problem in BEM computation inner skull

[chiaram]

Dear all,

I am having trouble with the function mne.bem.make_watershed_bem. I have preprocessed the T1w data with FastSurfer and I am now computing the BEM. However the inner skull seems to have problems (specifically it is outside the outer skull and has weird shapes on the bottom). I have tried the follwing:

• increased the preflood: it is slightly better until preflood=45, then gets worse (outer skulls extremely wide. I also tried with atlas and gcaatlas but it does not improve. Below, you can see a picture of the preflood=45 result.

• If I follow these tutorials, I manage to fix it until the inner skull surface does not exceed the outer skull one. But still the lines don’t follow well the brain even if they are inside (see below)

  

What should I try next? Manually running in FreeSurfer the mri_watershed command? are there any specific parameters that could be helpful for my case?

[bonokat (Ekaterina)]

I believe I solved this by adjusting --preflood height (-p) when generating watershed BEM in freesurfer:

mne watershed_bem -s subject_name -d SUBJECTS_DIR -p 15 --overwrite

I don’t remember, if I used -p 15, but it’s worth playing with this parameter. Hopefully it’ll help!