Hi Luke, mri_mc is newer and more flexible, and also implements marching cubes. You don't need to extract any labels from the volume, as mri_mc explicitly takes a label to cover the surface of (e.g. 2 or 41).
cheers Bruce On Wed, 22 Dec 2010, Luke Bloy wrote: > Hi Bruce, > > Basically what i would like to do is to generate a surface for the cerebral > Wm. additionally I would like to label each vertex based on the anatomy on > the other side of the boundary. This is mostly for a visualization but might > be useful in other contexts. > > My strategy is to extract the right and left cerebral WM as well as the > corpus callosum from the aseg result using the FreeSurferColorLUT.txt to tell > me the labels to extract. This i will most likely do in fslmaths or with afni > as I am more familar with them. If a freesurfer cmd is available that would > certainly work as well. > > Using this mask I'll compute a surface using either mri_mc or mri_tessellate. > what is the difference by the way? > > Then I'll compute the surface normals at each vertex and based on those label > each vertex. > > I'm certainly open to any suggestions on how to make this simpler. or perhaps > such a tool already exists in FS. > Thanks, > Luke > > On 12/22/2010 10:06 PM, Bruce Fischl wrote: >> Hi Luke, >> >> you could, but perhaps it would be easier if you explained what your bigger >> goal is? >> >> cheers, >> Bruce >> On Wed, 22 Dec 2010, Luke Bloy wrote: >> >>> Hi Allison, >>> >>> Sorry if i was unclear, what i'm interested in is the WM. As you say the >>> current WM surface provides good information in separating the WM from >>> the Gm, I would also like to have a surface which separates the WM from >>> the subcortical structures. Is this possible? >>> >>> Could i for instance take the volume information in aseg.mgz generate >>> surfaces of the subcortical structures then some how remove these areas >>> from the overall WM surface. >>> >>> Alternatively, if I had a WM volume mask, that didn't include the >>> subcoritcal regions. ie by sorting through aseg.mgz. could I somehow >>> generate a new surface the is the boundary of this mask? >>> >>> Thanks for the help. >>> Luke >>> >>> On 12/22/2010 04:35 PM, Allison Stevens wrote: >>>> Hi Luke, >>>> For subcortical structures, you would want to use the volume >>>> information provided by the aseg.mgz and not information from the >>>> surfaces (which are intended for cortical measures). >>>> Allison >>>> >>>> On Wed, 22 Dec 2010, Luke Bloy wrote: >>>> >>>>> Hello, >>>>> >>>>> I'm new to freeSurfer and just starting to look around so I apologize if >>>>> this question is a bit naive. >>>>> >>>>> When I look at segmentation results, that include deep brain nuclei >>>>> (thalamus etc) I see that they are all contained inside of the white >>>>> matter surface. is there away to edit the surface so that these >>>>> boundaries are represented? >>>>> >>>>> I imagine that this would change the topology of the WM region thus it >>>>> might be difficult, Is there away to generate surfaces form these >>>>> regions on there own? >>>>> >>>>> Thanks >>>>> Luke >>>>> _______________________________________________ >>>>> 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 >>> >>> >>> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
