BEM Model not configuring correctly

✉️ Mailing List Archive (read-only)
1

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

2

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