I have recently started to use FS to generate cortical surfaces for boundary element modelling in EEG source localization. In particular I would like to use the pial surface generated by FS. I have three problems:
1: I can only get FS to generate individual hemispheres. For the BEM, I need a single, connected, mesh for the entire brain. Is there a way to get this (perhaps by fooling FS into not disconnecting the hemispheres early in the segmentation process)?
2: The white/gray boundary mesh is topologically correct (no bridges / handles / holes etc..). Is the pial surface mesh also correct?
3: Is there a way to generate the volume inside the pial surface? That is - can I flood fill the pial surface in some way to extract the voxels that lie inside it as 3d volume?
Many thanks
Alex
A.R. Wade Ph.D. Associate Scientist The Smith-Kettlewell Eye Research Institute 2318 Fillmore Street San Francisco, CA 94115
tel. 415 345 2083 fax. 309 416 6533
On Mon, 14 Feb 2005, Alex Wade wrote:
I have recently started to use FS to generate cortical surfaces for boundary element modelling in EEG source localization. In particular I would like to use the pial surface generated by FS. I have three problems:
1: I can only get FS to generate individual hemispheres. For the BEM, I need a single, connected, mesh for the entire brain. Is there a way to get this (perhaps by fooling FS into not disconnecting the hemispheres early in the segmentation process)?
sorry, no easy way to do this.
2: The white/gray boundary mesh is topologically correct (no bridges / handles / holes etc..). Is the pial surface mesh also correct?
yes, all the surfaces should have the same topology at the end (except the ?h.qsphere, which you don't have to worry about)
3: Is there a way to generate the volume inside the pial surface? That is - can I flood fill the pial surface in some way to extract the voxels that lie inside it as 3d volume?
inside the entire surface? Or just between pial and white? There is something to do the filling, but I can never remember what it is. Tosa: what's it called?
cheers, Bruce
Many thanks
Alex
A.R. Wade Ph.D. Associate Scientist The Smith-Kettlewell Eye Research Institute 2318 Fillmore Street San Francisco, CA 94115
tel. 415 345 2083 fax. 309 416 6533
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Alex:
We have a program called "mri_surfacemask", which uses the surface to get the inside volume covered by the surface. The outside is set to zero (the volume must be UCHAR).
If you need this, please let me know.
Tosa
Bruce Fischl wrote:
On Mon, 14 Feb 2005, Alex Wade wrote:
I have recently started to use FS to generate cortical surfaces for boundary element modelling in EEG source localization. In particular I would like to use the pial surface generated by FS. I have three problems:
1: I can only get FS to generate individual hemispheres. For the BEM, I need a single, connected, mesh for the entire brain. Is there a way to get this (perhaps by fooling FS into not disconnecting the hemispheres early in the segmentation process)?
sorry, no easy way to do this.
2: The white/gray boundary mesh is topologically correct (no bridges / handles / holes etc..). Is the pial surface mesh also correct?
yes, all the surfaces should have the same topology at the end (except the ?h.qsphere, which you don't have to worry about)
3: Is there a way to generate the volume inside the pial surface? That is - can I flood fill the pial surface in some way to extract the voxels that lie inside it as 3d volume?
inside the entire surface? Or just between pial and white? There is something to do the filling, but I can never remember what it is. Tosa: what's it called?
cheers, Bruce
Many thanks
Alex
A.R. Wade Ph.D. Associate Scientist The Smith-Kettlewell Eye Research Institute 2318 Fillmore Street San Francisco, CA 94115
tel. 415 345 2083 fax. 309 416 6533
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
There's also mri_surf2vol. It won't flood fill, but it will create a binary volume of the ribbon with --fillribbon
doug
Yasunari Tosa wrote:
Hi, Alex:
We have a program called "mri_surfacemask", which uses the surface to get the inside volume covered by the surface. The outside is set to zero (the volume must be UCHAR).
If you need this, please let me know.
Tosa
Bruce Fischl wrote:
On Mon, 14 Feb 2005, Alex Wade wrote:
I have recently started to use FS to generate cortical surfaces for boundary element modelling in EEG source localization. In particular I would like to use the pial surface generated by FS. I have three problems:
1: I can only get FS to generate individual hemispheres. For the BEM, I need a single, connected, mesh for the entire brain. Is there a way to get this (perhaps by fooling FS into not disconnecting the hemispheres early in the segmentation process)?
sorry, no easy way to do this.
2: The white/gray boundary mesh is topologically correct (no bridges / handles / holes etc..). Is the pial surface mesh also correct?
yes, all the surfaces should have the same topology at the end (except the ?h.qsphere, which you don't have to worry about)
3: Is there a way to generate the volume inside the pial surface? That is - can I flood fill the pial surface in some way to extract the voxels that lie inside it as 3d volume?
inside the entire surface? Or just between pial and white? There is something to do the filling, but I can never remember what it is. Tosa: what's it called?
cheers, Bruce
Many thanks
Alex
A.R. Wade Ph.D. Associate Scientist The Smith-Kettlewell Eye Research Institute 2318 Fillmore Street San Francisco, CA 94115
tel. 415 345 2083 fax. 309 416 6533
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
-- Yasunari Tosa, Ph.D. Email: tosa@nmr.mgh.harvard.edu NMR Ctr, Mass. General Hospital TEL: 617-726-4050 Building 149, 13th Street Charlestown, MA 02129 USA
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Alex Wade -
Bruce Fischl -
Doug Greve -
Yasunari Tosa