My understanding is that you compute the ratio on the uncorrected images because the ratio will be free from bias (part of the motivation for doing it)

On 6/14/2021 1:23 PM, Marina Fernández wrote:

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Dear experts,

I would like to create myelin maps calculating the T1w/T2w ratio. Should I apply bias field correction and intensity normalization (i.e., "nu correction" in the Freesurfer pipeline) to T1w and T2w images separately before calculating the T1w/T2 ratio?

I applied nu correction to T1w images and worked fine but results were weird when nu correction was applied applied to T2w images. I am not sure if nu correction must only be applied to T1w images for this purpose, or if I have to modify some parameters to apply nu correction to T2w images.

Thank you in advance for your help.

Best, Marina

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