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A Brief Example MRI data and metadata on PTSD patients

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Presentation on theme: "A Brief Example MRI data and metadata on PTSD patients"— Presentation transcript:

1 A Brief Example MRI data and metadata on PTSD patients
Hippocampal volume from structural MRI Intracranial volume from structural MRI NAA levels from MRSI Age Education Level CAPS score (estimated PTSD severity based on psychological exam)

2 A Brief Example I - Get Data Into Readable Format - WEKA recognizes quite a few – ARFF (primary), CSV…

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4 A Brief Example Open Weka…

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8 A Brief Example Explore the data…

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16 A Brief Example Based on exploring the data, some thoughts on a preliminary analysis Reduce number of variables (there are also formal ways of “subset selection” – stepwise regression, criteria based (AIC), the lasso, pace regression,…) “Disctretize” CAPS (as measure of PTSD severity) and try classifying on discretized CAPS score

17 A Brief Example Select varible subset, discretize CAPS score in Weka and save result as an ARFF file

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22 A Brief Example Do some classifications in the Weka Epxplorer…

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24 A Brief Example C 4.5 Decision Tree: Age Education <= 13 > 13
Rt Hipp Vol Lt Hipp Vol PTSD- Age PTSD+ Intracr Vol >3.01 <= 13 > 13 <=3.01. <=43 >43 <=2.66 >2.66 <=2.43 >2.43 <= 15 > 15 <= 1403 > 1403 <= 33 > 33

25 A Brief Example Then can automate application of multiple algorithms on multiple data sets (e.g. discretization of CAPS scores into different numbers of bins) using the Weka Experimenter

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27 A Brief Example Results using Weka Experimenter (10 times, 10 fold corss validation) – prediction accuracy:


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