Have you checked the image and the mask with fslhd? For example, I would try 'fslhd img.nii' and 'fslhd mask.nii'. You will want to check the sform (or if that is not set, the qform). If both images are in identical space, the sform should be identical. I wonder if something got lost in translation. The coding of space is explicitly described in the NIfTI standard, you should get a spatial transformation matrix that looks like the following:

sform_code 1
sto_xyz:1 -3.250000 0.000000 -0.000000 104.000000
sto_xyz:2 0.000000 3.230991 -0.388798 -58.684311
sto_xyz:3 0.000000 0.350998 3.578943 -84.798035
sto_xyz:4 0.000000 0.000000 0.000000 1.000000