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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
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
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
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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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi! Thanks, Doug and Bruce, for your input. It seems to be a problem with the number of iterations (-n). It is currently hard coded to run 4 times. If I run it only once, grey and white are in a normal range (but there are still inhomogeneities). If I run it twice, grey is at 60 and white is at 100. With every following iteration I loose overall brightness. Caspar
Am Fr., 18. Sept. 2020 um 17:16 Uhr schrieb Douglas Greve < dgreve@mgh.harvard.edu>:
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 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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Fischl, Bruce