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
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