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MNE Tools & Scripts

MNE Tools & Scripts. Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies. MRI data. raw MEG data. (setup). fwd sol’n. meg average. inverse sol’n. mne_compute_mne. movie files. Real Data. Simulated Data. meg_stc_morph. Subject 1. Subject 2.

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MNE Tools & Scripts

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  1. MNE Tools & Scripts Karim Kassam

  2. meg_average • mne_simu • meg_stc_morph • ROI analysis in Excel • custom MNE movies

  3. MRI data raw MEG data (setup) fwd sol’n meg average inverse sol’n mne_compute_mne movie files

  4. Real Data Simulated Data

  5. meg_stc_morph Subject 1 Subject 2 Subject 3

  6. MRI data raw MEG data (setup) fwd sol’n meg average inverse sol’n mne_compute_mne movie files

  7. meg_average

  8. VBA in Excel

  9. Real Data Simulated Data

  10. mne_simu • Simulate a source

  11. mne_simu

  12. mne_simu +

  13. mne_simu

  14. mne_simu

  15. meg_stc_morph Subject 1 Subject 2 Subject 3

  16. meg_stc_morph • how bad is it? • spatial problems • statistical problems • now infamous intersubject averager • there are some problems • it’s not that bad, at least qualitatively

  17. Real Data Simulated Data

  18. Spatial problems • mne_make_uniform_stc

  19. Spatial Problems

  20. Spatial Problems

  21. Spatial Problems

  22. Spatial Problems

  23. Spatial Problems

  24. Spatial Problems

  25. , ... ROI analysis • avoid spatial problems

  26. ROI analysis • avoid spatial problems

  27. ROI analysis • avoid statistical problems ttest

  28. ROI analysis • avoid statistical problems Arithmetic Average subtract condition in xplotter (task - control) noise normalize convert f-statistics to p-stats

  29. ROI analysis • avoid statistical problems T Test calculate currents for main effects (task and control) generate ROI, perform ttest (ttest averaged over 50 ms)

  30. ROI analysis • avoid statistical problems Arithmetic Average T Test

  31. Subject 1 Subject 2 Subject 3

  32. MNE Movies • EasyMEG does a great job of rendering movies • But sometimes for talks we may want to show more • Can use a combination of programs to make custom movies

  33. MNE Movies • meg_snapshot_om  make pictures • for every frame and every view • photoshop • adjust contrast and put frames together • matlab (showtime toolbox) • control timing and make movie

  34. MNE Movies • meg_snapshot_om  make pictures for viewname in “lat med ven” do meg_snapshot_om \ --frameopt “0 10 10 20 20 30 30 40 40 50 50 60 60 70 ...” done

  35. MNE Movies • photoshop  adjust contrast

  36. MNE Movies • photoshop  create frame

  37. MNE Movies • matlab  create movie

  38. MNE Movies • matlab  create movie

  39. where to go for more info • Visual Basic in Excel http://www.engineering.usu.edu/cee/faculty/gurro/VBA&Excel.htm • mne_simu (type in command line for instructions) • mne_make_uniform_stc (type in command line for instructions)

  40. where to go for more info • Movies: • meg_snapshot_om (will post) • AppleScript for Photoshop (will post) • showtime.mex for Matlab (quicktime movie maker) www.psychtoolbox.org/download

  41. Moshe Bar Elissa Aminoff Jasmine Boshyan Mark Fenske Avniel Ghuman Nurit Gronau Irina Ostrovskaya Matti Hamalainen Ksenija Marinkovic Eric Halgren Brendan Cox Matt Cain Thomas Witzel Sari Levanen Seppo Ahlfors Steve Stufflebeam Daniel Goldenholz Dan Wehner thank you

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