[Freesurfer] Mismatched dimensions with T1 and Flair inputs

Dear mailing list, I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for pial surface refinement. This results in an error message saying the dimensions are mismatched. (The third dimension of the T1 and Flair are different by one slice. ) I do not, however, have a problem running recon-all with only one T1 input. I am using Freesurfer v 5.1 . I read in the release notes that in version 5.2 you can use the flag -FLAIR when you are using a flair image as input. I suppose this will not run in an earlier version? Would it be correct to use the following command : recon-all -s [subject] -i T1.nii -i flair.nii -all Kind regards,Vilde