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/ >>>> >>> >> >
