you should convert the patch to ascii using mris_convert -p and get the vertex #s from the ascii file. Also, I think you must have an old version of mris_convert (as every other area is 0, which it certainly shouldn't be). Try taking a new one from surfer.nmr.mgh.harvard.edu:/space/outgoing/fsdev.
cheers, Bruce On Thu, 13 Jun 2002, Tom Schoenemann wrote: > Thanks Bruce, > > A few more questions: > > On Thursday, June 13, 2002, at 03:00 PM, Bruce Fischl wrote: > > > 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. > > Here is the first few lines of the lh.area.asc file that we created this > way: > > %more lh.area.asc > 000 -9.50000 -97.50000 -23.50000 161.92000 > 001 -10.50000 -97.50000 -23.50000 0.00000 > 002 -11.50000 -97.50000 -23.50000 163.20000 > 003 -7.50000 -97.50000 -24.50000 0.00000 > 004 -8.50000 -97.50000 -24.50000 162.88000 > 005 -9.50000 -97.50000 -24.50000 0.00000 > 006 -10.50000 -97.50000 -24.50000 162.88000 > 007 -11.50000 -97.50000 -24.50000 0.00000 > > This doesn't match what the manual states should be the output (see > below). I assume that the first number of each line is the vertex > identifier. The next 3 are, I'm guessing, the X, Y, Z coordinates for > that vertex. Is the last number the average area of the triangles that > meet at that vertex? If so, what are the units? And why do all the odd > numbered vertices have 0.00000 as their last number? > > > 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. > > OK but how do we get the list of vertices in the patch? Don't we need > the .area file for this patch? How is this obtained, e.g., from our > rh.occip.patch.3d file? > > -Tom > > > > > 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/ > >>>> > >>> > >> > > >
