RE: [Freesurfer] Manual editing tips?

[Bruce Fischl]

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 mris_anatomical_stats rh
thickness for this same person.Visually, I've noticed that the pial and
wm surfaces intersects on some parts of the brain? Could this be the
problem?
Than ks again for your help,
Alex
-----Original Message-----
From:   Evelina Busa [mailto:[EMAIL PROTECTED]
Sent:   Sat 5/7/2005 6:51 AM
To:     Fornito, Alexander
Cc:
Subject:        RE: [Freesurfer] Manual editing tips?
Hi Alex,
The normalized brain volume is created quite early on in the process
--
first the raw data are converted from their native scanner format,
then
motion corrected into what we call the 'orig' volume, then the
intensities are normalised to what we call the T1 volume, then the
non-brain
tissues are stripped from the T1 and we have the 'brain' volume.
The WM volume is then segmented out of the brain volume, and that's
what
is edited, for the purpose of getting the surface topologically
correct.
So, although it's mostly true that the brain volume is what is used to
calculate the pial/white boundary and cortical thicknesses (thus
arbitrary edits to the WM volume won't change that), if the initial
surface (which is defined by the wm edits) is far enough off, it won't
find the correct location during the final surface deformation.
In other words, it's important that the wm edits be accurate, but rest
assured that your edits are not what Freesurfer ultimately uses to
determine the cortical surfaces.
This should be welcomed as good news!  ;)
Good luck!
On Thu, 5 May 2005, Fornito, Alexander wrote:
Hi once again,
Just wanted to also clarify your response:
"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."
This has me a bit confused. What exactly is the normalized brain
volume (ie., created at which step/which file name?), and if edits on
the WM volume don't affect thickness (and presumably therefore, surface
estimation) why do we edit them at all? There's something I a missing,
and I'd greatly appreciate it if you could point me in the right
direction!!
Thanks again,
Alex
-----Original Message-----
From:   Evelina Busa [mailto:[EMAIL PROTECTED]
Sent:   Thu 5/5/2005 4:23 AM
To:     Fornito, Alexander
Cc:
Subject:        RE: [Freesurfer] Manual editing tips?
Hi again,
The posterior portion connects to calcarine which makes the big
defect.
The tutorial pictures and instructions for filling in the posterior
ventricles may give the impression that *any* apparent "hole" in the
WM volume will necessarily result in a topological defect, but that's
not
true.  It depends on whether that hole when looked at in 3D will
still be
a hole.  This is kind of hard to gauge when going through the slices
but
the inflated surface tells the story.
Good luck and sorry for my delayed response!
On Wed, 4 May 2005, Fornito, Alexander wrote:
Thanks for your comprehensive response! Very helpful!
Just wanted to clarify, why is it that the posterior portion of the
lateral ventricles, and not the anterior portions, result in topological
defects, if both appear as 'islands' inside the white matter?
Thanks again,
Alex
        -----Original Message-----
        From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
        Sent: Wed 5/4/2005 2:06 PM
        To: Fornito, Alexander
        Cc: freesurfer@nmr.mgh.harvard.edu
        Subject: Re: [Freesurfer] Manual editing tips?

    Hello Alex,
	A helpful approach when editing the lateral ventricles is to
view the
	sagittal plane; usually the filling should not extend anterior
to the
	point where the posterior fornix is erased.   The axial plane is
also
	useful.  The tutorial focuses on the coronal plane, which isn't
optimal
        for determining when to stop the edits (moving anteriorly).
	Smoothness of the surface -- the aim of manual editing is
chiefly to
	eliminate the defects that the subsequent automated topology
fixer
	cannot likely handle, whether or not they are easily visible on
the
	surface.  The large defects outlined in the manual are pretty
safe bets
        for editing in this respect, and there are other anatomical
        idiosyncrasies that you'll find in normal or other populations
which you
	can anticipate having to edit in order to "force" a
topologically
	correct surface, e.g. brain lesions resulting in large gaps of
white
        matter voxels.
	It's hard to predict what will need to be edited without having
done
	quite a few brains, but in general your choice is to either:  a)
err on
	the side of caution and edit whatever corresponds with a visible
defect
	on the inflated surface,  or;  b)  run the topology fixer first
to see
	how/whether it could handle the remaining visible defects, with
the risk
	that you might need to edit the extra defects afterward, anyway.
And of
	course the Euler number calculation can give you precise
information
	about a hemisphere's topological defect index.   I'd recommend
routinely
	editing the standard areas that lead to topological defects (as
per the
	tutorial), then running the automated topology fixer, unless it
is a
	structurally unusual brain with quite large visible defects.
The
	automated topology fixer by and large works, and it's usually a
better
	use of operator time to wait on this 5-hour process rather than
spend an
        hour or so, perhaps pointlesssly, doing extra edits first.
	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.
        Hope this helps, if not, ask more -
Hi all,
I've noticed that the tutorial's instructions for manual editing of
	the ventricles stops at about slice 92 (for Bert's data). Does
this mean
	only the posterior portion of the lateral ventricles need to be
filled,
	and that there is no need to continue to fill in the ventricles
up to
	the anterior horns as well?
Also, a couple more queries re: manual editing:
- Sometimes I can see handles emanating from the surface that are
not
	in the areas listed in the manual. Are there any guidelines re:
what
	should be deleted as opposed to what should be filled?
- Are there any guidelines for just how smooth the brain surface
	should be before moving on to create the final surface? Some of
my
        surfaces appear quite smooth (ie., no obvious handles), although
        somewhat bumpy, esp. around the posterior-dorsal areas.
- Am I correct in assuming that what is tissue is edited or not
will
	affect surface generation and hence estimates of cortical
thickness? In
        this case, is it advisable to carry out some kind of reliability
        analysis for morphmoteric studies?
Thanks for your help,
Alex
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