Hi,
So if the volumes are estimated from the surfaces and not aseg.mgz, does
this mean it is unnecessary to edit aseg.mgz? Or is it still necessary,
but only for the subcortical structures? Is it best to make pial
surface/wm.mgz edits and control points for grey and white matter, and
aseg.mgz for the subcortical volumes?
I hope I am being clear enough.
Thanks,
Chris
Bruce Fischl wrote:
Hi Jim,
yes, I think that should be fine
Bruce
On Mon, 10 Dec 2007, James N. Porter wrote:
Hello Bruce-
From the wiki, I gather that I would rerun recon-all from -finalsurfs
onward, as that is the step that calls make_final_surfaces. In order
to insert the fix_mtl flag I'll have to run that section via a
separate command line outside of recon-all. Are there any other
subsequent steps that require manual intervention or nonstandard
parameters, or would something like the code below do the work?
for S in $SUBJ; do
for H in $HEMI; do
mris_make_surfaces --noaparc --mgz -T1 --fix_mtl brain.finalsurfs
$S $H
done
recon-all -s $S -cortribbon -autorecon3
done
Thanks,
Jim Porter
Graduate Student
Clinical Science & Psychopathology Research
University of Minnesota
Bruce Fischl wrote:
Hi Jim,
you can actually run mris_make_surfaces with -fix_mtl and it will
inhibit all deformations in these regions. I didn't enable that by
default as I was afraid it would mean missing a bit of entorhinal.
In general it doesn't really matter as the gray and white volumes
computed from the surfaces will exclude amygdala and hippocampal
voxels that are interior to the surface.
For your second question: we use the gray matter volume estimated
from the surfaces instead of the aseg, as we find it to be more
accurate than the voxel-based techniques.
cheers,
Bruce
On Tue, 27 Nov 2007, James N. Porter wrote:
Hello FreeSurfer Folks-
I've seen several threads in the archives discussing the expected
inaccuracies in the pial, white, and orig surfaces running through
subcortical structures. However, I've been unable to ascertain
exactly how much and what kind of inaccuracy is acceptable. It
makes sense to me that if the entirety of a structure, say the
amygdala, were included or excluded in the pial surface, then it
would be easy to adjust later measurements. However, what we see in
all of our subjects is a random pattern of half in/half out, with
weird shapes, when it comes to the surfaces running in and around
subcortical structures. For example, take a look the image at this
link.
http://www.tc.umn.edu/~norb0062/Amygdala.tiff
There you will see the how the hippocampus and amygdala are both
half included in the pial surface. Item 1 has a strange
guitar-shaped chunk taken out of the amygdala, and item 2 has a
triangle and a peanut-shaped area removed. Are these the types of
expected and accepted inaccuracies, or is there something afoul
here that needs to be corrected?
I have one other question regarding the interactions of aseg and
surface information. Item 3 in the image points out a section of
apparent subdural matter that has been classified as grey matter in
the aseg but has been excluded from the pial surface. When the
final statistics are spit out of recon-all, is there a section of
processing that says something like, "Based on the aseg values my
grey matter volume is X, but since Y of that is outside of the pial
surface I'll call my total volume X-Y"? Or, is this another item to
that requires correction and re-running of recon-all?
Many thanks in advance,
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