Hi, Sebastian and Bruce
I think I have found the reason: there are low intensity values at the
precentral region (~1) that are almost invisible when viewed using the gray
color scheme in FS. When I converted the wm.mgz to nifti format and viewed it
in FSL using red-yellow color scheme. They are readily shown there.
Is there any option in tkmedit that can show volume images with different color
schemes such as red-yellow or blue, green? I found the option very helpful in
detecting unwanted voxels with low intensity values when I am working on the
data in FSL.
Thank you for your help!
Leon
________________________________
From: Sebastian Moeller <sebastian.moell...@rwth-aachen.de>
To: Leon <leonad...@yahoo.com>
Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu>
Sent: Friday, May 25, 2012 1:28 PM
Subject: Re: [Freesurfer] Fw: wm surface does not follow wm.mgz
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 <fis...@nmr.mgh.harvard.edu>
> To: Leon <leonad...@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 <fis...@nmr.mgh.harvard.edu>
> > To: Leon <leonad...@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 <leonad...@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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--
Sebastian Moeller
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