Very interesting, Chris! The atlas is indeed designed to be symmetric, such that left-right differences arise from the data rather than the prior. Did you try on a larger sample? Are these differences in asymmetry significant? Cheers, /E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <[email protected]> on behalf of Chris Vriend <[email protected]> Reply-To: Freesurfer support list <[email protected]> Date: Tuesday, September 8, 2020 at 03:07 To: "[email protected]" <[email protected]> Subject: Re: [Freesurfer] Asymmetry whole thalamus with native vs Iglesias method External Email - Use Caution Dear Eugenio, Douglas referred me to you for this question. Do you have an explanation for the difference in asymmetry between the native (aseg) and ThalamicNuclei.v12 segmentation? kind regards, Chris I'm not sure about this. The FS segmentation atlas was not created to be symmetrical, so interpreting the asymmetry of aseg results can be tricky. I know that Eugenio often creates his atlases to be symmetric; unfortunately, he's away until next week. Thalamus is also quite tricky because the contrast with WM is so low it can make finding the border quite variable. You are right about LGN/MGN. So, try re-sending this next week and see what Eugenio has to say. Op ma 31 aug. 2020 om 17:21 schreef Chris Vriend <[email protected]<mailto:[email protected]>>: 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
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