Kristine, You should be able to use -ccseg which occurs after the aseg is created in -autorecon2. First, you will need to copy your aseg.mgz to aseg.auto.mgz as this is the file that -ccseg will work on (in the dev version of FS, it uses the aseg.mgz). Allison
On Tue, 22 Jan 2008 k.b.walhovd@psykologi.uio.no wrote:
Thanks!
The MRI_cc works fine. It's just that I want to use the entire wmparc, and I worry that it may be skewed when the cc is not in there. The cingulate parcellations look a little off. Do you think there's any step in -autorecon2 (before -cortribbon) after the aseg I might try to start reprocessing to fix this?
Best,
Kristine
Hi Kristine,
you can just run mri_cc directly if you want:
mri_cc -o aseg_with_cc.mgz $subject
cheers, Bruce On Tue, 22 Jan 2008 walhovd@nmr.mgh.harvard.edu wrote:
Hi
I have a dataset originally processed with the Autumn 2005 FS version (2.2?). I know need wm segs, and in order to get this, I've tried to run
-cortribbon -cortparc -cortparc2 -aparc2aseg -wmparc
But the cc doesn't get labeled in the cortparc, and consequently (?) not in the wmparc either.
I've also tried to rerun all of -autorecon3, but w/o difference.
When rerunning recon-all -all, it gets fixed, but I would like to keep as much as possible as is, since I did lots of edits due to a temporal bias field problem. I've edited the asegs in some instances, and that is not kept by default.
Grateful for tips on how far down in the processing stream I need to go to get correct wmparcs w/cc.
Thanks,
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