I don’t think adding 100 will work as once it scales everything down that far you only have a couple of bits of representation in the conformed ( 1 byte/voxel) images. Maybe someone else can comment on fixing nu_correct?

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Caspar M. Schwiedrzik
Sent: Friday, September 18, 2020 5:04 AM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output

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Hi!

I am having some issue at the interface between mri_nu_correct.mni and mri_normalize, using v5.3.

Specifically, the output when applying mri_nu_correct to a T1 is quite dark, with white matter in the range of 15. Contrast is ok. When I apply mri_normalize to nu, it does not scale the data to white matter 110. This happens with and without a brain mask, and with various other parameter choices.

I am tempted to just add 100 to all voxels.

Any advice?

Thank you,

Caspar