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Orientation in plot_bem #7221

@christian-oreilly

Description

@christian-oreilly

Describe the bug

Two things. The first one is more of a feature request: 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 in mne.viz.plot_bem.

Second, in the current code of MNE, the orientation argument of mne.viz.plot_bem only produce correct visualization when the MRI volumes are in the "conform" space (e.g, running mri_convert with --conform). E.g., here is the result with orientation == coronal for a volume that is not in the "conform" space:

image

To the extent that the volumes contain the metadata for the orientation, the plot_bem function should check the orientation metadata and either 1) throw an exception if using non-conform volumes would cause to many issues or 2) give an appropriate view of the volume if managing internally non-conform volumes is reasonable for MNE. I don't think the volume should be made "conform" by MNE, unless MNE also manage rotating all the other artifacts (e.g., BEM surfaces) so that they stay in registration with the volume.

Question: Are there other functions that would be impacted by non "conform" volume?

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