Dear freesurfer experts,

I’m currently using FreeSurfer 7.1 with the thalamus subsegmentation from Iglesias et al (version 12) to subsegment the thalamus. Something we noticed is that the asymmetry between the left and right whole thalamus is reversed when comparing the native thalamus segmentation by FreeSurfer itself and the Iglesias method. This is exemplified by the values below where we calculated the Asymmetry Index [ (Left – right)/(left + right) * 100 ] and shows that for some subjects the left thalamus is larger when looking at the results of the Iglesias method, but smaller with the native method.

To allow comparison between the two methods we subtracted the LGN and MGN volumes from the whole thalamus volume, because –  if I’m not mistaken –  these nuclei are not segmented by the standard recon-all pipeline?

We don’t know why we observe this and not just in one dataset or one subject but in multiple. Do you have any words of wisdom or explanation for this phenomenon?

Your advice is much appreciated.

Kind regards,

Chris Vriend