Hi Bruce,
I would like to be able to tell what proportion of a region of interest (ROI), as defined in atlas space by e.g. Desikan-Killiany, that shows a significant effect (based on a p-map). For now I overlay the p-map on the inflated surface of fsaverage in tksurfer and eyeball the proportion.
Given a p-map, if I find the FDR threshold and identify the vertices within a given ROI that have a p-value greater than the threshold, then I can find the proportion of the ROI that is suprathreshold. E.g., I find 1986 suprathreshold vertices in "bankssts" out of 2137, so 93% of vertices in bankssts show a significant effect.
My question is: Does that tell me anything about what proportion of the ROI's surface area is affected in atlas space? Obviously, if the faces were uniform, there would be a 1 to 1 relationship between #vertices and area. In the original tesselation of any dataset the size of the faces is uniform, but that changes with topology fix and deformation. I assume that is true also for fsaverage? (so I can't assume [#sig vertices] / [# tot vertices] == the proportion of the ROI's area that is significant in atlas space)
I can find the surface area of the suprathreshold region for my sample (or any subset thereof) by looking at a mean area map. But I'm unsure how to do that for fsaverage itself? Is there information on regional surface area directly available? Or would using getFaceArea.m or getFacesArea.m or similar functions be a solution?
Thank you!
LMR
--------------------------------------------------------------------------------------------------------------------- Hi Lars,
yes, the size of the faces is initially fixed - we cover the surface of each segmented wm voxel that borders non wm with 2 triangles. This gets changed by both the topology correction and the surface deformation. Note that the fsaverage surface area is less than any individual subject due to smoothing of the surface, which is why we include a correction factor in the fsaverage surfaces.
cheers, Bruce
On Wed, 16 Sep 2009, Lars M. Rimol wrote:
Hi,
I have a few questions about the surface processing stream:
I compared ?h.orig.nofix, ?h.orig, ?h.sphere and ?h.sphere.reg files. The number of triangles and vertices changes between the first two but after that they're constant. But the numbers are different across subjects. For fsaverage the number of vertices is consistently 163 842 and the number of faces 327 680.
Therefore, I assume that during the tesselation step in the processing stream, different subjects get different numbers of vertices due to differences in brain size. (And that the fsaverage numbers reflect average brain size.) Is that correct?
And does this mean that the size of the faces/triangles is uniform across all locations and subjects, at least before the topology fix?
Thank you!
Lars M. Rimol