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
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
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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" 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, you are *not* drawing the boundary. You are setting control points inside the wm in regions in which the white matter signal intensity in the normalized image (e.g. brain.mgz) is too low, meaning significantly lower than 110 On Tue, 8 Sep 2009, Nick Schmansky wrote:
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" 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Nick Schmansky -
Ritobrato Datta