[Mne_analysis] BEM model: watershed vs. flash

[Lin Wang]

        External Email - Use Caution        

Hi MNE-experts,

I'm trying to build a 3-compartment BEM model to source localize combined
MEG and EEG data.

At the beginning, I used the watershed algorithm and MPRAGE images to build
the three-layer model. The plot (watershed:
https://www.dropbox.com/s/ceyucikgvcpjka9/watershed.png?dl=0) shows that
the outer-skull surface is closer to the outer-skin surface, which is very
different from what was shown on the MNE documentation webpage here:
https://mne-tools.github.io/dev/auto_tutorials/plot_forward.html#sphx-glr-auto-tutorials-plot-forward-py

Later, I used flash algorithm and FLASH images to have a better estimation
of the three layers. This way, the plot ( flash:
https://www.dropbox.com/s/8c6l5fiosl7p19k/flash.png?dl=0) shows similar
segmentation results as shown in the documentation webpage, i.e. the
outer-skull surface is closer to the inner-skull surface.

My first question is: which algorithm was used for the plot on the
documentation webpage? Should I use flash for the 3-layer model?

My second question is: is it possible to have a relatively accurate 3-layer
model using watershed? We have 9 subjects missing the FLASH images.
Although I can still build the 3-layer head model using watershed for 8
subjects, I run into this error for one subject:  "the surface inner skull
is not completely inside surface outer skull". Is there any easy fix?

Thanks a lot for you help!

Lin
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