Kate,
If you have already transformed the atlases into the native space, then GM volumes are computed by summing the voxels in the c1*.nii segmentation maps within each atlas region. You then multiply by the volume of each voxel to convert the units mm^3. Sorry, I do not have code that I can provide for this, but it seems like you have already done the parts of it that are relatively more difficult. Eventually I plan to include code to compute GM volumes but this is not available yet and I do not have an ETA.
Best regards,
Chris