[Freesurfer] Running recon-all with multiple source files

Hi,

I would like to try running recon-all for some subjects using two source images in combination. The first image is a FLAIR with dimensions 288x288x30, while the second is a T1 with dimensions 256x256x165. Furthermore, the each FLAIR voxel has dimensions of 0.79x0.79x4.5 mm, while each T1 voxel has dimensions 1x1x1 mm.

I tried running the following command:

*recon-all -i FLAIR/FLAIR_P00004210_S0001.nii -i T1/T1_P00004210_S0001.nii -subjid FreeSurfer_FLAIR*

But I got the following error message:

*ERROR: inputs have mismatched dimensions!*

Is there an inbuilt command in FreeSurfer that will override this error message and perform a linear registration of the two images into the same space automatically, or do I need to perform the registration manually before starting with recon-all?

Thank you, Deirdre