Dear Josh,
The registration or resampling process should not be changing the intensities in any large way. There are always interpolation-related inaccuracies, which you would particularly notice at the edge of the bright bony areas, but the intensities in central part of the brain should not be changing much at all. Are you using the MRI as the reference and then looking at the resampled input (CT) image?
If you think the intensities really are changing a lot then please give us an example of the values and also describe how you are doing the registration in more detail.
All the best,
Mark
> On 9 Jul 2019, at 22:39, Josh Cain <[log in to unmask]> wrote:
>
> I am attempting to warp CT images to MRI images for purposes of running simulations through bone.
>
> So I need to be able to warp the geometry of the CT images without changeing the intensity values of the CT images (which denote different tissue types). Is this possible? Flirt changes these values dramatically, essentially making the CT an MRI image.
>
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