Dear Mark
I have tried again and have uploaded the nifti images with the reference number: 380594.
Hope that it is better.
Thanks a lot
Sermin Dzaferov
> Date: Tue, 24 May 2011 14:19:27 +0100
> From: [log in to unmask]
> Subject: Re: [FSL] segmentation error
> To: [log in to unmask]
>
> 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,
> > > >
