Registration errors
In the slicesdir_T1toMNI, open the "index" web page. This shows the outline of the MNI brain traced onto the rigid-body registered T1 file. Look only for gross errors; different brain shapes will mean the outlines rarely line up perfectly.
If there is an error, make sure the manual T1 registration in the T1preprocess subfolder has been done. If the misregistration persists, remove the subject from the analysis (create a new set and re-run).
Segmentation errors
First note that a registration error means the segmentation will fail (because the segmentations are based in part on probabilities in MNI space).
In the "slicesdir_segmentations" folder, open the "index" web page. This shows the outline of structures on the T1 for each study. Look through for gross errors; it can be easiest to pick one or two slices, and just scroll down through those.
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.