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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![Page 1: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/1.jpg)
MNE Tools & Scripts
Karim Kassam
![Page 2: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/2.jpg)
• meg_average
• mne_simu
• meg_stc_morph
• ROI analysis in Excel
• custom MNE movies
![Page 3: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/3.jpg)
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
![Page 4: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/4.jpg)
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
![Page 5: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/5.jpg)
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
![Page 6: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/6.jpg)
MRI data
fwd sol’n
(setup)
movie files
mne_compute_mne
meg average
raw MEG data
inverse sol’n
![Page 7: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/7.jpg)
meg_average
![Page 8: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/8.jpg)
VBA in Excel
![Page 9: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/9.jpg)
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
![Page 10: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/10.jpg)
mne_simu
• Simulate a source
![Page 11: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/11.jpg)
mne_simu
![Page 12: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/12.jpg)
mne_simu
+
![Page 13: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/13.jpg)
mne_simu
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
![Page 14: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/14.jpg)
mne_simu
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
![Page 15: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/15.jpg)
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
![Page 16: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/16.jpg)
• 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
![Page 17: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/17.jpg)
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
![Page 18: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/18.jpg)
Spatial problems
• mne_make_uniform_stc
![Page 19: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/19.jpg)
Spatial Problems
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
![Page 20: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/20.jpg)
Spatial Problems
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
![Page 21: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/21.jpg)
Spatial Problems
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
![Page 22: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/22.jpg)
Spatial Problems
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
![Page 23: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/23.jpg)
Spatial Problems
![Page 24: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/24.jpg)
Spatial Problems
QuickTime™ and aQuicktime for Linux decompressor
are needed to see this picture.
![Page 25: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/25.jpg)
ROI analysis
• avoid spatial problems
, ...
![Page 26: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/26.jpg)
ROI analysis
• avoid spatial problems
![Page 27: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/27.jpg)
ROI analysis
• avoid statistical problems
ttest
![Page 28: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/28.jpg)
ROI analysis
• avoid statistical problems
Arithmetic Average
1. subtract condition in xplotter (task - control)
2. noise normalize
3. convert f-statistics to p-stats
![Page 29: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/29.jpg)
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)
![Page 30: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/30.jpg)
ROI analysis
• avoid statistical problems
Arithmetic Average T Test
![Page 31: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/31.jpg)
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
![Page 32: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/32.jpg)
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
![Page 33: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/33.jpg)
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
![Page 34: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/34.jpg)
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
![Page 35: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/35.jpg)
MNE Movies
1. photoshop adjust contrast
![Page 36: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/36.jpg)
MNE Movies
2. photoshop create frame
![Page 37: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/37.jpg)
QuickTime™ and aSorenson Video 3 decompressorare needed to see this picture.
MNE Movies
3. matlab create movie
![Page 38: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/38.jpg)
MNE Movies
3. matlab create movie
QuickTime™ and aSorenson Video 3 decompressorare needed to see this picture.
![Page 39: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/39.jpg)
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)
![Page 40: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/40.jpg)
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
![Page 41: MNE Tools & Scripts Karim Kassam. meg_average mne_simu meg_stc_morph ROI analysis in Excel custom MNE movies](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d585503460f94a3818b/html5/thumbnails/41.jpg)
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