Thx Nick for the reply.
Then how do I make sure that the spline (that I have used control points to demarcate) is included in the white matter boundary ?
Ri
----- Original Message ----- From: "Nick Schmansky" nicks@nmr.mgh.harvard.edu To: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Cc: "Ritobrato Datta" ridatta@mail.med.upenn.edu, "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 8, 2009 1:45:04 PM GMT -05:00 US/Canada Eastern Subject: Re: [Freesurfer] problem with intensity normalization control points
Ritobrato,
The control points mark voxels as belonging to white matter, and should be marked sparingly. They are not points on a spline, as it appears you were trying to do in the image.
Nick
On Tue, 2009-09-08 at 13:39 -0400, Bruce Fischl wrote:
Hi Ri,
you have to be careful to only put the control points in voxels that are completely white matter (no partial voluming). I also don't know what you mean by "the control points didnt get converted to a continuous line". Can you elaborate?
cheers, Bruce On Tue, 8 Sep 2009, Ritobrato Datta wrote:
Hello All,
I followed the steps in exercise C in the following page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints and added control points manually and then saved the Control Points by File > Save Control Points
Then I ran recon-all -autorecon2-cp -autorecon3 -s <subjid>
After completion, I opened the viewer to check if it is implemented by tkmedit <subjid> brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white
But saw that the image where I added the control points didnt get converted to a continuous line. I have attached a figure as an illustration. What am I doing wrong ?
Thanks
Ri
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