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If there is an error, it's probably simplest to remove the subject from the analysis (create a new set and re-run).
Checking individual files
The subject folders in FSL contain a nifti file with the segmentations. You can open the T1 file and overlay the segmentations.
You might want to choose a different colormap. The structures have different values(CMA Standard Labels) which you can see in the bottom-left of the mricron window.