MNE Tools

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MNE Tools Scripts

• Karim Kassam

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

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Real Data
Simulated Data
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Subject 1
Subject 2
Subject 3
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meg_average
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VBA in Excel
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Real Data
Simulated Data
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mne_simu

• Simulate a source

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mne_simu
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mne_simu

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mne_simu
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mne_simu
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Subject 1
Subject 2
Subject 3
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meg_stc_morph

• how bad is it?
• spatial problems
• statistical problems

• now infamous intersubject averager
• there are some problems
• its not that bad, at least qualitatively

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Real Data
Simulated Data
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Spatial problems

• mne_make_uniform_stc

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Spatial Problems
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Spatial Problems
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Spatial Problems
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Spatial Problems
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Spatial Problems
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Spatial Problems
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ROI analysis

• avoid spatial problems

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ROI analysis

• avoid spatial problems

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ROI analysis

• avoid statistical problems

ttest
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ROI analysis

• avoid statistical problems

Arithmetic Average

• subtract condition in xplotter (task - control)
• noise normalize
• convert f-statistics to p-stats

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ROI analysis

• avoid statistical problems

T Test

• calculate currents for main effects (task and
  control)
• generate ROI, perform ttest
• (ttest averaged over 50 ms)

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ROI analysis

• avoid statistical problems

Arithmetic Average
T Test
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Subject 1
Subject 2
Subject 3
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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

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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

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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
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MNE Movies

• photoshop ? adjust contrast

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MNE Movies

• photoshop ? create frame

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MNE Movies

• matlab ? create movie

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MNE Movies

• matlab ? create movie

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where to go for more info

• Visual Basic in Excel
• http//www.engineering.usu.edu/cee/faculty/gurro/V
  BAExcel.htm
• mne_simu (type in command line for instructions)
• mne_make_uniform_stc (type in command line for
  instructions)

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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

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thank you

• 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