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" <fis...@nmr.mgh.harvard.edu> An: "Fabian Schrumpf" <schru...@cbs.mpg.de> CC: "Matti Hamalainen" <m...@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" <fis...@nmr.mgh.harvard.edu> > An: "Fabian Schrumpf" <schru...@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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
