Hello, You may prefer to write your own code for calculating the patch, but I thought I would just mention that this functionality is implemented in Caret (http://brainmap.wustl.edu/resources/caretnew.html). Caret can read FreeSurfer surfaces. It will calculate the distance of all nodes from a given seed node, along your chosen surface. Then it is easy to select all nodes at or within a certain radius.
best, Rutvik On Wed, 9 Mar 2005, Daniel Goldenholz wrote: > Hi Bruce > > Yes, I'm sorry I wasn't clear in my previous posting. I think that you and > I are talking about the same thing... > > The surface distance along the sphere from my vertex point... let's call > that arc length. So I want to have all freesurfer points which are less > than or equal to an arc length of R. Lets now consider the boundary > condition, where I am looking at only locations that are arc length R. Now > I could calculate the euclidean distance from vertex to any point on the > sphere which has exactly arc length R. It turns out that a > circle is formed on the sphere surface. The euclidean distance that I > measure is a constant value - M. Therefore, I could identify that boundary > in another way. I could get the intersection of two spheres: 1 the > original freesurfer sphere, and 2, a sphere with my vertex at the origin, > and the radius M. Intersecting these two spheres gives me that same > boundary. Indeed, if I take all the points from the freesurfer ?h.sphere > which are inside the second sphere, then I should now have my patch. > > Whew. Now the question is this: if I do all that (which I believe is > equivalent to Bruce's suggestion) then do I correctly generate a patch > which: > a. has a centroid at my vertex > b. has an area given approximately by pi*R^2 > c. from a surface point of view, has radial symmetry > (meaning an ant could walk in any direction from the centroi > along the surface, and until he reaches distance R, he is > still inside the patch) > > ? > > > Thanks > > Daniel > > On Tue, 8 Mar 2005, Bruce Fischl wrote: > > > Hi Daniel, > > > > don't use Euclidean distance. Use the length of the great circle connecting > > each point to the central vertex on the ?h.sphere surface. > > > > Bruce > > > > On Tue, 8 Mar 2005, Daniel Goldenholz wrote: > > > >> Doug > >> > >> I was thinking of trying something like that. > >> If I took all vertices which are a radius M or less from my centriod, > >> aren't I basically done? > >> (M is defined as the maximum euclidean distance between the centroid on > >> the sphere and the ring of outer vertices. If my surface distance max is > >> called R, I can use some geometry to figure out the relation between R and > >> M) > >> > >> What tweaks would I need to do at the folded surface level? > >> > >> On Tue, 8 Mar 2005, Doug Greve wrote: > >> > >>> > >>> You might try starting off with the ?h.sphere. It's easy to parameterize > >>> these things on the sphere. The sphere, of course, has some metric > >>> distortion, but if the patch is small, it might not be to bad. Once > >>> you've identified the vertices in the patch (or maybe a slightly bigger > >>> patch), then you can refine it in the folded space. > >>> > >>> doug > >>> > >>> > >>> Daniel Goldenholz wrote: > >>>> > >>>> Hi. I have a graph theory question: > >>>> > >>>> I would like to make a definition of a particular patch of cortex, > >>>> that > >>>> has a centroid at position (x,y,z) and has a total area of A. > >>>> > >>>> I thought that this was going to be somewhat hard, but I soon learned > >>>> that > >>>> it is very hard. > >>>> > >>>> First, I found some code for the Dijkstra algorithm, which can quickly > >>>> tell me what is the minimum number of jumps needed from one vertex to > >>>> another. IF the freesurfer surface triangles were all of EXACTLY the > >>>> same > >>>> euclidean distances on each side, then this alone could solve my > >>>> problem. > >>>> I could simply take all vertices which have a jump distance less than > >>>> some number. > >>>> > >>>> However, because the side lengths of the triangles in a freesurfer > >>>> surface > >>>> are NOT the same, I need to get more sophisticated. > >>>> > >>>> Ideally, what I would like is the following: > >>>> If I were an ant, walking along on the surface of the folded > >>>> brain, I could walk from the centroid in any direction for a certain > >>>> distance, and still be within my "patch." > >>>> Knowing that distance (radius), I could just use pi*r^2 and > >>>> call > >>>> that the area of the patch. > >>>> > >>>> But how do I find this idealized patch in real life? > >>>> > >>>> Thanks > >>>> Daniel Goldenholz > >>>> _______________________________________________ > >>>> 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 > >>> [EMAIL PROTECTED] > >>> Phone Number: 617-724-2358 > >>> Fax: 617-726-7422 > >>> > >> > >> > > > > -- > Daniel Goldenholz > ----------------------------------------------------- > Cell: 617-935-9421 http://people.bu.edu/danielg/ > _______________________________________________ > 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
