Hi Krista
I've never seen that happen before. Can you upload this subject and we will take a look?
thanks
Bruce
On Wed, 2 Oct 2013, krista kelly wrote:
Hi Bruce,
I've tried twice to post this to the freesurfer mail list but it hasn't
worked, I'm assuming because of the attached pictures. I'm going to try this
again with only one picture and see if it works.
I'm using the V1 labels that are automatically generated during recon-all (I
think at autorecon step 28??). There are also V2 and MT labels that get
generated. Are they the Hinds ones? I'm using freesurfer version 5.0 and
have tried in 5.1 as well.
Here are the commands I ran:
recon-all -all -notal-check -cw256 -force -subjid BV20 -i
~/Desktop/New_CT_niis/BV20.nii.gz
By holes, I mean that when I look at the label on the 3d brain in tksurfer,
there are areas on the surface that are coloured in by the label. I've
attached a photograph of the left hemisphere with the V1 label overlaid.
It's even worse, and in both hemispheres, when I look at the cuneus label
automatically generated with freesurfer. Is there something I'm doing wrong?
Please let me know you're not able to see the snapshots.
Thanks!
Krista
On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
Hi Krista,
which V1 label are you talking about? And when you say holes
when you load it onto the 3D brain with tksurfer, what exactly
do you mean? Can you send us a snapshot?
Bruce
On Mon, 23 Sep 2013, krista kelly wrote:
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
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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https://gate.nmr.mgh.harvard.edu/filedrop2
>
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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