It's been a while since 5.3, but I vaguely remember something like this happening because there were one or two super bright voxels in the image. If this is the case, then you can find them and clip them.

On 9/18/20 10:32 AM, Fischl, Bruce wrote:

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

 

        External Email - Use Caution        

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

 

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