Hello Paul,
Thank you for the quick reply! Here's what the output of the @djunct_overlap_check tool looks like for the two problematic subjects (top image - weirdly rotated/stretched brain, bottom image - cut-off parietal lobe).
The tool also produces _DEOB images which show a somewhat closer alignment to the MNI template. I don't do deobliquing as part of my pipeline. Is it something that could potentially be helpful?
Best,
Katya
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