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.edu> wrote:
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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