I don't use any prior alignment and it always works fine for me.
Just name the mri_convert output "001.mgz" if you have one anatomical volume (001 and 002 if you have two to be aligned and averaged by Freesurfer) and put it into the subject subfolder /mri/orig
One note: I have encountered problems with volumes where one FOV (any) dimension is larger than 255mm. Freesufer resamples the volume to 1mm resolution and some of the progs used in the scripts don't seem to like indices larger than 255.
Wolfgang