Hello, Group
I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface?
Thank you in advance.
Xin
it depends why it's not getting out far enough. Usually you need to add control points in the nearby white matter that are <110 on the brainmask.mgz volume.
On Mon, 9 Jul 2007, Wang, Xin wrote:
Hello, Group
I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface?
Thank you in advance.
Xin
Dear, Dr. Fischl Thank you for your suggestion. My problems are around hippocampus. The grey/white surface is OK now. but some grey matters are not included in the pial surface. How to change the Pial surface? Thank you again,
Xin
________________________________
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Mon 7/9/2007 5:53 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] add the gray matter
it depends why it's not getting out far enough. Usually you need to add control points in the nearby white matter that are <110 on the brainmask.mgz volume.
On Mon, 9 Jul 2007, Wang, Xin wrote:
Hello, Group
I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface?
Thank you in advance.
Xin
oh, I wouldn't worry about the surfaces in the hippocampus. They aren't meant to be accurate there. There is too much internal structure there - we model is separately in the aseg.mgz files.
cheers, Bruc
On Tue, 10 Jul 2007, Wang, Xin wrote:
Dear, Dr. Fischl Thank you for your suggestion. My problems are around hippocampus. The grey/white surface is OK now. but some grey matters are not included in the pial surface. How to change the Pial surface? Thank you again,
Xin
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Mon 7/9/2007 5:53 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] add the gray matter
it depends why it's not getting out far enough. Usually you need to add control points in the nearby white matter that are <110 on the brainmask.mgz volume.
On Mon, 9 Jul 2007, Wang, Xin wrote:
Hello, Group
I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface?
Thank you in advance.
Xin
This is an example of my problem area (labeled with * in the fig). Do I need to correct the pial surface? If so, how to do it? Does this problem effect the values of hippocampus in the aseg.mgz? Many thanks,
Xin
________________________________
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 7/10/2007 10:39 AM To: Wang, Xin Cc: freesurfer Subject: RE: [Freesurfer] add the gray matter
oh, I wouldn't worry about the surfaces in the hippocampus. They aren't meant to be accurate there. There is too much internal structure there - we model is separately in the aseg.mgz files.
cheers, Bruc
On Tue, 10 Jul 2007, Wang, Xin wrote:
Dear, Dr. Fischl Thank you for your suggestion. My problems are around hippocampus. The grey/white surface is OK now. but some grey matters are not included in the pial surface. How to change the Pial surface? Thank you again,
Xin
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Mon 7/9/2007 5:53 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] add the gray matter
it depends why it's not getting out far enough. Usually you need to add control points in the nearby white matter that are <110 on the brainmask.mgz volume.
On Mon, 9 Jul 2007, Wang, Xin wrote:
Hello, Group
I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface?
Thank you in advance.
Xin
Xin, You do not have to correct the pial surface for that area - these surfaces do not affect the aseg.mgz. You will often see the surfaces in the hippocampus/amygdala regions as inaccurate, however your aseg will look fine. Allison
On Fri, 13 Jul 2007, Wang, Xin wrote:
This is an example of my problem area (labeled with * in the fig). Do I need to correct the pial surface? If so, how to do it? Does this problem effect the values of hippocampus in the aseg.mgz? Many thanks,
Xin
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 7/10/2007 10:39 AM To: Wang, Xin Cc: freesurfer Subject: RE: [Freesurfer] add the gray matter
oh, I wouldn't worry about the surfaces in the hippocampus. They aren't meant to be accurate there. There is too much internal structure there - we model is separately in the aseg.mgz files.
cheers, Bruc
On Tue, 10 Jul 2007, Wang, Xin wrote:
Dear, Dr. Fischl Thank you for your suggestion. My problems are around hippocampus. The grey/white surface is OK now. but some grey matters are not included in the pial surface. How to change the Pial surface? Thank you again,
Xin
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Mon 7/9/2007 5:53 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] add the gray matter
it depends why it's not getting out far enough. Usually you need to add control points in the nearby white matter that are <110 on the brainmask.mgz volume.
On Mon, 9 Jul 2007, Wang, Xin wrote:
Hello, Group
I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface?
Thank you in advance.
Xin
freesurfer@nmr.mgh.harvard.edu
-
Allison Stevens -
Bruce Fischl -
Wang, Xin