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, > >