower than the FLAIR then that will make the effects worse. If you still do not think it is just interpolation effects then can you describe how you are testing this and give us some numerical examples? All the best, Mark On 17 Jun 2010, at 22:40, Anil Vasireddi wrote: > Hi, > > I have been using FLIRT to register FLAIR volumes of a given brain > to the corresponding proton density (PD) volumes. I am using the > following simple command for this purpose: > > flirt -in <FLAIR volume> -ref <PD volume> -out <registered FLAIR > volume> > > The input and reference volumes were similar enough for the above > command to be sufficient for a successful registration. > > However, the I have been noticing that the image intensities of > voxels in the output FLAIR volumes are considerably larger than the > intensities from the input FLAIR volumes. It doesn't seem as though > the intensities were simply multiplied by a scalar factor either. > > Is it possible to use the flirt command without altering the image > intensities from the input volumes during registration? > > Any help would be greatly appreciated. > > -Anil >