[Mne_analysis] BEM coregistration

[Christian O'Reilly]

        External Email - Use Caution        

Hi,

I am using the mne.viz.plot_bem function and I get some co-registration
issues between the volume and the surfaces:
[image: image.png]

I am working with Lilla Zöllei pipeline, which do not produce the T1.mgz
file that is expected by the mne.viz.plot_bem function (as a side note, it
might be nice to have an optional mri arguments to mne.viz.plot_bem to
explicitly pass the location of the MRI file to use), so I generated it
from the original mprage.nii.gz volume expected as input by
infant_recon_all:

mri_convert $SUBJECT_DIR/mprage.nii.gz $SUBJECT_DIR/mri/T1.mgz

The different surfaces co-register well in freeview:

freeview -v $SUBJECT_DIR/brainmask.nii.gz \
                  $SUBJECT_DIR/mri/T1.mgz \
               -f $SUBJECT_DIR/surf/lh.pial:edgecolor=red \
                  $SUBJECT_DIR/surf/rh.pial:edgecolor=red \
                  $SUBJECT_DIR/surf/lh.white:edgecolor=blue \
                  $SUBJECT_DIR/surf/rh.white:edgecolor=blue \
                  $SUBJECT_DIR/bem/outer_skin.surf:edgecolor=yellow \
                  $SUBJECT_DIR/bem/outer_skull.surf:edgecolor=yellow \
                  $SUBJECT_DIR/bem/inner_skull.surf:edgecolor=yellow

produces

[image: Screenshot from 2020-01-15 12-41-39.png]
I am trying to pinpoint the source of this missmatch in mne.viz.plot_bem. I
am not that worry about mne.viz.plot_bem per se, but I am worry that it
might be indicative of how volumes and surfaces will be (wrongly)
co-registered when I will compute the source model.

Thanks for any advice on how to troubleshoot this. Best wishes,

Christian
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