Hi Keyma!
Could you send the command you used, and possibly more output? (say, the
last 15 lines before the error message?)
Thanks!
On Mon, 26 Jul 2004, Chekema Nayasha Prince wrote:
Hello,
I'm trying to normalize an MPRAGE dataset and I received the following message
from the mri_normalize:
MRI
Hi Kevin,
Are you using Talairach co-ordinates? Is the talairach.xfm okay -- does
it look reasonable?
On Thu, 9 Sep 2004, Kevin DeSimone wrote:
> i have a subject (who is not out of the ordinary) where the cerebellum
> is sticking to one hemisphere. i make the usual edits on the
> segmenta
Hi
If you are new to fMRI then it's likely you will be dissatisfied with the
level of exchange on the freesurfer mailing list. Might we recommend
several excellent online sources for NMR neophytes? This seems like a
good one with links to some very active fMRI research centers:
http://www.
On Wed, 5 Jan 2005, Joongnam Yang wrote:
> Hi,
>
> Sounds like trivial questions...
>
> (1) How do you check if the talairach.xfm is OK?
You load the mri/orig in tkmedit as main volume, then:
File--> Load Transform for Main Volume --> and select
SUBJECTNAME/mri/transforms/talairach.xfm *or
It isn't useless but being a GUI it is less stable, and the command line
outputs a recon-all.log, at least the tail line of which you should
include with any enquiries to the freesurfer list, otherwise it is
sometimes difficult to say what caused an undesirable freesurfer result.
On Fri, 14 J
Hi Wan,
Looks like it had difficulty automatically finding the corpus callosum
cutting plane, so you'll have to give it the coordinates manually. To do
so:
Load the WM volume, and click in the dead center of the corpus callosum,
in coronal view. Then switch to a sagittal plane. You should
Hi Margaret,
How does the talairach transform look?
On Wed, 2 Feb 2005, Margaret Duff wrote:
> Hello, I am trying to reconstruct brains of patients who had one
> structural scan during each of 2 visits, a month apart. I averaged the
> two images together, but since they are from different vis
t also
> has a rimming/shadowing effect.
>
> On Wed, 2 Feb 2005, Evelina Busa wrote:
>
> >
> > Hi Margaret,
> >
> > How does the talairach transform look?
> >
> > On Wed, 2 Feb 2005, Margaret Duff wrote:
> >
> > > Hello, I am tryin
not control for the position of the coil, etc.), then
definitely be prepared to ditch the worse scan. Unfortunately!
> On Wed, 2 Feb 2005, Evelina Busa wrote:
>
> > Hi again,
> >
> > If the shadowing/rimming effect appears to be because of an artifact in
> > one o
brain volume, and it looks better, but also
> has a rimming/shadowing effect.
>
> On Wed, 2 Feb 2005, Evelina Busa wrote:
>
> >
> > Hi Margaret,
> >
> > How does the talairach transform look?
> >
> > On Wed, 2 Feb 2005, Margaret Duff wrote:
> >
>
Hi Daniel,
Is it possible to get the original dicom data? You said the data were
already processed by Freesurfer when they got to you, so maybe whoever
gave them to you can point you to the whereabouts of the raw dicom files?
Ev
On Tue, 20 Sep 2005, Daniel Goldenholz wrote:
Hi Bruce
I a
Hi Dahlia
Since it seems unclear whether or not you edited the WM volume of this
second subject whose surface files were overwritten, it might be helpful
for you to first look at the recon-all.log text files in that subject's
scripts/ directory, to see what commands you ran.
Probably what h
rect surfaces from the (currently correct) mri/wm?
Thanks!
Dahlia.
On Thu, 27 Oct 2005, Evelina Busa wrote:
Hi Dahlia
Since it seems unclear whether or not you edited the WM volume of this
second subject whose surface files were overwritten, it might be helpful
for you to first look at the r
e is still
correct, will I now get the correct old surfaces?
Thanks!
Dahlia.
On Thu, 27 Oct 2005, Evelina Busa wrote:
Hi again,
Yes, assuming you are using the same version of FreeSurfer and since the WM
volume is the same, the new surfaces you created should be similar to
the Septembe
Hi Aaron,
First, is it something simple and annoying like that your script doesn't
look for an orig.mgz volume (vs. the 'orig' which was standard until fairly
recently)? I have needed to edit my scripts to accommodate for this.
okay!
On Wed, 2 Nov 2005, Goldman, Aaron (NIH/NIMH) wrote:
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