yeah, the ?h.area file is the area of the ?h.white surface. The surface
specified for mris_convert is only used to get the # of
vertices/faces/etc... I think the only way to write out the area of other
surfaces is to read them into tksurfer and use the tcl commands:
% set area lh.pial_area
% write_binary_areas
cheers,
Bruce
On Thu, 5 Jan 2006, Fornito, Alexander wrote:
Great, thanks.
On another issue, I've noticed that using mris_convert to convert ?h.area to
ascii produces the same area values in the resulting file, irrepsective of
whether pial or white surfaces are specified in the command. This contrasts
mris_anatomical_stats, which gives different values. Is it possible to extract
pial and white surface area separately for sulcal and gyral regions?
Thanks again,
Alex
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
________________________________
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thu 5/01/2006 12:42 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] .sulc in tksurfer
yes, that makes sense.
On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi Bruce,
I'm trying to extract thickness for sulci and gyri separately. From what I
understand, positive .sulc values suggest sulci and negative .sulc values suggest
gyri. I'd like to play around with this distinction (e.g., call everything with a
.sulc value < .35 'gyral'), and am wandering if adjusting the midpoint in
tksurfer allows me to precisly visualize what changing this threshold does.
Basically, I'd like to know if it's correct for me to pick a midpoint I'm happy
with in tksurfer, say .35, than go back and split the .thickness file into
vertices with .sulc values above and below .35, knowing that this distinction
between sulcal and gyral will correspond to the one shown by the colour display I
visualized in tksurfer.
I'm pretty sure the values in the tksurfer threshold midpoint scale correspond
to those in the curvature file, since they seem to change depednig on the
curvature file loaded (e.g., the range for .sulc files is different to the
range for .thickness files). Just want to double-check.
Hope this makes sense,
Alex
the threshold midpoint in the curvature display just sets where the
transition is from red to green (or light gray to dark gray if using
binary colors)
On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi,
Does the 'threshold midpoint' value in tksurfer's curvature display control
correspond to values in the .sulc file (assuming the .sulc file is loaded), or
are they arbitrary values? For example, if I set the value to .50, does this
make all vertices with a .sulc value of .50 or less lighter (lighter, if using
binary colouring)?
Thanks,
Alex
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
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