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ucl-pond / pySuStaIn

Subtype and Stage Inference (SuStaIn) algorithm with an example using simulated data.
MIT License
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Question on Using pySuStaIn on ADNI #36

Closed lmz123321 closed 2 years ago

lmz123321 commented 2 years ago

Hi, Thanks for releasing pySuStaIn !

I am interested in AD pathology and currently trying to reproduce your subtyping results on ADNI dataset (i.e. the resulst reported in your Nat.Comm. 2018 paper).

I am confused of two problems:

  1. Some subjects in ADNI 3T and 1.5T dataset have longitudinal data (datapoints collected at different time). So, how did you decide which datapoint to use?
  2. Can you provide the positional variance diagrams (containing all brain regions) learned by SuStaIn on ADNI 3T/1.5T dataset? Because the qualitative results of disease progression in your paper are rather rough to understand detailed pathology.

Grateful for your help 😁

noxtoby commented 2 years ago
  1. We used the first available ("baseline") visit for each individual.
  2. I don't have the PVDs (maybe @ayoung11 does), but you should be able to reproduce them very closely using the pySuStaIn codebase and the ADNI data.
lmz123321 commented 2 years ago

Thanks for replying.

I note that pySuStaIn provides very good documentations, thus I believe it should be easy to use.

However, since we do not have the identical data pre-processing codes (those used to compute the z-scores), we still hope to obtain the PVDs so that we can confirm our reproduction. @ayoung11

Thanks a lot.

noxtoby commented 2 years ago

I tried to explain how to calculate a z-score in this response to an earlier issue you raised.

Suggest you have a go yourself.