[Freesurfer] Question about rotating the segmentation

Hello,

Several of our scans are slightly misaligned along the horizontal plane, and we are currently looking for a way to align them using tkmedit. We've tried using the "Rotate volume" function. However, when we do this, our segmentation (aseg.mgz) does not rotate along with the anatomical image. Is there any way to rotate the segmentation along with the volume file (e.g. a coregistration function)? Also, has anyone found a benefit to aligning scans with the horizontal plane for manual segmentation of subcortical regions (we are segmenting hippocampal volumes into anterior and posterior regions using the tkmedit tool)? Would rotation improve or distort the volume measurements?

Thanks,

Tim Al-Khindi