Ritobrato, The user doesnt have explicit control over where the surface boundaries are drawn. Rather, you just have to be very careful not to put a control point in grey matter, or any thing partial-volumed. I can't quite tell from the resolution of the image you posted, but it appears some of the point are in grey matter, which would mark that whole region as white matter.
Nick On Tue, 2009-09-08 at 13:48 -0400, Ritobrato Datta wrote: > 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" <ni...@nmr.mgh.harvard.edu> > To: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > Cc: "Ritobrato Datta" <rida...@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 > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
