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 <chrisvri...@gmail.com
<mailto:chrisvri...@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
<chrisvri...@gmail.com <mailto:chrisvri...@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
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