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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