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

Whole_thalamus_lh_Iglesias	whole_thalamus_rh_Iglesias	AI	Fsnative_Left-Thal	Fsnative_Right-Thal	AI
4913.391	5129.889	-2.155650345	5987.2	5764.6	1.894177913
6019.185	6235.017	-1.761289719	6793.9	6732.4	0.454669791
6374.575	6574.893	-1.546920692	7543.9	7592.1	-0.318446089
6974.051	6983.314	-0.066366395	7661.3	7624.8	0.238779021
5907.853	5798.037	0.93812602	6756.4	6485.2	2.048090865
6316.792	6382.639	-0.518503546	7191.2	6959.7	1.63593835