...
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 used for segmentation contain the T1, a nifti file with the segmentations, and a folder with logs including errors. The error files have "e" in them, and if there are none then everything ran ok. However, even if there are some errors the segmentations can still be ok. To check, open the T1 file in mricron 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.
CMA Labels
10 Left-Thalamus-Proper 40
11 Left-Caudate 30
12 Left-Putamen 40
13 Left-Pallidum 40
16 Brain-Stem /4th Ventricle 40
17 Left-Hippocampus 30
18 Left-Amygdala 50
26 Left-Accumbens-area 50
49 Right-Thalamus-Proper 40
50 Right-Caudate 30
51 Right-Putamen 40
52 Right-Pallidum 40
53 Right-Hippocampus 30
54 Right-Amygdala 50
58 Right-Accumbens-area 50