Hi Nick,

Thanks for your reply. I've tried nuintentistycor as you suggested, but it didn't help with the problem. I've even tried nuiterations up to 100.

Thanks,

- David

On Wed, Nov 26, 2008 at 11:40 AM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:

David,

Have you tried increasing the number of iterations during the nu_correct step? Thats the first normalization step (so, you may have tried this already).

You can increase the iterations from the default of 2, like this:

recon-all -s <subjid> -nuintensitycor -nuiterations 6

Inspect the file nu.mgz for any improvement after running this.

Nick

On Wed, 2008-11-26 at 10:26 -0500, David Qixiang Chen wrote:

...

Hi all,

I tried to post this a few days ago, but didn't see it on the mailing list, so I'm sending this again.

I'm running into a problem where some of my scans have varied brightness between slices. What happens is that this results in heavy banding of the resulting scans, and this creates major problem for freesurfer to segment out wm because of the variation in signal intensity.

Intensity normalization doesn't seem to correct this kind of signal problems.

I'm wondering what would be a good way to go about correcting this? I'm been doing control points and wm edits, but because the wm intensity is not standarized across the slices, I think it's just an exercise in futility so far.

I've attached a screen shot.

Thanks!

• David Qixiang Chen

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