External Email - Use Caution
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
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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.
On 8/31/2020 11:21 AM, Chris Vriend wrote:
External Email - Use Caution
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
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6485.2
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6382.639
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6959.7
1.63593835
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 chrisvriend@gmail.com:
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
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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: 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: Tuesday, September 8, 2020 at 03:07 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 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 <chrisvriend@gmail.commailto:chrisvriend@gmail.com>: 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
External Email - Use Caution
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?
Cheers, Chris
Op di 8 sep. 2020 om 09:05 schreef Chris Vriend chrisvriend@gmail.com:
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 chrisvriend@gmail.com:
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
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6732.4
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1.63593835
Yea, I would not say it is the best way to do QC. But just correlating the volumes themselves should be meaningful
On 9/9/2020 10:29 AM, Chris Vriend wrote:
External Email - Use Caution
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?
Cheers, Chris
Op di 8 sep. 2020 om 09:05 schreef Chris Vriend <chrisvriend@gmail.com mailto:chrisvriend@gmail.com>:
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 <chrisvriend@gmail.com <mailto:chrisvriend@gmail.com>>: 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
See attached spreadsheet!
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, September 9, 2020 at 11:19 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Asymmetry whole thalamus with native vs Iglesias method
Yea, I would not say it is the best way to do QC. But just correlating the volumes themselves should be meaningful
On 9/9/2020 10:29 AM, Chris Vriend wrote:
External Email - Use Caution
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?
Cheers, Chris
Op di 8 sep. 2020 om 09:05 schreef Chris Vriend <chrisvriend@gmail.commailto:chrisvriend@gmail.com>: 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 <chrisvriend@gmail.commailto:chrisvriend@gmail.com>: 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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Op wo 9 sep. 2020 om 16:29 schreef Chris Vriend chrisvriend@gmail.com:
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?
Cheers, Chris
Op di 8 sep. 2020 om 09:05 schreef Chris Vriend chrisvriend@gmail.com:
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 chrisvriend@gmail.com:
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
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
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
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
Op wo 9 sep. 2020 om 16:29 schreef Chris Vriend <chrisvriend@gmail.commailto:chrisvriend@gmail.com>:
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?
Cheers, Chris
Op di 8 sep. 2020 om 09:05 schreef Chris Vriend <chrisvriend@gmail.commailto:chrisvriend@gmail.com>: 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 <chrisvriend@gmail.commailto:chrisvriend@gmail.com>: 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
freesurfer@nmr.mgh.harvard.edu
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Chris Vriend -
Douglas N. Greve -
Iglesias Gonzalez, Juan E.