afni.nimh.nih.gov

It sounds like you have at least one subject with a different dimension image. In the folder that you have all of your data files try the following:

3dinfo -header_line -prefix -d3 -n4 *.HEAD

Which will output the dataset name, three values depicting voxel dimensions, 3 depicting grid size. Adding -same_grid to the command will add a column testing if the datasets are on the same grid.