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 Bruce Fischl <fis...@nmr.mgh.harvard.edu>
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 NHP data.
cheers
Bruce
On Fri, 4 Oct 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
another update: I now set more than 2000 control points which
significantly
improved the pial surface. I am still fighting with a few places
though, in
particular medially and orbitofrontal.
I attached a screenshot of the problem that I am facing medially. Is
this a
situation where even more control points can help?
Orbitofrontally, the issue seems to be that I cannot clearly discern
white
matter from some point on, so there is nothing to grow out from
Caspar
2013/10/3 Caspar M. Schwiedrzik <cschwie...@rockefeller.edu>
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. See occipital lobe.
Caspar
2013/10/3 Bruce Fischl <fis...@nmr.mgh.harvard.edu>
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 Fischl
<fis...@nmr.mgh.harvard.edu>
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 the coil) and some of
the brain pretty
dark (far away from the
coil). In the screenshot that I
sent you, there is
some gray matter that has
values between 95-100, which is
well captured by the
pial surface, while the
grey matter in the more medial
areas has values
between 70 and 80. The
transition where the pial surface
starts to fail is
when the gray matter
values drop from above 90 to below
90.
Caspar
2013/10/3 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
hmmmm. 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
<fis...@nmr.mgh.harvard.edu>
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
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 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
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.
Interestingly, the
pial
surface growing
process fails
where the grey
matter
is
fairly dark. I have
tried several rounds
of
normalizing using the
N3
tool
but that didn't
change
anything.
Thanks for any advice
on this,
Caspar
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