Hi Eyal,

you need to make your axes square in matlab to unsquash it. Not sure what the other vertices are though. There is some code around that removes "orphan" vertices (ones that have no valid neighbors)

cheers Bruce

On Fri, 1 Oct 2010, Eyal Dechter wrote:

Hi, I'm trying to get the coordinates of vertices on a flattened patch that I've cut out of an inflated surface using tksurfer in fs 4.5.0. I save the patch, use mris_flatten, and then mris_convert -p. However, the coordinates I'm getting render the patch somewhat distorted and I'm wondering how I can recover the original geometry. Loading the ascii file back into tksurfer results in the correct geometry, so is there some distortion that tksurfer accounts for when loading up a patch. At the link below I've put a screen shot of the ascii coordinates plotted (ignore the black line) and the flat patch as it looks in tksurfer. I've also put the patch files I'm using. Note how the patch seems squashed.

http://web.mit.edu/~edechter/Public/

After saving the patch I run:

mris_flatten -w 10 patch_file patch_file.flat mris_convert -p patch_file.flat patch_file.flat.asc

Also, there are a number of extraneous random vertices that show up in the ascii files. They are speckled around the patch in the left hand plot. What are these? And how do I get rid of them?

Thanks, Eyal Dechter

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edechter@mit.edu Kanwisher Lab MIT