[Freesurfer] wmparc.mgz transformation

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Dear All, I would like to transform individual wmparc.mgz into MNI space for each of my subjects. I have tried using this command:mri_vol2vol --targ /data/mri/wmparc.mgz --mov /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz --inv --reg /usr/local/freesurfer/subjects/fsaverage/mri/transforms/reg.mni152.2mm.dat --o test.mgz

However, when I compare this output file with my FSL normalized functional data (MNI space), they didn't really match well - not a one-to one exact match (orientation slightly different), although the dimension and space are all in MNI 2mm. Do I need to use bbregister or other commands to transform it better? Thanks!Catherine