Could you try loading up the *pvc.label.nii.gz (label volume of tissue types) file superimposed over your brain image? (Load either the unprocessed brain image or the bias field corrected (*bfc.nii.gz image) as Volume and load *pvc.label.nii.gz file as Label). From here, you can visually check the quality of the tissue segmentation. As you move your cursor around in the images, the bottom bar of your window will tell you which tissue type it has been labeled.
If your image has been poorly segmented, you may want to try editing your brain mask (Skull Stripping) or bias field correction (Nonuniformity Correction) parameters. I hope this helps!