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
e: bernhardt@cbs.mpg.de
http://www.cbs.mpg.de/~bernhardt
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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: bernhardt@cbs.mpg.de
http://www.cbs.mpg.de/~bernhardt
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