fsaverage/mri.2mm/subcort.mask.mgz
--targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
--o ./subcort.mask152.nii
--reg $FREESURFER_HOME/average/mni152.register.dat

but when I check the registration with the MNI152 template I find that the 152 normalized subcortical mask does not align with the template. The problem is somewhat resolved when I specify a 180 degree rotation along the x axis (though there still appears to be some translation error). However, I feel uncomfortable using rotations/translations without understanding why the registration is incorrect in the first place.

In fact, this problem is making me question whether a transformation is really necessary since, technically, both the mask and the target are in MNI space and the registration of the original MNI 305 subcortical mask with the MNI152 template looks more accurate than the 152 normalized mask. Any help that you can offer would be greatly appreciated.

Cheers,
Elisa