Dear all,
I have successfully run the freesurfer-steps for my subject and completed it without errors. After that I started MNE to create my BEM meshes. The manual tells me, for MNE to do that, the mri_watershed routine from freesurfer is used. Also, this runs fine, as far as the four surfaces (brain, inner_skull, outer_skull and outer_skin) are produced.
Here is the problem: when MNE wants to create the BEM geometry file, it checks whether the surfaces are overlapping or not. Apparently they do:
outer skin CM is 0.20 -3.31 10.19 mm Going from 5th to 4th subdivision of an icosahedron (ntri: 20480 -> 5120)
outer skin CM is 0.20 -3.31 10.19 mm outer skull CM is 0.20 -3.19 9.75 mm inner skull CM is 0.08 -5.38 17.14 mm Checking that outer skull surface is inside outer skin surface...[ok] Checking that inner skull surface is inside outer skull surface...[failed] Surface inner skull is not completely inside surface outer skull(sum of solid angles = -3.98566e-16 * 4*PI). Coulnd't create the geometry file
Though I do not know what CM or these numbers in mm given mean, I can tell by using freeview, that the surfaces indeed overlap. My questions are now: which of all the files freesurfer created in the recon-all processes does the mri_watershed routine use? In other words, which of the surfs or transform do I have to check and manually edit to get rid of this problem? And which recon-processes do I have to run again? Is there an easier way around this problem? As always, help is very much appreciated. Thanks. Maria