afni.nimh.nih.gov

You can compute volumes, the simplest is count voxels in the mask with 3dBrickStat, but the problem you are having is one of segmentation. The volume will be off to the extent that the mask you have for the volume of interest is off. Whether or not the errors will affect your results is something you will have to consider. But the safest bet is to touch up the segmentation so that your estimates of volume are reliable.

cheers,
ziad