Wouldn't that occur by using the MNI tools anyway?
-----Original Message-----
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wed 5/18/2005 9:39 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] WMFilll and talairach coordinates
just that you have sacrificed resolution.
On Wed, 18 May 2005, Fornito,
Alexander wrote:
> Other than that though, should there be any problem if I align my
images prior to starting with freesurfer?
> Provided I align to the MNI 152 brain, it should still be in
talaraich space...
>
> -----Original Message-----
> From: Bruce Fischl [mailto:[EMAIL PROTECTED]
> Sent: Wed 5/18/2005 10:55 AM
> To: Fornito, Alexander
> Cc: peggy christidis; freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] WMFilll and talairach coordinates
>
>
>
> 1. to report talairach coords.
> 2. To get cutting planes to separate the hemispheres when the
head is at an
> angle.
> 3. To find the callosum if other heuristics fail.
> 4. To pick some control points in the white matter for intensity
> normalization.
>
> cheers,
> Bruce
>
>
> On Wed, 18 May 2005, Fornito, Alexander
> wrote:
>
> > Hi,
> > Just to toss my hat into the ring, can I ask why the
transform is kept. Is it used later on?
> > I've also been having trouble with the MNI tools, and was
thinking of using FLIRT or AIR to align the images first. What is th point of
having the .xfm?
> > Thanks,
> > Alex
> >
> > -----Original Message-----
> > From: Bruce Fischl [mailto:[EMAIL PROTECTED]
> > Sent: Wed 5/18/2005 6:00 AM
> > To: peggy christidis
> > Cc: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] WMFilll and talairach
coordinates
> >
> >
> >
> > Hi Peggy,
> >
> > we don't apply the transform, just keep it around, so
blurring isn't a
> > problem. I don't know if AFNI knows how to write out
.xfm files (the mni
> > transform format), but that would be the best solution.
> >
> >
> > Bruce
> >
> > On Tue, 17 May 2005,
> > peggy christidis wrote:
> >
> > > Hello,
> > >
> > > I'm having a bit of trouble with the "Create Surface"
step in FreeSurfer. I
> > > have a single mprage scan that creates a decent first
pass surface, but
> > > there's still some brainstem and cerebellum attached
to it. I followed the
> > > troubleshooting guidelines in the FreeSurfer manual
regarding Failure of
> > > Automatic Cutting Planes. I went to Expert
Preferences --> WMFill, and
> > > inputed the appropriate coordinates to separate the
brainstem and cerebellum.
> > > The coordinates I used were not in Talairach space,
but I assumed this was
> > > okay because the manual says to use original
coordinates if you don't have
> > > Talairach coordinates. However, when I re-ran
"Create Surface", nothing
> > > happened (i.e., filled volume and surface both still
show the
> > > pons/cerebellum/brainstem attached). I read through
the FreeSurfer mailing
> > > list archives and read that Talairach coordinates are
indeed needed.
> > >
> > > Here's my question: The volume I'm using shows a
head that's slightly tilted
> > > about 10 degrees to the left, so I should probably do
the Taliarach
> > > transformation anyway. However, I don't have the
mni_tools installed on my
> > > computer (I had major installation problems with
them). Anyway, could I do a
> > > taliarach transformation outside of Freesurfer (like
in AFNI) and then
> > > tranfer that talairached volume to FreeSurfer? My
concern is that the
> > > transformation will blur the volume, making
segmentation difficult. What
> > > should I do?
> > >
> > > Thanks,
> > > Peggy
> > > _______________________________________________
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> > >
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> > >
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> >
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> >
> >
> >
>
>
>
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