[Mne_analysis] mne_surf2bem dense head problem

[Dan G Wakeman]

Hi Eric,

This is when the image generates very "sharp" surfaces. The typical problem is sharp "icicles" that grow up from the base of the neck (it can also happen with people that blink a lot during their MRI and have noise around the eyes). If you load the surface in freeview (or whatever app you use), you can select the vertex and likely find the area causing it to be a problem.

One slight added kink is that mne_check_surface (at least by default) stops when it reaches a single problem vertex. It does not search for more, so fixing a single problem location can require you to lather rinse repeat several times. That is why I offer solution b below. Solution a is for a single problem location.

a
load surface identify the location of the "problem vertex"
Next load the MRI that you are feeding seghead
Edit the location to encourage the surface to be "smoother" (this means making at least two contiguous voxels deep and across)
Save
Rerun mri seghead

b
load the mri that you are feeding into seghead
cut a section of the neck as far up as you like.
Fill in the two slices dorsal to it from the skin inwards with a value of 255.
Erase any noise around the eyes.
Save
Rerun mri seghead


On 2011 Oct 31, at 18:08 , Eric Larson wrote:

> Hey all,
> 
> I'm having trouble making the dense head used for coregistration for a
> couple of my subjects. When I run:
> 
> mne_surf2bem --surf ../surf/lh.seghead --id 4 --check --fif
> ${SUBJECT}-head-dense.fif
> 
> I get the error:
> 
> New quad file : nvert = 207742 nquad = 207794
> 	Triangle and vertex normals and neighboring triangles...[done]
> 	Vertex neighbors...Too many neighbors for vertex 104979.
> 
> This "too many neighbors" error occurs with or without the "--check"
> option, if it matters. Has anyone run into this before and/or know a
> solution? I had run the command "mkheadsurf -subjid ${SUBJECT} -srcvol
> T1.mgz" to get the surface that mne_surf2bem is complaining about, so
> I'm going to look for an option in there that could fix it.
> 
> Eric
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