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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
