Hi all,
I ran into an issue similar to the manual editing problem discussed yesterday and earlier today. The pial surface seems to cut into the gray matter regions. However, there seems to be no wm problem in the neighborhood. Are there any tools to fix this?
I have attached snapshots for your reference. Any advice on how to include the gray matter would be helpful!
Thanks, Sindhuja
Hi,
How is the intensity of the wm between the putamen and the white surface? If it's lower than 110, you can place a string of control points along the inside border of the white surface. That might help extend the pial surf to include all the gm.
-Khoa
On Fri, 16 Sep 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi all,
I ran into an issue similar to the manual editing problem discussed yesterday and earlier today. The pial surface seems to cut into the gray matter regions. However, there seems to be no wm problem in the neighborhood. Are there any tools to fix this?
I have attached snapshots for your reference. Any advice on how to include the gray matter would be helpful!
Thanks, Sindhuja
Looks like there might be some kind of gray matter pathology there as well
On Sep 16, 2011, at 3:07 PM, Khoa Nguyen khoa@nmr.mgh.harvard.edu wrote:
Hi,
How is the intensity of the wm between the putamen and the white surface? If it's lower than 110, you can place a string of control points along the inside border of the white surface. That might help extend the pial surf to include all the gm.
-Khoa
On Fri, 16 Sep 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi all,
I ran into an issue similar to the manual editing problem discussed yesterday and earlier today. The pial surface seems to cut into the gray matter regions. However, there seems to be no wm problem in the neighborhood. Are there any tools to fix this?
I have attached snapshots for your reference. Any advice on how to include the gray matter would be helpful!
Thanks, Sindhuja
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Khoa and Bruce,
I added control points along the white surface - it did not help much in extending the pial surface.
Looks like there might be some kind of gray matter pathology there as well
On Sep 16, 2011, at 3:07 PM, Khoa Nguyen khoa@nmr.mgh.harvard.edu wrote:
Hi,
How is the intensity of the wm between the putamen and the white surface? If it's lower than 110, you can place a string of control points along the inside border of the white surface. That might help extend the pial surf to include all the gm.
-Khoa
On Fri, 16 Sep 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi all,
I ran into an issue similar to the manual editing problem discussed yesterday and earlier today. The pial surface seems to cut into the gray matter regions. However, there seems to be no wm problem in the neighborhood. Are there any tools to fix this?
I have attached snapshots for your reference. Any advice on how to include the gray matter would be helpful!
Thanks, Sindhuja
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
What command did you run? Do you want to upload the dataset?
On Sep 16, 2011, at 10:52 PM, "Sindhuja Tirumalai Govindarajan" sindhuja@nmr.mgh.harvard.edu wrote:
Hi Khoa and Bruce,
I added control points along the white surface - it did not help much in extending the pial surface.
Looks like there might be some kind of gray matter pathology there as well
On Sep 16, 2011, at 3:07 PM, Khoa Nguyen khoa@nmr.mgh.harvard.edu wrote:
Hi,
How is the intensity of the wm between the putamen and the white surface? If it's lower than 110, you can place a string of control points along the inside border of the white surface. That might help extend the pial surf to include all the gm.
-Khoa
On Fri, 16 Sep 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi all,
I ran into an issue similar to the manual editing problem discussed yesterday and earlier today. The pial surface seems to cut into the gray matter regions. However, there seems to be no wm problem in the neighborhood. Are there any tools to fix this?
I have attached snapshots for your reference. Any advice on how to include the gray matter would be helpful!
Thanks, Sindhuja
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
recon-all -autorecon2 -autorecon3 -subjid <subj>
Actually, I am sorry, I just noticed the processing is not over yet. I will check after it is done and get back to you.
What command did you run? Do you want to upload the dataset?
On Sep 16, 2011, at 10:52 PM, "Sindhuja Tirumalai Govindarajan" sindhuja@nmr.mgh.harvard.edu wrote:
Hi Khoa and Bruce,
I added control points along the white surface - it did not help much in extending the pial surface.
Looks like there might be some kind of gray matter pathology there as well
On Sep 16, 2011, at 3:07 PM, Khoa Nguyen khoa@nmr.mgh.harvard.edu wrote:
Hi,
How is the intensity of the wm between the putamen and the white surface? If it's lower than 110, you can place a string of control points along the inside border of the white surface. That might help extend the pial surf to include all the gm.
-Khoa
On Fri, 16 Sep 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi all,
I ran into an issue similar to the manual editing problem discussed yesterday and earlier today. The pial surface seems to cut into the gray matter regions. However, there seems to be no wm problem in the neighborhood. Are there any tools to fix this?
I have attached snapshots for your reference. Any advice on how to include the gray matter would be helpful!
Thanks, Sindhuja
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce and Khoa,
I've attached the snapshots after adding control points and using autorecon2. So it looks like the control points extended the pial surface by a bit, but there is still some gray matter is left out.
The same was observed in some other dataset as well.
What command did you run? Do you want to upload the dataset?
On Sep 16, 2011, at 10:52 PM, "Sindhuja Tirumalai Govindarajan" sindhuja@nmr.mgh.harvard.edu wrote:
Hi Khoa and Bruce,
I added control points along the white surface - it did not help much in extending the pial surface.
Looks like there might be some kind of gray matter pathology there as well
On Sep 16, 2011, at 3:07 PM, Khoa Nguyen khoa@nmr.mgh.harvard.edu wrote:
Hi,
How is the intensity of the wm between the putamen and the white surface? If it's lower than 110, you can place a string of control points along the inside border of the white surface. That might help extend the pial surf to include all the gm.
-Khoa
On Fri, 16 Sep 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi all,
I ran into an issue similar to the manual editing problem discussed yesterday and earlier today. The pial surface seems to cut into the gray matter regions. However, there seems to be no wm problem in the neighborhood. Are there any tools to fix this?
I have attached snapshots for your reference. Any advice on how to include the gray matter would be helpful!
Thanks, Sindhuja
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Sindhuja
is this a patient population? It looks to me like there are lesions in the gray matter which will definitely mess up the pial surface deformation. We can try some things if you want to upload the data
cheers Bruce
On Sat, 17 Sep 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi Bruce and Khoa,
I've attached the snapshots after adding control points and using autorecon2. So it looks like the control points extended the pial surface by a bit, but there is still some gray matter is left out.
The same was observed in some other dataset as well.
What command did you run? Do you want to upload the dataset?
On Sep 16, 2011, at 10:52 PM, "Sindhuja Tirumalai Govindarajan" sindhuja@nmr.mgh.harvard.edu wrote:
Hi Khoa and Bruce,
I added control points along the white surface - it did not help much in extending the pial surface.
Looks like there might be some kind of gray matter pathology there as well
On Sep 16, 2011, at 3:07 PM, Khoa Nguyen khoa@nmr.mgh.harvard.edu wrote:
Hi,
How is the intensity of the wm between the putamen and the white surface? If it's lower than 110, you can place a string of control points along the inside border of the white surface. That might help extend the pial surf to include all the gm.
-Khoa
On Fri, 16 Sep 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi all,
I ran into an issue similar to the manual editing problem discussed yesterday and earlier today. The pial surface seems to cut into the gray matter regions. However, there seems to be no wm problem in the neighborhood. Are there any tools to fix this?
I have attached snapshots for your reference. Any advice on how to include the gray matter would be helpful!
Thanks, Sindhuja
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Yes, this is patient population. I ran the following command after adding control points along the white surface:
recon-all -autorecon2 -autorecon3 -subjid <subj>
Thanks for the offer to try out reconstruction in the data. I have uploaded the dataset and allowed access by you and Khoa. Kindly let me know if I should include others.
Thanks and regards, Sindhuja
Hi Sindhuja
is this a patient population? It looks to me like there are lesions in the gray matter which will definitely mess up the pial surface deformation. We can try some things if you want to upload the data
cheers Bruce
On Sat, 17 Sep 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi Bruce and Khoa,
I've attached the snapshots after adding control points and using autorecon2. So it looks like the control points extended the pial surface by a bit, but there is still some gray matter is left out.
The same was observed in some other dataset as well.
What command did you run? Do you want to upload the dataset?
On Sep 16, 2011, at 10:52 PM, "Sindhuja Tirumalai Govindarajan" sindhuja@nmr.mgh.harvard.edu wrote:
Hi Khoa and Bruce,
I added control points along the white surface - it did not help much in extending the pial surface.
Looks like there might be some kind of gray matter pathology there as well
On Sep 16, 2011, at 3:07 PM, Khoa Nguyen khoa@nmr.mgh.harvard.edu wrote:
Hi,
How is the intensity of the wm between the putamen and the white surface? If it's lower than 110, you can place a string of control points along the inside border of the white surface. That might help extend the pial surf to include all the gm.
-Khoa
On Fri, 16 Sep 2011, Sindhuja Tirumalai Govindarajan wrote:
> Hi all, > > I ran into an issue similar to the manual editing problem discussed > yesterday and earlier today. The pial surface seems to cut into the > gray > matter regions. However, there seems to be no wm problem in the > neighborhood. Are there any tools to fix this? > > I have attached snapshots for your reference. Any advice on how to > include > the gray matter would be helpful! > > Thanks, > Sindhuja _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Khoa Nguyen -
Sindhuja Tirumalai Govindarajan