Hello Alex,
This warning message appears during the watershed segmentation process. The final brain shape is compared to a statistical atlas and the correctness of the segmentation (of the shape) is evaluated.
It turns out that the validation is often too restrictive and often generates a useless warning message. As a consequence, you should most often ignore this message. If the skull stripping appears to be incorrect, this message might then become of interest.
In any case, we'll shortly fix this.
Best,
Florent
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