[Mne_analysis] MRI scaling in mne coreg do not scale / copy skull / skin bem surfaces

Leonardo Barbosa lsbarbosa at gmail.com
Fri Nov 11 11:48:31 EST 2016
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Dear list,

I'm trying to scale the MRI of some subjects from which the digitization
files are missing.

After saving the -trans file, a new MRI folder was also created with the
scaled MRI surfaces (surf, labels and bem directories).

However I could not create the forward model because the bem files
gernerated by the watershaed algorithm (skin / skull bem model) were

I then tried to generate the bem files of the scaled subjects using

mne watershed_bem -d /data/project1/MRI/ -s USER_2005_T1_scaled

But got an error saying:

(project1) {16-11-11 10:11}host:/data/project1/Digitization leonardo% mne
watershed_bem -d /data/project1/MRI/ -s USER_2005_T1_scaled

Traceback (most recent call last):
line 63, in <module>
line 59, in run
    gcaatlas=gcaatlas, preflood=preflood, verbose=verbose)
  File "<string>", line 2, in make_watershed_bem
  File "/home/leonardo/projects/project1/mne-python/mne/utils.py", line
684, in verbose
    return function(*args, **kwargs)
  File "/home/leonardo/projects/project1/mne-python/mne/bem.py", line 1068,
in make_watershed_bem
    raise RuntimeError('Could not find the MRI data')
RuntimeError: Could not find the MRI data

What would be the correct pipeline for scaling the MRI?
I guess I could copy the MRI data from the original folder and run mne
watershed, but since it was not scaled I guess it wouldn't represent the
correct surface for the skin / skull bem models.

Best Regards,
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