Hi Tom, the mris_convert command line for converting curvature files is a bit arcane (my fault). You need to specify that it is a "curvature" format file with the -c option, and which one you want, but then you still need an input surface in order to read it. So, from the surf directory you could do:
mris_convert -c ./lh.area lh.orig lh.area.asc the values in the file lh.area.asc will then be the surface area of each vertex. Note that the vertex #s are invariant across the different surface representations, so you should be able to relate it to the vertices in the patches with no trouble. I don't really use the surf-sess stuff, I just start it from the command line: tksurfer <subject name> <hemi> <surface name> e.g. tksurfer tom lh inflated cheers, Bruce -------------------------------------------------------- Bruce Fischl email: [EMAIL PROTECTED] Mass. General Hosp. NMR Center. tel:(617)-726-4897 Rm. 2328, Building 149, 13th Street fax:(617)-726-7422 Charlestown, MA 02129 USA On Thu, 13 Jun 2002, Tom Schoenemann wrote: > Hi again, > > On Friday, June 7, 2002, at 06:38 PM, Bruce Fischl wrote: > > > Hi Tom, > > > > we write out an ?h.area file that contains the area of every vertex in > > the tessellation (the average area of all triangles it is a member of). > > You > > should be able to convert it to ascii using mris_convert in the usual > > way. > > When you say you "write out an ?h.area file...", what exactly does this > mean? In the process of following the tutorial, the program has > produced files in the surf directory of the subject we are working on > named: rh.area and lh.area, as well as a files for patches named > rh.occip.patch.3d and rh.occip.patch.flat. The manual mentions a "-p" > flag for mris_convert to use for patches. Does this mean we don't need > to produce some sort of a .area file for patches? > > We tried doing "mris_convert rh.area rh.area.asc" while in the surf > directory and got only a segmentation fault after a fair amount of time > (it was doing something). Any thoughts about what is wrong? > > Also, in the manual under the section for mris_convert (p. 128-129), > nothing is said about the area of every vertex being listed: > > "The first (non-comment) line contains the number of vertices > <nvertices> and the number of faces <nfaces> in the tessellation. The > is followed by the <nvertices> lines of 3 floating point numbers and > one integer. The 3 floats are the x y z coordinates of that vertex, and > the integer is a flag indicating whether the vertex is part of the > tessellation (i.e. whether it has been cut out (1) or not (0)). > Directly following the vertex description are a list of the faces. Each > line describing a face contains 4 integers. The first three are the > indices of the vertices making up that face, and the fourth is a flag, > similar to the one above, indicating whether the face has been cut out > of the tessellation (1) or not (0)." > > ??? > > > > > Also, note that the vertex index is invariant across the different > > surface > > representations, including flattened, so you can always relate data > > across > > them. As far as getting used to looking at the flatmaps, it takes a > > little > > bit of time, but it's not that bad. Probably the best thing to do is run > > two copies of tksurfer, one with the inflated and one with the flattened > > surfaces, and use send and goto point to see how they are related. > > > > In the tksurfer guide > (http://surfer.nmr.mgh.harvard.edu/docs/tksurfer_doc.html) is says: > > "TkSurfer can be started in any of three ways: launching it from > FreeSurfer with the Surface button, using the tksurfer-sess script, and > calling it from the command line. Depending on which method you use, you > may see different types of data loaded, but all methods require a > surface data set to be loaded." > > How exactly would one start another copy of tksurfer using the > "tksurfer-sess script" or the command line? > > Thanks for any help you can provide, > > -Tom > > > > > On Fri, 7 Jun 2002, Tom Schoenemann wrote: > > > >> Is there any way to get a measure of absolute surface area of, e.g., > >> the > >> pial surface of an individual? If so, can this be run on cut portions > >> of the cortical surface (e.g., the occipical pole)? We worked our way > >> to > >> the point at which freesurfer has created a model of the surface of > >> each > >> hemisphere. We are beginning to experiment with cuts as a prelude to > >> flattening. We would like to make comparisons between individuals in > >> the size and distribution of surface area across the cortex. > >> > >> Also, it isn't clear from the guide how easy it would be to interpret > >> the flattened cortex map. That is, how do we know which part of the > >> map > >> corresponds to which part of the cortex, just by looking at the map > >> itself. Is the flattened map presented in some standardized > >> perspective? > >> > >> Apologies if we have overlooked this in the guide and/or tutorial! > >> > >> -Tom > _________________________________________________ > P. Thomas Schoenemann > Assistant Professor > Department of Anthropology > University of Pennsylvania > Philadelphia, PA 19104-6398 > > Phone: (215) 573-7671 > Fax: (215) 898-7462 > E-mail: [EMAIL PROTECTED] > Homepage: http://www.sas.upenn.edu/~ptschoen/ > >> > > >
