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 <[EMAIL PROTECTED]>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 > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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