You don't want to get the surface area from the faces of fsaverage. Instead use the values in fsaverage/surf/lh.white.avg.area.mgh (this is the average of the group used to create fsaverage), or, probably better, get an average area map for your cohort doug
On 07/30/2014 08:38 AM, Lars M. Rimol wrote: > 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 > > -- > yours, > > Lars M. Rimol, PhD > St. Olavs Hospital > Trondheim, > Norway > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
