Hi Leon,
On May 25, 2012, at 12:55 PM, Leon wrote:
> Hi, Sebastian
>
> I think you are right: the final wm surface not only considers wm.mgz and
> filled.mgz, but the brain.finalsurf.mgz as well. Even though I deleted these
> voxels with low intensity values in the wm.mgz, the lump at the precentral
> gyrus still show in the final wm surface.
Yeaeh I struggled with this in the past, but you can always just use
the orig surface.
> I assume this is due to the high variations of the subjects in this area,
> causing high intensity values in brain.finalsurf.mgz in these regions.
Are you in any case building a surface for an average subject? In that
case it would be better to reconstruct all input individuals and create an
averaged surface from those. A lot of NHP people would be happy if a good
averaged free surfer monkey would exist (that would mean that you have to build
your own template out of all the individual surfaces though).
>
> Also, loading wm.mgz as a segmentation mask works for detecting the voxels
> with low values. Adjusting only the brightness and contrast seems not enough
> (see the attached file).
Well in my laptops screen it works well enough. But this is really
irrelevant as the orig surface does not include this bit of cortex, so the
value of 1 does not hurt there…
Best
Sebastian
>
> Thank you!
> Leon
>
> From: Sebastian Moeller <[email protected]>
> To: Leon <[email protected]>
> Sent: Friday, May 25, 2012 2:15 PM
> Subject: Re: [Freesurfer] Fw: wm surface does not follow wm.mgz
>
> Hi Leon,
>
>
>
> On May 25, 2012, at 10:51 AM, Leon wrote:
>
> > 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.
>
> Now that seems weird, as far as I know the wm.mgz should only contain
> values around 110. But that said, the orig surface looks fine so the wm.mgz
> is most likely not your problem. Please have a look at brain.mgz or
> brain.finalsurf.mgz and look for the intensities in that area. BTW
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable gives a nice
> overview aout the free surfer steps and the inputs and outputs My
> interpretation is that the whitematter surfaces take in the intensity
> gradients from brain.finalsurfs.mgz and refine the orig surface. But I have
> last used free surfer 4.5 for surface reconstruction so things might have
> changed. But please humor me and show that the brain.finalsurf.mgz at
> corresponding slices looks fine :)
>
> >
> > 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.
>
> The best workaround is to use Ctrl-b to open the brightness contrast
> dialog and set brightness to 0 and contrast to 30 (both sliders to the
> right), that way even values of 1 can be seen (to some degree).
>
> Best
> Sebastian
>
> >
> > Thank you for your help!
> > Leon
> >
> > From: Sebastian Moeller <[email protected]>
> > To: Leon <[email protected]>
> > Cc: FreeSurfer <[email protected]>
> > 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 <[email protected]>
> > > To: Leon <[email protected]>
> > > 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 <[email protected]>
> > > > To: Leon <[email protected]>
> > > > 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 <[email protected]> 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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> >
> >
> > The information in this e-mail is intended only for the person to whom it is
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> --
> Sebastian Moeller
>
> telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616
> fax: 626-395-8826
> German GSM: +49 - 15 77 - 1 90 31 41
> mobile: +1-626-325-8598
> +1-626-807-5242
> US CDMA: +1-626-807-5242
> [email protected]
>
> Division of Biology
> MC 114-96
> California Institute of Technology
> 1200 East California Boulevard
> CA 91125, Pasadena
> USA
>
>
>
> <WM_Contrast_WM_Seg_Brain.jpg>
--
Sebastian Moeller
telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616
fax: 626-395-8826
German GSM: +49 - 15 77 - 1 90 31 41
mobile: +1-626-325-8598
+1-626-807-5242
US CDMA: +1-626-807-5242
[email protected]
Division of Biology
MC 114-96
California Institute of Technology
1200 East California Boulevard
CA 91125, Pasadena
USA
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