[caret-users] Distorted COMPMEDWALL

Donna Dierker donna at brainvis.wustl.edu
Thu Feb 13 11:02:28 CST 2014


Hi Ahmad,

Even if your anatomical volume is in LPI orientation, I don't think your surface is.  Does the segmentation volume used to generate that surface align properly with the anatomical volume (T1/T2)?

The attached capture shows what I see when I set your fiducial surface to medial view (ferret_medial.jpg).  It doesn't look medial to me.

But the source of your compressed medial wall woes is the hole shown in the ventral view (ventral_hole.jpg).  I'm not sure this really is ventral; I suspect it might be the real medial view, but it is closer to what you see when you press the V button on the toolbar.  The fact that the subcortical stuff isn't filled in the segmentation used to generate the surface means your surface is more topologically equivalent to a sheet than a sphere, and Caret needs the latter to do its CMW/registration thing.

So can you fill the subcortical stuff and regenerate the surface, so it's more sphere-like?

Donna





On Feb 12, 2014, at 4:54 PM, Ahmad Khan <110ahmadkhan at gmail.com> wrote:

> Hi Donna,
>  
> I have uploaded the file as zip file name Data_Ferret.
> Thanks for your timely help.
>  
> With Regards
> Ahmad
>  Ahmad Raza Khan
> (Postdoctoral fellow)
> Advanced Imaging Research Center (AIRC),Division of Neuroscience
> Oregon National Primate Research Center (ONPRC)
> Oregon Health and Science University (OSHU),Portland
> Oregon- 97006
> Ph no.    503-614-3755
> Mob No.-503-799-7204
> 
> 
> On Wed, Feb 12, 2014 at 6:41 AM, Donna Dierker <donna at brainvis.wustl.edu> wrote:
> Can you trim your working directory down to a gigabyte zipped and upload it here:
> 
> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
> 
> The only other thing that comes to mind is that maybe your mesh density is so high that inflation isn't taking out enough folds for the projection to sphere / compressed medial wall thing to happen properly.
> 
> Looking at the data seems like the most efficient way to troubleshoot.
> 
> 
> On Feb 11, 2014, at 6:19 PM, Ahmad Khan <110ahmadkhan at gmail.com> wrote:
> 
> > Hi,
> >
> > I am still getting the same problem and the orientation is
> > x axis: increases left to right
> > y axis: increases posterior to anterior
> > z axis: increases inferior to superior.
> > Surface don't have any topological defects or other defects.
> >
> > Please help!
> >
> >
> > <image.png>
> >
> >  Ahmad Raza Khan
> > (Postdoctoral fellow)
> > Advanced Imaging Research Center (AIRC),Division of Neuroscience
> > Oregon National Primate Research Center (ONPRC)
> > Oregon Health and Science University (OSHU),Portland
> > Oregon- 97006
> > Ph no.    503-614-3755
> > Mob No.-503-799-7204
> >
> >
> > On Thu, Jan 16, 2014 at 5:42 PM, Donna Dierker <donna.dierker at sbcglobal.net> wrote:
> > When I see something like that, I wonder if your fiducial surface was in the right orientation:
> >
> > x axis: increases left to right
> > y axis: increases posterior to anterior
> > z axis: increases inferior to superior
> >
> >
> > On Jan 16, 2014, at 6:45 PM, Ahmad Khan <khaah at ohsu.edu> wrote:
> >
> > > Hi,
> > >
> > > I am  wondering that despite of having good fiducial surface , when I try to make inflated and ellipsoidal surface from fiducial.
> > > I get this type of COMPMEDWAL surface. Please help me in this regard.
> > >
> > >
> > > Thanks
> > > Ahmad
> > >
> > > <image003.png>
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