Dear Sermin,
Are you sure that these are not connected in the other
planes? In 3D if you have slightly jagged boundaries
then sometimes it looks like there is a hole in one 2D slice,
but if you look at the other slices you'll see that it is
actually just part of the boundary.
I was expecting to get the nifti images, rather than
screenshots, so I can't really say anymore than that.
I would also look at the non-boundary-corrected image
and see if it might be the case that the boundary
correction is not doing well and might be changed.
All the best,
Mark
On 24 May 2011, at 14:06, SERMIIIN Dz wrote:
> Dear Mark
>
> Thank you for your reply. For your information we are dealing with children in the age 7-12 years old. I've uploaded 2 examples illustrating my problem. The reference number is 700071.
> Hope to hear from you soon.
> Thanks a lot,
>
> Sermin Dzaferov
> Bachelor-student
> Technical University of Denmark,
>
>
>
>
> > Date: Mon, 23 May 2011 18:03:08 +0100
> > From: [log in to unmask]
> > Subject: Re: [FSL] segmentation error
> > To: [log in to unmask]
> >
> > Dear Sermin,
> >
> > You should not get holes in structures.
> > You should also not use FIRST with children younger than 4 years
> > old, as that is the limit of the age range for the training data used.
> > If it helps you can upload an example segmentation (and original
> > image) to:
> > http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
> > and send us the reference number so that we can see the problem.
> >
> > All the best,
> > Mark
> >
> >
> > On 23 May 2011, at 15:57, SERMIIIN Dz wrote:
> >
> > > Hi
> > >
> > > My partner and I have segmented some subcortical structures using FSL-FIRST. As we want to check the segmentation in FSL-view, we discover some "unsegmented" areas which appear as a hole. Why does this happen? and how can this be avoided? Our study goes on children and the brain-maturation. Does the program have any problems dealing with a child's brain? I've tried to read the Technical report/thesis by Brian Patenuade but without success.
> > >
> > > Thanks in advance.
> > >
> > > /Sermin Dzaferov
> > > Bachelor-student
> > > Technical University of Denmark,
> > >
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