-----Original Message-----
From: Fornito, Alexander
Sent: Mon 5/9/2005 1:14 PM
To: Bruce Fischl
Cc:
Subject: RE: [Freesurfer] Manual editing tips?
That did the trick. So then the ?.thickness file contains data needed
to calculate thickness stats (and I assume the same is true for the ?.sulc and
?.curv, and ?.area files). Is it possible to visualize them? I've noticed that
you display thickess in fig 2 of you PNAS paper. I was wandering if there is an
output surface that can be overlaid onto the inflated surface that displays
thickness variations across the cortex.
Thanks for your quick responses!!!
Alex
-----Original Message-----
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Mon 5/9/2005 11:52 AM
To: Fornito, Alexander
Cc: Evelina Busa; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Manual editing tips?
because thickness isn't a surface - it's a scalar field (it has no
geometry information, just a list of vertex indices and thickness
values). You can only run mris_euler_number on a surface
On Mon, 9 May 2005,
Fornito, Alexander wrote:
> Hi Bruce,
> So then if my euler numbers for the white and pial surfaces are okay,
any tips as to why I get the "Segmentation Fault" message when I run
mris_anatomical_stats rh thickness? Is this a problem with the initial wm
segmentation?
> Thanks,
> Alex
>
> -----Original Message-----
> From: Bruce Fischl [mailto:[EMAIL PROTECTED]
> Sent: Mon 5/9/2005 10:38 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
> >>>>
> >>>> _______________________________________________
> >>>> Freesurfer mailing list
> >>>> Freesurfer@nmr.mgh.harvard.edu
> >>>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>
> >>
> >
> >
>
>
>
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