Yes, all exacerbated by the noise in the volumes introduced by the low contrast boundaries of the thalamus.
We are working on an improved version of the thalamic nuclei tool that will exploit diffusion MR data (when available) to improve the thalamic boundaries, but it’s going to take a while to get it FS-ready.
Cheers,
/E
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Chris Vriend <chrisvriend@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, September 11, 2020 at 03:11
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Asymmetry whole thalamus with native vs Iglesias method
External Email - Use Caution
thanks Eugenio and Douglas! So to sum up: correlations between raw volumes of left and right thalamus derived from both method are high. correlations between the difference in L + R volume (or asymmetry) is low but this is likely due to
the fact that the segmentation method used to create aseg in itself already produces asymmetry + any asymmetry in the data itself, whereas the prior used in ThalamicNuclei.v12 is symmetric and therefore any asymmetry is due to the data only. correct?
best wishes, Chris
Dear Eugenio,
I tested it on 103 subjects. The asymmetry index is significantly different from 0 (symmetric) for both aseg and ThalamicNuclei.v12. Also when you compare the asymmetry index across segmentation methods (either using paired or independent
t-tests) the AI is significantly different. The correlation of the AI between methods is also 'only' r = 0.377 ( P < 0.001). I've attached an xls file with the data. Based on the reply from Douglas and yourself, does this mean that AI for aseg stems from both
the method and data, while the asymmetry shown by your method is due to the data only and therefore comparing the AI between the two methods is meaningless and definitely not suitable as a quality (or sanity) check?
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?
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.
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
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Whole_thalamus_lh_Iglesias
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whole_thalamus_rh_Iglesias
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AI
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Fsnative_Left-Thal
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Fsnative_Right-Thal
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AI
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4913.391
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5129.889
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5987.2
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5764.6
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1.894177913
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6019.185
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6235.017
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6793.9
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6732.4
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0.454669791
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6374.575
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6574.893
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7592.1
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6974.051
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7661.3
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7624.8
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0.93812602
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6485.2
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2.048090865
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6316.792
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6382.639
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7191.2
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6959.7
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1.63593835
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