Hi Leon,

if I recall correctly the wm surface is looking at intensity gradients in the brain.finalsurfs.mgz (I think). So please have a look at that file and see whether you have some weird issues in that file. The orig surface is created from the wm.mgz and so will reflect edit you made there. BTW I think the filled is created from wm.mgz,  so I guess it is guaranteed to match the orig surface… I do wonder why your wm.mgz shows so much structure, as I am under the impression the wm.mgz should basically be of the wm voxel value (I am wondering about the basal ganglia /caudate intensity I guess)

Best
    Sebastian


On May 25, 2012, at 10:15 AM, Leon wrote:

> Hi, FreeSurfer experts
>
> I am posting it here again since I still have not had the issue solved. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached files). It is strange that such a problem is only located at the precentral gyrus. I checked  the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. I also checked the orig.nofix with defects_label overlaied as suggested by Bruce and I do not see red marks close to the region (see attached file). So I wonder if anyone would help on solving the issue.
>
> Many thanks in advance
>
> Leon
>
> ----- Forwarded Message -----
> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> To: Leon <leonado78@yahoo.com>
> Sent: Friday, May 25, 2012 11:23 AM
> Subject: Re: [Freesurfer] wm surface does not follow wm.mgz
>
> Hi Leon
>
> can you cc the list so others can answer? I don't have any experience
> with monkey recons so I'm not going to be able to be all that helpful.
> Check the filled.mgz and see if the surface follows it, and if so we'll
> have to figure out why that region is being turned on in the filled
> cheers
> Bruce
>
>
> On Fri, 25
> May 2012, Leon wrote:
>
> > Hi, Bruce
> >
> > I checked the orig.nofix and do not see any obvious defect there (see the
> > attached file). Do you have any suggestions on how I should check the
> > defects other than visual check? I loaded the defect_label and there is no
> > red label near this region.
> >
> > Thank you!
> > Leon
> >
> > ____________________________________________________________________________
> > From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> > To: Leon <leonado78@yahoo.com>
> > Sent: Wednesday, May 23, 2012 7:28 PM
> > Subject: Re: [Freesurfer] wm surface does not follow wm.mgz
> >
> > That almost certainly means there is a topological defect there. Check the
> > orig.nofix
> >
> >
> > Cheers
> > Bruce
> >
> >
> >
> > On May 23, 2012, at 2:49 PM, Leon <leonado78@yahoo.com> wrote:
> >
> >      Hi, FreeSurfer experts
> >
> > I have seen similar posts before but did not think that I could solve
> > the issue based on the answers from the previous posts. So I am
> > posting it here again. Basically, I find that white matter surface
> > does not follow the wm.mgz file (see the attached file). It is strange
> > that such problem is only located at the precentral gyrus. I checked
> > the white matter original surface and the inflated surface and they
> > look fine. I also went through wm.mgz slice by slice to see if there
> > is abrupt gradient between slices and it doe not seem to have that
> > either. So I wonder if anyone would help on solving this issue.
> >
> > Thanks in advance!
> > Leon
> >
> >      <RightPreCentralGyri.jpg>
> >
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>
> <OrigNoFix_vs_WM.jpg><RightPreCentralGyri.jpg>_______________________________________________
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--
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