Yes, this is the command that comes with the Infant version of the FreeSurfer pipeline. I don't know about this issue of MRI and surfaces not being co-registered put I did many post-processing steps beside using this command (e.g., extraction of the head surfaces) before trying to import my surfaces into Brainstorm so it is possible that I solved such an issue along the way. This notebooks contain all the manipulations I used: https://github.com/christian-oreilly/infant_template_paper/blob/master/process_infants_freesurfer.ipynb if it may be of any help...