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The offsets are most likely caused by the asymmetric view frustums that are generated for non-HMD stereo displays, which is expected. Make sure you specify the viz.HMD flag with viz.go() when using an HMD. If you are using shutter glasses then you should not be using the viz.HMD flag, instead you should use the viz.MainWindow.screenDistance(meters) command to specify the distance between the user and the screen.
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