you can do it here:
https://gate.nmr.mgh.harvard.edu/filedrop2/
On Thu, 3 Oct 2013, krista kelly wrote:
Sure! Where/how do I upload the subject's folder? I've tried attaching a
zipped copy to my email but it exceeds the size limit.
Thanks!
Krista
On Thu, Oct 3, 2013 at 8:23 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
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
> FileDrop:
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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>
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>
>
> The information in this e-mail is
intended only
for the person to whom it is
> addressed. If you believe this e-mail
was sent to
you in error and the e-mail
> contains patient information, please
contact the
Partners Compliance HelpLine at
> http://www.partners.org/complianceline
. If the
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.