Hi Oliver,
you might check with Mike Chee (ccd) who has some tools for editing of
the mesh. Alternatively you could draw in some white matter (even if you
can't see it) to get the pial surface a closer initialization.
cheers,
Bruce
On Sat, 16 May 2009, Olivier Piguet wrote:
Thanks for the info. In severe cases of semantic dementia, you will see
overall atrophy where the anterior temporal pole becomes almost non existent
(combination of neuronal loss and white matter loss), probably also
contributing to reduced white/grey differentiation.
Is there a way to manually trace the pial surface on these slices or not?
Because I have a large group of patients with semantic dementia that I would
like to process, I am likely to encounter this problem again in the future.
Thanks again for any suggestions and comments
Olivier
On 16/05/2009, at 0:20, Bruce Fischl wrote:
thanks Mike. Was it the same situation, where there is no nearby white
matter? I guess I don't really understand the anatomy. Is there really a
place where you have 10mm of gray matter with no underlying white matter?
Or is it unmeylinated white matter that we just can't see?
On Fri, 15 May 2009, Michael Harms wrote:
As an aside, in a Alzheimer/ elderly cohort of ~250, we had 12 subjects
that we had to exclude for what sounds like a very similar reason -- we
just couldn't get the pial surface in the anterior temporal lobe to
properly encapsulate the gray matter.
-Mike H.
On Fri, 2009-05-15 at 12:24 +1000, Olivier Piguet wrote:
That is correct. This is case of semantic dementia where left anterior
temporal region is markedly atrophic.
Olivier
On 15/05/2009, at 9:15, Bruce Fischl wrote:
so there's 10mm or so of gray matter with no underlying wm? I didn't
think that was ever the case. What pathology is this in? And you're
sure it's cortex, not amygdala? Jean: any thoughts?
On Fri, 15 May 2009, Olivier Piguet wrote:
Hi Bruce,
In the coronal plane, slice 152 is the last slice where white
matter is clearly visible. Then, slices 153-158, only grey matter
is recognised but not all of it, and slices 159-164, grey matter
is not recognised at all.
I added control points on slice 151-153 in the hope that it would
help but no luck.
Olivier
On 15/05/2009, at 8:39, Bruce Fischl wrote:
Hi Oliver,
how far away is the nearest white matter?
Bruce
On Fri, 15 May 2009, Olivier Piguet wrote:
Hi there,
I haven't received a reply to my question below.
Just to clarify, I ran autorecon1 and autorecon2 on this subject.
When examining the surfaces in tkmedit, the left temporal pole is
not included in the pial surface. Is there a way to force
freesurfer to recognise this as valid brain tissue, bearing in
mind that there is no visible white matter underneath (and
therefore the option of adding control points is not possible).
Thanks for any suggestion to resolve this problem.
Olivier
On 13/05/2009, at 12:57, Olivier Piguet wrote:
Hi there,
I've run autorecon2 on a subject who has significant unilateral
atrophy in the anterior temporal region. In the last few slices
anteriorly, the pial surface does not include what is clearly
atrophied cortical tissue without underlying white matter. What
is the method to correct for this? Looking at previous queries,
all of them refer to spots where one can manipulate the
segmentation by adding control points in the neighbouring white
matter, which is not present in this instance.
Any suggestion appreciated.
Olivier
~~~~~~~~~~~~~~~~~~~~~
Olivier Piguet Ph.D.
NHMRC Fellow (Clinical Career Development Award)
Conjoint Senior Lecturer UNSW
Prince of Wales Medical Research Institute
Barker St
Randwick NSW 2031
Australia
Voice: +61 2 9399 1113
Fax: +61 2 9399 1047
E-mail: o.pig...@powmri.edu.au
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