Hi all, 

I'm having trouble with V1 labels that are mapped automatically in freesurfer. I've noticed that there are holes in the label when I load it onto a 3d brain in tksurfer. This happens more often for the left hemisphere and not so much for the right. I've found the problem persists even after doing manual edits of the borders and fixing the brain extraction. I was just wondering if anyone has had the same problem or knows how to fix it (see message previously posted below).

Thanks!

Hi Doug,

Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below:

recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.nii.gz

then

recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.nii.gz

I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right.  When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem?  Is this label the same as the Hinds label and if not, should I run that instead?

Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the process and I wouldn't want to mess with that too much.


Thanks!



On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
>
> How did you do the transfer? What was your cmd line?
> doug
>
> On 09/10/2013 05:31 PM, krista kelly wrote:
> > Hello,
> >
> > I am looking at cortical thickness and surface area using Freesurfer.
> > I have transferred label V1 from freesurfer onto the brains of my
> > participants and when I view them on the inflated brains in tksurfer ,
> > I notice that there are holes in the label. Is this an issue when
> > calculating mean cortical thickness and total surface area
> > estimations? Should I fill these in somehow?
> >
> > I've attached a picture to show as an example. Please let me know if
> > the picture cannot be viewed.
> >
> > Thanks!
> > Krista
> >
> >
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
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