mne tools & scripts karim kassam. meg_average mne_simu meg_stc_morph roi analysis in excel...

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