if you can
On Mon, 7 Oct 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
it sounds very possible that the bright spots (which are gadolinium-enhanced
blood vessels)
cause the problem.
I guess I will have to remove them. Does it make sense to manually delete them
from brain.mgz?
Caspar
2013/10/7
Hi Bruce,
it sounds very possible that the bright spots (which are
gadolinium-enhanced blood vessels) cause the problem.
I guess I will have to remove them. Does it make sense to manually delete
them from brain.mgz?
Caspar
2013/10/7 Bruce Fischl
> Hi Caspar
>
> I'm not sure what to tell you. Th
Hi Caspar
I'm not sure what to tell you. There are bright spots and rings out near
the pial surface that are probably part of your problem, and the images
even in the zoom look really inhomogenous. I don't think we ever have to
add thousands of control points, but I have no experiences with NH
Hi Bruce,
sorry, I meant to say that data is conformed.
It is primate data. I am having trouble with this particular data set only;
the other ones are at the same resolution and worked fine.
I am attaching another screenshot to show that the control points
unfortunately do not solve the problem. Se
Hi Caspar,
that's probably part of the problem. Is this human data? If you actually
run it at 1mm (conforming it) does it work better?
Bruce
On Thu, 3 Oct 2013,
Caspar M. Schwiedrzik wrote:
It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm.
Caspar
2013/10/3 Bruce Fisch
It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm.
Caspar
2013/10/3 Bruce Fischl
> what resolution?
>
> On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
>
> This was a fairly regular MPRAGE, unfortunately not very well optimized
>> for
>> contrast. However, the main issue see
what resolution?
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
This was a fairly regular MPRAGE, unfortunately not very well optimized for
contrast. However, the main issue seems to be that the data were acquired
with a surface coil here. That made some of the brain extremely bright
(close to
This was a fairly regular MPRAGE, unfortunately not very well optimized for
contrast. However, the main issue seems to be that the data were acquired
with a surface coil here. That made some of the brain extremely bright
(close to the coil) and some of the brain pretty dark (far away from the
coil)
h. Can you tell us more about the acquisition?
On Thu, 3 Oct 2013,
Caspar M. Schwiedrzik wrote:
the white matter is mostly between 100 and 110 in these regions. at least in
the center of the wm, the voxels are almost all 110.
caspar
2013/10/3 Bruce Fischl
is the WM in those region
the white matter is mostly between 100 and 110 in these regions. at least
in the center of the wm, the voxels are almost all 110.
caspar
2013/10/3 Bruce Fischl
> is the WM in those regions already close to 110? No, there is no way to
> normalize GM intensity (it has too much biological variabil
is the WM in those regions already close to 110? No, there is no way to
normalize GM intensity (it has too much biological variability over the
brain)
On Thu, 3 Oct 2013, Caspar M.
Schwiedrzik wrote:
> Thanks, Bruce. The problem is fairly extensive. There is no way to do
> normalize grey matte
Thanks, Bruce. The problem is fairly extensive. There is no way to do
normalize grey matter intensity (the white surface looks pretty good)?
Caspar
On Thursday, October 3, 2013, Bruce Fischl wrote:
> Hi Caspar
>
> try putting control points in the white matter where the pial surface
> doesn't get
Hi Caspar
try putting control points in the white matter where the pial surface
doesn't get out far enough.
cheers
Bruce
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
> Hi Freesurfer Experts,
> I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having
> trouble getting the p
Hi Freesurfer Experts,
I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having
trouble getting the pial surface to go all the way through the grey matter.
Please see screenshot attached. These data were acquired with a surface
coil and the grey matter varies a lot in intensity. I
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