# BEM Model not configuring correctly

**URL:** <https://mne.discourse.group/t/bem-model-not-configuring-correctly/460>\
**Category:** Mailing List Archive (read-only)\
**Tags:** list-archive\
**Created:** [June 19, 2012, 3:06pm UTC](https://mne.discourse.group/t/bem-model-not-configuring-correctly/460 "2012-06-19T15:06:45Z")\
**Posts on this page:** 2\
**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:** [June 19, 2012, 3:06pm UTC](https://mne.discourse.group/t/bem-model-not-configuring-correctly/460/1 "2012-06-19T15:06:45Z")

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Hey Minimum Norm Estimators,

I ran a subject before using the spacing of 7, but I was told it would  
be a good counter-model to try a spacing of 5. However, when I run: the  
command to set up the BEM model, it gives me this error:

\> Solution ready.  
\> Saving...Could not update directory!  
\>  
\> Saved the result to  
/autofs/space/huygens\_001/users/dgow/PTC2/MRI/PTC2\_12/bem/PTC2\_12-20480-20480-20480-bem-sol.fif  
\>  
\> BEM geometry computations complete.  
\>  
\> The model  
/autofs/space/huygens\_001/users/dgow/PTC2/MRI/PTC2\_12/bem/PTC2\_12-20480-20480-20480-bem-sol.fif  
is now ready for use  
\> Complete.

I am not sure why it could not update the directory. My disk has more  
than 50 GB left, and there is a ...-sol.fif file but it takes 3.7GB of  
space, the spacing 7 file takes only 0.23 GB. The forward solution  
process cannot load the ...-sol.fif file. The BEM/MEGMRI portion of my  
commands look like this:

mne\_setup\_source\_space --overwrite --spacing 5 --subject PTC2\_12  
mne\_setup\_mri --overwrite --subject PTC2\_12  
mne\_watershed\_bem --overwrite --subject PTC2\_12  
mne\_setup\_forward\_model --subject PTC2\_12 --surf --ico 5 --overwrite

Additionally, the mne\_setup\_forward\_model command takes about 12 hours  
to compute. In the past (with fewer vertices) it has only taken 12  
minutes, so I am not sure what is the slowdown.

Do you know why the mne\_setup\_forward\_model function did not work or why  
it takes so long? Can I provide any additional information?

- Conrad

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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:** [June 19, 2012, 3:16pm UTC](https://mne.discourse.group/t/bem-model-not-configuring-correctly/460/2 "2012-06-19T15:16:41Z")

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You are trying to solve the BEM on very high resolution HEAD-surface,  
which is not required due to the smoothing of the potentials

mne\_setup\_forward\_model --subject PTC2\_12 --surf --ico 5 --overwrite

This will be enough,  
mne\_setup\_forward\_model --subject ${subject} --surf --homog --ico 4  
--overwrite

ico-5 you needed is for mne\_setup\_source\_space, which is setting up the  
cortical surface where dipole will be placed

mne\_setup\_source\_space --subject ${subject} --ico 5 --cps --overwrite

Hope this helps

Sheraz