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,
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
