Hello,
I'm hoping someone can help me clear something up about the different
parcellations now performed as part of autorecon3.
In tksurfer, when I select file-->Label-->Import Annotation, I can choose
from (for the lh, for example) lh.aparc.annot or lh.aparc.a2005s.annot. I
understand that one of these is the "old" parcellation and one is the
newer one done in (for the moment) the dev version of Freesurfer.
My question is which of the aseg.mgz's correspond to which parcellation,
and also which list in FREESUFER_HOME contains the list of labels created
by which parcellation. When I look in $FREESURFER_HOME, there are several
texts with numbered lists of cortical and subcortical areas.
Having the correct "match" between aseg and $FREESURFER_HOME/<list> seems
to be necessary in the sense that, to load a segmentation in tkmedit, the
aseg volume that is loaded must correspond to the appropriate color list
in order to get the segmentation labeled properly. My experience has been
that aparc+aseg.mgz and FreeSurferColorLUT.txt match one another and that
these correspond to the annotation lh.aparc.annot when loaded upon a
surface.
It has also been my experience that the labels/regions in
lh.aparc.a2005s.annot correspond to the list contained in
$FREESURFER_HOME/Simple_surface_labels2005.txt. I am hoping someone can
help me figure out which aseg volume, if any, contains this particular
parcellation. As it happens, my area of interest is the superior temporal
gyrus, which is subdivided in this aparc.a2005s.annot but not in the
aparc.annot, and because I will be extracting functional and volumetric
data about these ROI, I would like to work with as small anatomical areas
as possible.
The way that this ROI extraction works (as the scripts I am using are set
up) involves inputing a particular aseg volume and the number of a given
label as it appears on the appropriate corresponding list, and I have been
unable to find a way to use the cortical areas identified in the
aparc.a2005s.annot annotation.
Sorry this email is long, and likely not using the most accurate
terminology, but I hope I got my question across. Thanks so much!
Best,
Eli Diamond
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