just visually inspect the surfaces, and if they look accurate you're all
set.
On Thu, 12 May 2005, Fornito, Alexander wrote:
So generally speaking, the thickness values obtained before and after manual
editing should be quite similar across the brain.
How smooth should the surface be before you can move on? I tend to get slight
protrusions here and there across the surface and it generally appears to be
smooth. Is it just a matter of checking the euler numbers and being happy with the white
and pial surfaces when overlaid on the T1?
Also, beyond fix topology correction, what additional processing is done when running
create final surfaces?
Sorry to labour the points, just trying to get an idea of what is/isn't
acceptable.
Many thanks,
Alex
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wed 5/11/2005 11:30 PM
To: Fornito, Alexander
Cc: Evelina Busa; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Manual editing tips?
Hi Alex,
the thickness is the distance between the ?h.white and ?h.pial surfaces.
These are initialized with the wm volume, so if it is too far off, they
won't converge to the right answer. It's pretty robust, but if you're
missing 5-6mm of wm at the crown of a gyrus for example, it probably
won't recover the entire thing.
cheers,
Bruce
On Wed, 11 May 2005, Fornito, Alexander
wrote:
Hi,
Just a bit confused re: Evelina's comment:
The surfaces are generated using the normalized brain volume and not
strictly the segmented white matter volume, so edits on the WM volume
do
not arbitrarily affect the cortical thickness measures.
And Bruce's comment:
the manual editing can certainly effect the final surface placement.
Mostly if a large piece of wm is missed, or sometimes we edit the
brain
volume
directly to remove some dura that gets kept within the pial surface.
My questions are:
- What surfaces (and at what point) is the thickness calculated from?
Is
it from the edited wm and pial surfaces used when create final
surfaces
is run?
- To what degree do variations in manual editing affect thickness
estimates?
- Would it be advisable to perform a reliability study to make sure
the
manual editing process does not affect thickness estimates too much?
Thanks again,
Alex
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Monday, May 09, 2005 10:39 AM
To: Fornito, Alexander
Cc: Evelina Busa; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Manual editing tips?
Hi Alex,
the manual editing can certainly effect the final surface placement.
Mostly
if a large piece of wm is missed, or sometimes we edit the brain
volume
directly to remove some dura that gets kept within the pial surface.
The qsphere is used to guide the topology correction, but itself is
not
corrected, so it won't have an Euler # of 2. You can't run
mris_euler_number on thickness, since it's not a surface (but a scalar
field over the surface). You can run it on the ?h.white and ?h.pial
surfaces if you want.
There is actually a means for manual intervention in the spherical
morph,
but it's rarely needed.
cheers,
Bruce
On Mon,
9 May 2005, Fornito, Alexander wrote:
Hi Evelina,
Let's see if I understand you...
The pial and white boundaries are calculated on the intensity
normalized/motion/corrected/averaged image, irrespective of manual
editing.
Then the manual editing is only done to obtain a surface
representation that is visually accurate for display of inflated
and/or
flattened surfaces, but has not effect whatsoever on the surface
estimation used for thickness and curvature calculations?
How about inter-subject registration? Is it affected by manual
editing?
I've been having problems with my surfaces and am trying to work out
what's going wrong. My euler numbers are 2 for the white and pial
surfaces, but I get the following message when I comupte it for the
qsphere (for one rh.qsphere case):
euler # = v-e+f = 2g-2: 156076 - 468733 + 312496 = -161 -- 81 holes
F =2V-4: 312496 != 312152-4 (-348)
2E=3F:937466 != 937488 (-22)
total defect index = 185
Also, I get a segmentation fault when I run
