Hi bruce,
At first I want to build a voxel-based FEM-Model based on the surfaces freesurfer creates. For finally creating the models I want to use the MATLAB toolbox iso2mesh. But I would also be interested in building BEM models as a second approach.
best regards
Fabian
----- Ursprüngliche Mail ----- Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Fabian Schrumpf" schrumpf@cbs.mpg.de CC: "Matti Hamalainen" msh@nmr.mgh.harvard.edu Gesendet: Dienstag, 25. September 2012 15:36:50 Betreff: Re: [Freesurfer] Brain segmentation (gray, white, csf) using freesurfer
Hi Fabian
can you cc the list so others can answer? Do you want a voxel-based head model? We generate surface models for BEM analysis that Matti (ccd) can tell you about if you are interested. You could generate a volume by fillin the interior of the various surfaces with mris_fill if you prefer.
cheers Bruce
On Tue, 25 Sep 2012, Fabian Schrumpf wrote:
Hi Bruce,
thank you for your reply. I'm new to freesurfer. What I'm trying to do is to build a head model für MEG source localization. Therefore I have to divide the human brain in white matter, gray matter and CSF. After doing WM segmentation and cut/fill freesurfer comes up with a good segmentation of the brain in aseg.mgz. Unfortunately, this segmentation also contains many sub-cortical structures that I don't want to take into account for my head model. I'm trying to find a way to do a segmentation that only considers WM, GM and CSF. Additionally, reducing diversity of segmented tissue should perhaps reduce computation time?
Best regards
Fabian
----- Ursprüngliche Mail ----- Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Fabian Schrumpf" schrumpf@cbs.mpg.de CC: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 25. September 2012 15:08:11 Betreff: Re: [Freesurfer] Brain segmentation (gray, white, csf) using freesurfer
Hi Fabian
What are you trying to achieve? The easiest thing to do is to run recon-all with the -all flag so we generate an aseg, then that can be collapsed into different measures.
cheers Bruce
On Tue, 25 Sep 2012, Fabian Schrumpf wrote:
Hi folks,
I successfully managed to do a brain segmentation using freesurfer. But the result after mri_fill has too much detail. I'd like to do a segmentation only dividing the brain into white matter, gray matter and csf. I suppose that I have to alter some options when registering and aligning the volume to the gca atlas. But i don't know which option that would be. On the other hand, is there any way to edit the atlas itself so that it just contains the regions I am interested in? Thanks in advance for your help.
Best regards
Fabian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
try using mris_fill then to create a volume that is the filled interior of any of the surfaces.
cheers Bruce On Tue, 25 Sep 2012, Fabian Schrumpf wrote:
Hi bruce,
At first I want to build a voxel-based FEM-Model based on the surfaces freesurfer creates. For finally creating the models I want to use the MATLAB toolbox iso2mesh. But I would also be interested in building BEM models as a second approach.
best regards
Fabian
----- Ursprüngliche Mail ----- Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Fabian Schrumpf" schrumpf@cbs.mpg.de CC: "Matti Hamalainen" msh@nmr.mgh.harvard.edu Gesendet: Dienstag, 25. September 2012 15:36:50 Betreff: Re: [Freesurfer] Brain segmentation (gray, white, csf) using freesurfer
Hi Fabian
can you cc the list so others can answer? Do you want a voxel-based head model? We generate surface models for BEM analysis that Matti (ccd) can tell you about if you are interested. You could generate a volume by fillin the interior of the various surfaces with mris_fill if you prefer.
cheers Bruce
On Tue, 25 Sep 2012, Fabian Schrumpf wrote:
Hi Bruce,
thank you for your reply. I'm new to freesurfer. What I'm trying to do is to build a head model für MEG source localization. Therefore I have to divide the human brain in white matter, gray matter and CSF. After doing WM segmentation and cut/fill freesurfer comes up with a good segmentation of the brain in aseg.mgz. Unfortunately, this segmentation also contains many sub-cortical structures that I don't want to take into account for my head model. I'm trying to find a way to do a segmentation that only considers WM, GM and CSF. Additionally, reducing diversity of segmented tissue should perhaps reduce computation time?
Best regards
Fabian
----- Ursprüngliche Mail ----- Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Fabian Schrumpf" schrumpf@cbs.mpg.de CC: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 25. September 2012 15:08:11 Betreff: Re: [Freesurfer] Brain segmentation (gray, white, csf) using freesurfer
Hi Fabian
What are you trying to achieve? The easiest thing to do is to run recon-all with the -all flag so we generate an aseg, then that can be collapsed into different measures.
cheers Bruce
On Tue, 25 Sep 2012, Fabian Schrumpf wrote:
Hi folks,
I successfully managed to do a brain segmentation using freesurfer. But the result after mri_fill has too much detail. I'd like to do a segmentation only dividing the brain into white matter, gray matter and csf. I suppose that I have to alter some options when registering and aligning the volume to the gca atlas. But i don't know which option that would be. On the other hand, is there any way to edit the atlas itself so that it just contains the regions I am interested in? Thanks in advance for your help.
Best regards
Fabian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Fabian Schrumpf