Motion Correction (-<no>motioncor)
When there are multiple source volumes, this step will correct for small motions between them and then average them together. The input are the volumes found in file(s) mri/orig/XXX.mgz. The output will be the volume mri/orig.mgz. If no runs are found, then it looks for a volume in mri/orig (or mri/orig.mgz). If that volume is there, then it is used in subsequent processes as if it was the motion corrected volume. If no volume is found, then the process exits with errors.
The output of the motion corrected average is mri/rawavg.mgz which is then conformed to 255 cubed char images (1mm isotropic voxels) in mri/orig.mgz.