[Mne_analysis] BEM coregistration

[Eric Larson]

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

This sort of problem has occurred before, and I think it had to do with
handling volume information / orientation properly.

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
>

We might assume that the T1.mgz is in some standard orientation. Can you
see if adding `--conform` fixes things? I think plot_bem assumes a specific
slice orientation.


The different surfaces co-register well in freeview:
>

Internally freeview probably does this conforming, we probably do not. I
guess we could in theory use nibabel's resampling to get it in the correct
orientation.

I agree it would also make sense to:

1. Be able to specify the MRI image to use
2. Ensure the MRI is conformed to the correct orientation / reslice it if
necessary

Can you open an issue on GitHub and we can go from there?

Eric
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