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.