That is just a color lookup table that has an exhaustive list of possible regions. We do not label all of these, and some of them appear in some segmentations and not in others. I don't know who (or what program) does that thalamus labeling (it is not part of a2005s). It is probably part of the tract-based labeling that Zeynep Saygin does. doug
Kern, Mark wrote:
Hi Doug,
I must be misunderstanding the contents of the a2005s. From the LUT at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurfer..., there is a section under the color table listing for the a2005s for index numbers in the 7000's and 8000's that list thalamic and subcortical regions. If these indices are not part of the a2005s scheme, are they available in any other segmentation schemes? Thanks for considering this matter.
Best, Mark
From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, March 08, 2012 10:37 AM To: Kern, Mark; freesurfer Subject: Re: [Freesurfer] aparc.a2005s+aseg.mgz
Hi Mark, I don't think thalamic structures were part of the a2005s. I think it was only cortical structures. The aparc.a2005s+aseg.mgz will have a whole thalamus segmentation, but that is inherited from the aseg.mgz doug
Kern, Mark wrote:
Hi Doug,
Yes, the aparc.a2009s+aseg.mgz files were created and I have used them in a great deal of our analysis of large scale network connectivity of cerebral cortical regions. We have a desire to look at some subcortical structures that are part of the a2005s scheme but not included in the a2009s treatment, especially the subdivision of the thalamus. Any help in this matter would be greatly appreciated.
Best Wishes, Mark
On Mar 7, 2012, at 10:47 PM, Douglas Greve wrote:
Hi Mark, was aparc.a2009s+aseg.mgz created? That is the new one. doug
On 3/7/12 8:43 AM, Kern, Mark wrote:
Dear Freesurfer Mavens,
After running "recon-all -all" on a set of anatomical data, I wished to used the aparc.a2005s+aseg.mgz in a connectivity analysis pipeline to create some ROI masks. I was particularly interested in the subcortical regions contained in the a2005s scheme. However, the aparc.a2005s+aseg.mgz file was not created during the recon-all processing run. Is there a way to get the a2005s segmentation data?
Thanks for your help.
Best,
Mark
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