[Freesurfer] comparing long and cross FS aparc+aseg

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Hi all, I am running a test of long FS on some subjects to see if I can improve the segmentation accuracy compared to cross FS. The aparc+aseg.mgz output of long FS, however, is not aligned with the original timepoint structural scan, but rather to the T1 image in the "base" folder (which I believe is an average of the original timepoints).

I was wondering if there was a way to directly compare the results of long FS segmentation to those of cross FS segmentation, essentially having both the original aparc+aseg image and the new one in the same space and aligned, or if that does not make sense since we are doing the long FS segmentation on an effectively new image.

Thank you, Michele