Hi Eli,
the .annot files have the proper colortable embedded in them (and have for a long time), so they'll never be wrong. For the aseg just use the FreeSurferColorLUT.txt file.
cheers, Bruce
On Thu, 2 Mar 2006, Eli Diamond wrote:
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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