That should be fine (-ccseg -cortribbon -cortparc -aparc2aseg -wmparc).
Allison
On Wed, 23 Jan 2008 [EMAIL PROTECTED] wrote:
Thanks, I'll try that. Will I then need to redo all steps fromm -ccseg
onwards if I want a correct wmparc at the end, or can I safely skip some?
For instance, I could do -ccseg -cortribbon -cortparc -aparc2aseg -wmparc?
Best,
Kristine
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
[EMAIL PROTECTED] 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
[EMAIL PROTECTED] 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,
Kristine
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