Hi Boris,
For now I am taking the geometric average between pial and white
surface coordinates.
Is that the right way to do it, or is there a more precise way?
To obtain a surface that lies in the geometric middle between white and
pial surfaces, it is correct to take the average of the coordinates.
This surface is not guaranteed to coincide with any biologically
meaningful cortical layer, but it has advantages over pial or white for
not over/under-representing gyri or sulci.
Also: If I decided to represent the stuff on the mid-surface, would it
then also make sense to also take the average of pial.avg.area.mgh
white.avg.area.mgh as the area estimation at each vertex?
No no, to take the average of the areas is not the same as take the
average of the coordinates, because the areas depend quadratically on
linear distances. An average of the areas would not necessarily
represent a surface at the middle, most likely representing an
(invisible) surface that would be closer to the white in some places and
closer to the pial in others, depending on local folding.
Hope this helps!
All the best,
Anderson
On 2011-05-12, at 4:08 PM, Douglas Greve wrote:
Yes, the avg.area files have the average over the input subjects at each
vertex. I've used it to overcome this problem.
doug
On 5/12/11 8:04 AM, Bruce Fischl wrote:
Hi Boris,
1. Doug can say for sure, but I believe so.
2. No. The mid surface doesn't correspond to any boundary in the
image and
so we are always hesitant to provide any morphometric measures for
it. We
are working on a more explicit estimation of the location of layer
IV, but
that is a future direction. You could generate it yourself easily enough
though.
cheers
Bruce
On Thu, 12 May 2011, Boris Bernhardt
wrote:
Hi Bruce,
Thanks a lot for your reply.
2. The surface area of fsaverage is less than any individual, so
you *definitely* don't want to use it. You should map the ROI back
to individuals and compute it in the native space.
I have two follow-up questions:
1) Do .pial.avg.area.mgh and/or .white.avg.area.mgh then store the mean
native space surface areas for the individuals that were used to create
fsaverage, and can I use these values to approximate the surface
area of my
ROIs then?
2) Do the avg.area files also exists somewhere for the
half-thickness mid-surface? If not, does it make sense to
approximate the mid-thickness surface area at each vertex by taking
the mean of the corresponding pial.avg.area and white.avg.area entries?
Many thanks,
Boris
cheers
Bruce
On Wed, 11 May 2011, Boris Bernhardt wrote:
Hello Freesurfer-experts,
I just analyzed some FreeSurfer cortical thickness data that have
been surface-resampled to fsaverage (using mris_surf2surf with -s
fsaverage).
For the visualization and reporting of my findings, I have a two
questions:
1. Is there anything that conceptually speaks against showing my
results on non-inflated surfaces of fsaverage, such as the white
matter surface, the pial surface, or even a mid-surface model?
2. I have a couple of ROIs defined on the surface of fsaverage
and want
to report the surface area of a given ROI in mm^2. Should I
calculate the area of a ROI directly from the given surface of
fsaverage, or to take the area computations from
?h.pial.avg.area.mgh/?h.white.avg.area.mgh which represent the
averages of the individuals that went into fsaverage.
I am asking because I was slightly unclear of the wiki-instructions:
https://surfer.nmr.mgh.harvard.edu/fswiki/GroupAverageSurface
suggests to use ?h.pial.avg.area.mgh;
on the other hand, the more recently edited
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAverage
says that "The surface area of the new average subject
(fsaverage) is that of a typical subject"
I am using freesurfer 4.5.0.
Hope my questions make sense and thank you very much for
answering them,
Boris
---
Boris Bernhardt, PhD
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstr. 1a, 04103 Leipzig, Germany
p: +(49) 341 9940 2658
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---
Boris Bernhardt
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstr. 1a, 04103 Leipzig, Germany
p: +(49) 341 9940 2658
e: bernha...@cbs.mpg.de <mailto:bernha...@cbs.mpg.de>
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