I figured out that what i want to be calling is mri_tessellate but on a mask of the cortical WM. I can create this mask from aseg.mgz provided I know what the labels that i want extracted are.
Is there a file somewhere that says that 2 and 41 are the cortical WM. ideally I'd like to know all of the labels so that i won't have to bother people everytime i want to look at a different region. Thanks. Luke On 12/22/2010 05:10 PM, Allison Stevens wrote: > Oh, I see - the Total wm volume reported in the aseg.stats will not > include these structures even though they look included by the surfaces. > Allison > > 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
