mne tools & scripts karim kassam. meg_average mne_simu meg_stc_morph roi analysis in excel...
Post on 21-Dec-2015
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MNE Tools & Scripts
Karim Kassam
• meg_average
• mne_simu
• meg_stc_morph
• ROI analysis in Excel
• custom MNE movies
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
mne_simu
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
MRI data
(setup)
movie files
mne_make_uniform_stc
Real Data Simulated Data
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
Subject 1 Subject 2 Subject 3
meg_stc_morph
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
meg_average
VBA in Excel
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
mne_simu
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
Real Data Simulated Data
mne_simu
• Simulate a source
mne_simu
mne_simu
+
mne_simu
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
mne_simu
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
Subject 1 Subject 2 Subject 3
meg_stc_morph
• how bad is it?– spatial problems– statistical problems
meg_stc_morph
• now infamous intersubject averager– there are some problems– it’s not that bad, at least qualitatively
MRI data
(setup)
movie files
mne_make_uniform_stc
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
Real Data Simulated Data
Spatial problems
• mne_make_uniform_stc
Spatial Problems
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
Spatial Problems
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
Spatial Problems
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
Spatial Problems
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
Spatial Problems
Spatial Problems
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
ROI analysis
• avoid spatial problems
, ...
ROI analysis
• avoid spatial problems
ROI analysis
• avoid statistical problems
ttest
ROI analysis
• avoid statistical problems
Arithmetic Average
1. subtract condition in xplotter (task - control)
2. noise normalize
3. convert f-statistics to p-stats
ROI analysis
• avoid statistical problems
T Test
1. calculate currents for main effects (task and control)
2. generate ROI, perform ttest
(ttest averaged over 50 ms)
ROI analysis
• avoid statistical problems
Arithmetic Average T Test
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
Subject 1 Subject 2 Subject 3
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
MNE Movies
1. meg_snapshot_om make pictures• for every frame and every view
2. photoshop• adjust contrast and put frames together
3. matlab (showtime toolbox)• control timing and make movie
MNE Movies
1. 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
MNE Movies
1. photoshop adjust contrast
MNE Movies
2. photoshop create frame
QuickTime™ and aSorenson Video 3 decompressorare needed to see this picture.
MNE Movies
3. matlab create movie
MNE Movies
3. matlab create movie
QuickTime™ and aSorenson Video 3 decompressorare needed to see this picture.
where to go for more info
• Visual Basic in Excelhttp://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)
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
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