25 May
2010
25 May
'10
3:21 p.m.
Yes, you would just run the command for the fix that happens earliest on in the processing stream. The order these fixes occur in the processing stream is: control points wm edits pial edits
So if you've done all 3, you only need to run recon-all -autorecon2-cp -autorecon3 -s <subjid>
and it will take care of all those edits for you. Allison
--
On Tue, 25 May 2010, Deniz Ozgen wrote:
> Hello all,
>
> I am new to FreeSurfer and still trying to understand how things work.
> I am currently trying to understand how the manual correction works.
>
> Following the online tutorials I was able to fix the brainmask and
> wm.mgz, and also add control points in the wm so that low intensity wm
> is also included in the segmentation.
>
> In the tutorials it is suggested to run the FreeSurfer after doing the
> brainmask correction by
> recon-all -autorecon2 -subjid <subject name>
>
> After the wm control point addition, the tutorial says that "run the
> program with -autorecon2-cp"
>
> Is it possible to do brainmask correction, white matter edits and
> control points in one session and run the FreeSurfer again to fix all
> this at once? Is there a different command for this?
>
> I apologize if this has been answered before.
>
> Thanks a lot.
> Deniz.
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