# Intersecting MNE BEM meshes

**URL:** <https://mne.discourse.group/t/intersecting-mne-bem-meshes/514>\
**Category:** Mailing List Archive (read-only)\
**Tags:** list-archive\
**Created:** [November 29, 2012, 10:08pm UTC](https://mne.discourse.group/t/intersecting-mne-bem-meshes/514 "2012-11-29T22:08:44Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [November 29, 2012, 10:08pm UTC](https://mne.discourse.group/t/intersecting-mne-bem-meshes/514/1 "2012-11-29T22:08:44Z")

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Dear All,

I would like to compute nonintersecting decimated (~\<=5000 triangles)  
MNE BEM meshes, however using MNE on several patients with the default  
mne\_watershed seems to lead to intersecting surfaces. Is there a  
workaround this ?  
Thank you,

Octavian.

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [November 29, 2012, 10:27pm UTC](https://mne.discourse.group/t/intersecting-mne-bem-meshes/514/2 "2012-11-29T22:27:03Z")

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Hi Octavian,

There are several things to consider about this

Do you have any EEG data?

If NO

Just use a single layer BEM (This is supported by the literature).

If you do have EEG data,

First I would say you need to try to get better MR data FreeSurfer has  
pages on their wiki about this. Also, I highly recommend using the  
multi-echo flash sequences as these dramatically improve the BEM (I  
would argue they are necessary, but I imagine many others would  
disagree).

If it is too late for that, you can try to generate them by utilizing  
the -less and -more options described on the FreeSurfer wiki for  
mri\_watershed (the mne\_watershed\_bem script can help you find a good  
place to start). vary the names of the output files and use the best  
ones you can get. This is slow and difficult, but could work.

D

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [November 30, 2012, 9:41am UTC](https://mne.discourse.group/t/intersecting-mne-bem-meshes/514/3 "2012-11-30T09:41:47Z")

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hi,

when you do:

mne\_setup\_forward\_model --surf --ico 4

as in :

[https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run\_meg\_tutorial.sh#L25](https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_meg_tutorial.sh#L25)

you properly decimate the bem meshes.

the -bem.fif file then contains the triangulations you want with  
an acceptable resolution for BEM computation.

hope this helps,

Alex