I have a dataset of children who have had hemispherectomy surgery to treat epilepsy.  I want to be able to run recon-all on these children.  I have masked out the remaining tissue from the excised side so that only tissue from the healthy hemisphere remains, and aligned this single hemisphere to a template.  To mimic a whole brain, I have flipped the single hemisphere over the X-axis and added it to the other half.  Thus, I have the original hemisphere, and the "mirrored" hemisphere in one scan.  This is my input to recon-all.  However, as the scans were acquired some time after surgery, the remaining hemisphere was not perfectly aligned at the midline and expanded / grew into to the empty cranial space, and there are gaps and overlap between the mirrored side and the original side.

Is there a way to run recon-all on the single hemisphere alone, so that I do not have to mirror the brain?  Perhaps by supplying a mask, to apply to the FreeSurfer atlases?

Thanks

Kristian