SIFT Manual 0.1 Alpha
SIFT_manual
SIFT_manual_0.1_alpha
SIFT_manual
User Manual: Pdf
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Page Count: 69
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Source'Information'Flow'Toolbox'(SIFT)!
An#Electrophysiological#Information#Flow#Toolbox#for#EEGLAB!!
Theoretical+Handbook(and(User(Manual!
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1.# Table#of#Contents#
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2.# Introduction#
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Structural connectivity denotes networks of anatomical (e.g., axonal) links. Here the
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5.2.1.# Bootstrap#resampling#
!
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stat_bootSignificanceTests()
5.2.2.# Phase#Randomization#
!
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!
B\!
6.# Using#SIFT#to#analyze#neural#information#flow#dynamics#
!
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!
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5-..1441-+@!!
24 Subjects
!
B]!
6.1.# System#Requirements#
!
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path>/external/!!$[*&*!<SIFT-path>!14!'[*!,022!/%'[!'-!'[*!#7VH!1+4'%22!81&*5'-&=@!
6.2.# Configuring#EEGLAB#
!
V1&4'!4'%&'!0/!EEFQIL!,&-.!'[*!GIHQIL•!5-..%+8K/&-./'Z!!
>> eeglab@!!
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!
!
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6.3.# Loading#the#data#
!
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'[*+!U&67T#00<6&3!2-5%'*8!1+!'[*!<SIFT-path>/Data/!,-28*&@!
!
B#]&W(!F+!5UQX!RespWrong.set!T_()!RespCorr.set!
!
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!
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,-&.%'4@!
!
6.4.# The#SIFT#analysis#pipeline#
!
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!
B#]&W(!;+!:,B"!0QTQ!^WUZ(SS#)]!^#^('#)(!
!
6.5.# Preprocessing##
!
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>> EEG = pop_pre_prepData(EEG)@!!
Pre-processing
Statistics
Visualization
Group Analysis
Model Fitting
and Validation
Connectivity
Modeling
!
CB!
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!
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!
!
6.6.# Model#Fitting#and#Validation#
!
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Oest_fitMVARKalman()P@!!!!
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>> EEG = pop_est_fitMVAR(EEG);
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!
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6.6.1.# Theory:#selecting#a#window#length#
!
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6.6.1.3.% Sufficient%amount%of%data%
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6.6.2.# Selecting#the#model#order#
!
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^'UTT(X![(WS&S!$UX('!UWX(W+!-UT(!T_QT!BC8!Q)X!7,2!^'UTS!QW(!Q'$UST!#X()T#ZQ'+!.#]_TP!0#STW#R&T#U)!U[(W!Q''!
`#)XU`S!UV!U^T#$Q'!$UX('!UWX(W!&S#)]!?A! #)VUW$QT#U)!ZW#T(W#U)+!6(WT#ZQ'!$QWb(WS!X()UT(!X#STW#R&T#U)!
$(Q)+!-UT(!T_(!X#STW#R&T#U)!#S!SU$(`_QT!R#$UXQ'!`#T_!U)(!^(Qb!QWU&)X!D!Q)X!Q)UT_(W!QWU&)X!<3+!!
!
6.6.3.# Fitting#the#final#model#
!
>*'0&+1+:!'-!-0&!.-8*2!-&8*&!4*2*5'1-+!F<76!$*!+-$!4*'!'[*!.-8*2!-&8*&!-/'1-+!'-!<F!%4!/*&!
'[*!/&*;1-04!81450441-+@!H[*!,1+%2!4*'!-,!/%&%.*'*&4!4[-028!%//*%&!%4!1+!V1:0&*!"R!%+8!'[*!
'%a2*!a*2-$Z!
J/'1-+!
N%20*!
:('(ZT!%67.!Q']UW#T_$!
6#(#WQ@%UWV!
N#)XU`!'()]T_!KS(ZL!!
E+3!!OD??!.4P!
:T(^!S#a(!KS(ZL!
E+E<!!O"?!.4P!
%UX('!UWX(W!
<F!
!
!
DD!
!
B#]&W(!<G+!/&W!V#)Q'!S(T!UV!S('(ZT(X!^QWQ$(T(WS!VUW!$UX('!V#TT#)]+!3-'*!'[%'!$*![%;*!4*2*5'*8!'[*!N1*1&%KG-&,!
.%(#013+-6!%!$1"'#$)%&"(3+!-,!?@D!4*5-+84!$1'[!%!63&7)61;&!-,!?@?"!4*56!%+8!%!-#'&%)#0'&0!-,!"A@!</-+!5215b1+:!JT6!
%!/&-:&*44!a%&!$122!4[-$!04!'[*!4'%'04!-,!'[*!.-8*2K,1''1+:!%2:-&1'[.@!!
!
)215b!/O!'-!5-+'1+0*@!J0&!4%+1'=!5[*5b!4[-028!/&-5**8!%+8!:*+*&%'*!+-!$%&+1+:4!-&!*&&-&4!
1+815%'1+:! $*! 5[-4*+! %! ;%218! 4*'! -,! .-8*2! /%&%.*'*&4@! V-&! *%5[! 5-+81'1-+6! '[*! NI>m"An!
.-8*2! $122! +-'! a*! ,1'! ,-&! *%5[! -,! '[*! "\R! $1+8-$4@! U*! 4[-028! +-$! 4**! %! /&-:&*44! a%&!
1+815%'1+:! '[*! .-8*2! ,1''1+:! /&-:&*44!,-&! *%5[! 5-+81'1-+@! 9*/*+81+:! -+! '[*! 4/**8! -,! =-0&!
5-./0'*&6! '[14! .%=! '%b*! %! $[12*6! 4-! =-0! .1:['! $%+'! '-! :*'! %! 5-,,**! -&! 8-! %! 21''2*! =-:%! -&!
4-.*'[1+:@!7,!=-0![%;*!21''2*!5-./0'*&!.*.-&=!-&!/&-5*44-&!4/**8!1440*46!=-0!5%+!1"20&.6&)
3+&)63&7)61;&)3#)V<V`)6&2@!H[14!$122!:&*%'2=!&*805*!'[*!5-./0'%'1-+!'1.*!8*.%+84!$[12*!4'122!
/&-8051+:!41.12%&!&*402'4!%4!1+!'[*!&*.%1+8*&!-,!'[14!*f*&514*@!!
6.6.4.# Validating#the#fitted#model#
!
I,'*&! =-0! %&*! &*,&*4[*8! ,&-.! '[%'! W-:%! 4*441-+! %+8! '[*! .-8*2! [%4! a**+! ,1'! ,-&! *%5[!
5-+81'1-+6! $*! $122! +**8! '-! ;%218%'*! -0&! ,1''*8! .-8*2@! #*2*5'! :,B"!%UX('! B#TT#)]! Q)X!
6Q'#XQT#U)!!!6Q'#XQT(!%UX('!,&-.!'[*!EEFQIF!.*+0@!H[14!5%+!%24-!a*!%5[1*;*8!,&-.!'[*!
5-..%+8K21+*!041+:Z!
>> pop_est_validateMVAR(EEG);
W-0! 4[-028! +-$! a*! /&*4*+'*8! $1'[! '[*! F<7! 4[-$+! 1+! V1:0&*! "X!O2*,'P@! S*&*! $*! [%;*! '[*!
-/'1-+!'-!5[*5b!'[*!$[1'*+*44!-,!'[*!&*4180%246!/*&5*+'!5-+414'*+5=6!%+8!.-8*2!4'%a121'=!,-&!
*%5[! O-&! %! &%+8-.! 40a4*'P! -,! -0&! $1+8-$4@! I4! $*! 8145044*8! 1+! 4*5'1-+! C@R@! 6! &*4180%2!
$[1'*+*44! '*4'4! 1+5208*! M-&'.%+'*%0! %+8! %0'-5-&&*2%'1-+! '*4'4! ,-&! 5-&&*2%'1-+! 1+! '[*!
&*4180%24!-,!'[*!.-8*2!O$[15[!5-028!1+815%'*!%!/--&!.-8*2!,1'P@!S*&*!$*
!
DA!
J/'1-+!
N%20*!
2_(Zb!N_#T()(SS!UV!.(S#X&Q'S!
Z_(Zb(X!%+8!S('(ZT!Q''!
S#])#V#ZQ)Z(!'([('!
E+EF!
2_(Zb!^(WZ()T!ZU)S#ST()Z\!
Z_(Zb(X!
2_(Zb!$UX('!STQR#'#T\!
Z_(Zb(X!
l!`#)XU`S!TU!SQ$^'(!
<EE!
!
!
B#]&W(!<;+!%UX('!6Q'#XQT#U)!91,!]()(WQT(X!R\!pop_est_validateMVAR().S*&*!$*!5%+!5[--4*!'-!5[*5b!
'[*!$[1'*+*44!-,!&*4180%246!/*&5*+'!5-+414'*+5=6!%+8!.-8*2!4'%a121'=!,-&!%22!O-&!4-.*!&%+8-.!40a4*'P!-,!$1+8-$4@!
7+!'[14!*f%./2*6!$*![%;*!5[-4*+!%!41:+1,15%+5*!'[&*4[-28!-,!/t?@?A!,-&!-0&!$[1'*+*44!'*4'4@!!
!
)215b!/O!'-!5-+'1+0*@!W-0!4[-028!+-$!4**!%!4*e0*+5*!-,!/&-:&*44!a%&4!,-&!*%5[!5-+81'1-+!%4!
4[-$+!1+!V1:0&*!"X!O&1:['P@!H[14!.%=!'%b*!%!$[12*6!4-!:-!%[*%8!%+8![%;*!%+-'[*&!5-,,**!-&!
O/&*,*&%a2=P!,1+14[!'[%'!W-:%!4*441-+@!!
J+5*! .-8*2! '[*! .-8*2! ;%218%'1-+! &-0'1+*4! [%;*! 5-./2*'*86! =-0! 4[-028! 4**! '[*! &*402'4!
4[-$+!,-&!*%5[!5-+81'1-+!%4!1+!V1:0&*!"\@!H[*!'-/!/%+*2!-,!*%5[!,1:0&*!4[-$4!'[*!&*402'4!-,!
'[*!$[1'*+*44!'*4'4!%4!%!,0+5'1-+!-,!$1+8-$!1+8*f!O4-&'*8!1+!-&8*&!-,!'*./-&%2!/&*5*8*+5*P@!!
V-&!'[*!M-&'.%+'*%0!'*4'46!$*![%;*!/2-''*8!'[*!/K;%20*!,-&!%55*/'%+5*!-,!'[*!+022![=/-'[*414!
-,! 5-&&*2%'*8! &*4180%24! O+%.*2=! "K7!$[*&*! 7) 14! '[*! /K;%20*! ,-&! &*c*5'1-+! -,! '[*! +022!
[=/-'[*414P@!N%20*4!:&*%'*&!'[%+!?@?A!Oa20*!8%4[*8!21+*P!1+815%'*4!'[*!&*4180%24!%&*!$[1'*!%'!
'[*! /t?@?A! 2*;*2@! V-&! '[*! I)V!'*4'! O:&**+P! $*![%;*! /2-''*8! '[*!/&-a%a121'=! -,! %+! -a4*&;*8!
I)V!5-*,,151*+'!'-!a*!$1'[1+!'[*!*f/*5'*8!1+'*&;%2!,-&!$[1'*!&*4180%24@!!N%20*4!:&*%'*&!'[%+!
?@]A!1+815%'*4!'[*!&*4180%24!%&*!$[1'*!%'!'[*!/t?@?A!2*;*2@!H[*!,&%5'1-+!-,!$1+8-$4!'[%'!/%44!
'[*!$[1'*+*44!'*4'!%&*!+-'*8!1+!'[*!2*:*+8@!!3-'*!'[%'!'[*!I)V!'*4'4!52%441,1*4!%22!$1+8-$4!%4!
[%;1+:!$[1'*!&*4180%246!$[12*!'[*!M-&'.%+'*%0! '*4'4!O$[15[! %&*!.05[!.-&*! 5-+4*&;%'1;*P!
1+815%'*!'[%'!'[*!.%c-&1'=!-,!$1+8-$4!%&*!$[1'*@!H[*!,%5'!'[%'!%!&%+:*!-,!$1+8-$4!+*%&!'[*!
*+8!-,! '[*!*/-5[! .%&:1+%22=!,%12!'[*!/-&'.%+'*%0!'*4'4!.%=!1+815%'*!'[%'! $*! .%=! $%+'!'-!
!
DR!
04*!%!421:['2=!2%&:*&!.-8*2!-&8*&!O*@:@6!7]P_P!-&!/*&[%/4!%!4.%22*&!$1+8-$!41(*!O'-!1./&-;*!
2-5%2!4'%'1-+%&1'=P@!
H[*!.1882*!/%+*2!4[-$4!'[*!/*&5*+'!5-+414'*+5=!/2-''*8!;*&404!1+5&*%41+:!$1+8-$!1+8*f@!
3-'*!'[%'!'[*!M)!14!&*21%a2=
!
DX!
!
B#]&W(!<I+!.(S&'TS!UV!$UX('![Q'#XQT#U)!VUW!.(S^NWU)]!KTU^L!Q)X!.(S^2UWW!KRUTTU$L!ZU)X#T#U)S+!V-&!*%5[!
5-+81'1-+!%!;%218%'1-+!4'%'14'15!14!/2-''*8!;*&404! $1+8-$!+0.a*&!O4-&'*8!1+! -&8*&!-,!'*./-&%2!/&*5*8*+5*P@!!7,!
-+2=! -+*! $1+8-$! 14! %;%12%a2*6! a%&! /2-'4! %&*! :*+*&%'*8! 1+4'*%8@! H[*! '-/! /%+*2! 4[-$4! '[*! 41:+1,15%+5*! 2*;*2! ,-&!
&*c*5'1-+!-,!'[*![=/-'[*414!-,!5-&&*2%'*8!&*4180%24@!V-&!M-&'.%+'*%0!'*4'4!OQGM6!L-fKM1*&5*6!Qc0+:KL-fP6!%!;%20*!
:&*%'*&!'[%+!?@?A!O8%4[*8!a20*!21+*P!.*%+4!$*!5%+!&*c*5'!'[*!+022![=/-'[*414!%'!'[*!/!≤!?@?A!2*;*2!O'[*!&*4180%24!
%&*!$[1'*P@!V-&!'[*!I)V!'*4'!O:&**+!21+*P6!%!;%20*!:&*%'*&!'[%+!?@]A!1+815%'*4!$[1'*!&*4180%24!%'!'[*!/!≤!?@?A!2*;*2@!
H[*!.1882*!/%+*2!4[-$4!'[*!/*&5*+'!5-+414'*+5=@!H[*!a-''-.!/%+*2!4[-$4!'[*!4'%a121'=!1+8*f@!
!
6.7.# Connectivity#Estimation#
!
3-$!'[%'!-0&!.-8*2![%4!a**+!,1'6!$*j8!21b*!'-!5%2502%'*!4-.*!,&*e0*+5=K8-.%1+!.*%40&*46!
405[! %4! '[*! 4/*5'&0.6! 5-[*&*+5*6! %+8! :&%+:*&K5%04%21'=@! L&1+:! 0/! '[*! )-++*5'1;1'=!
E4'1.%'1-+!F<7!a=!4*2*5'1+:!:,B"!2U))(ZT#[#T\@!W-0!5%+!4'%&'!'[14!,&-.!'[*!5-..%+8K21+*!
,-&!%!41+:2*!8%'%4*'!EEF!041+:Z!
>> EEG.CAT.Conn = pop_est_mvarConnectivity(EEG);
W-0! 4[-028! +-$! 4**! '[*! F<7! 4[-$+! 1+! V1:0&*! "]!O2*,'P@! S*&*! $*! 5%+! 5-./0'*! %22! '[*!
.*%40&*4!O%+8!.-&*P!214'*8!1+!H%a2*!D!1+!4*5'1-+!D@C@!!U*!5%+!4/*51,=!%!214'!-,!,&*e0*+51*4!%'!
$[15[! '-! 5-./0'*! '[*! .*%40&*O4P! %+8! $*! 5%+! 8-! 4-.*! 41./2*! 5-+;*&41-+4! -,! 5-./2*f!
.*%40&*4!%+8!4/*5'&%2!8*+41'1*4@!!!
!
D\!
V-&! -0&! *f%./2*6! 2*'j4! 5-./0'*! '[*! 81&*5'! 9HV! O$1'[! ,022! 5%04%2! +-&.%21(%'1-+6! 8*+-'*8!
89HV?\P6!'[*! 5-./2*f!5-[*&*+5*6!'[*!/%&'1%2!5-[*&*+5*6!%+8!'[*!5-./2*f! 4/*5'&%2!8*+41'=!
-;*&!'[*!,&*e0*+5=!&%+:*!BKA?!S(!O$1'[!"!S(!&*4-20'1-+P@!W-0&!-/'1-+4!4[-028!a*!4*'!%4!1+!
V1:0&*!"]!%+8!'[*!'%a2*!a*2-$Z!!!
J/'1-+!
N%20*!
:('(ZT!ZU))(ZT#[#T\!$(QS&W(S!
0#W(ZT!0"B!K`#T_!V&''!ZQ&SQ'!)UW$+L!
2U$^'(Y!2U_(W()Z(!K2U_L!
CQWT#Q'!2U_(W()Z(!K^2U_L!
2U$^'(Y!:^(ZTWQ'!0()S#T\!K:L!
W(T&W)!Se&QW(X!Q$^'#T&X(!UV!ZU$^'(Y!$(QS&W(S!
Z_(Zb(X!
ZU)[(WT!S^(ZTWQ'!X()S#T\!TU!X(Z#R('S!
Z_(Zb(X!
BW(e&()Z#(S!K?aL!
*PFE!
!
!
B#]&W(! <D+! 2U))(ZT#[#T\! (ST#$QT#U)! 91,!]()(WQT(X! R\! pop_est_mvarConnectivity().!S*&*! $*! [%;*!
5[-4*+!'-!*4'1.%'*!'[*!91&*5'!9HV!O$1'[!,022!5%04%2!+-&.%21(%'1-+k!89HV?\P6!'[*!)-./2*f!)-[*&*+5*!O)-[P6!'[*!
M%&'1%2!)-[*&*+5*!O/)-[P6!%+8!'[*!#/*5'&%2!9*+41'=!O#P@!!
U[12*! 4*2*5'1+:! %881'1-+%2!.*%40&*4! -+2=! .%&:1+%22=! 1+5&*%4*4! '[*! 5-./0'%'1-+%2! '1.*6!
8-0a21+:!'[*!+0.a*&!-,!.*%40&*4!$122!:*+*&%22=!8-0a2*!'[*!.*.-&=!8*.%+84@!)215b!/O!'-!
5-+'1+0*@!W-0!4[-028!+-$!:*'!%!/&-./'!+-'1,=1+:!=-0!-,
!
D]!
%+8!40&&-:%'*!4'%'14'154!Oa--'4'&%//1+:6!/[%4*!&%+8-.1(%'1-+P@!H[*!4'%'14'154!.-802*!1+!#7VH!
14! 50&&*+'2=! 0+8*&:-1+:! .%c-&! &*;141-+4! '-! 1./&-;*! 1'4! 5-./%'1a121'=! $1'[! EEFQILj4!
4'%'14'154!&-0'1+*4!%+8!'[*!#H<9W!.-802*!1+!EEFQIL@!H[046!40//-&'!,-&!4'%'14'154!1+!#7VH![%4!
a**+!$1'[8&%$+!/*+81+:!'[*!a*'%!&*2*%4*@!
6.9.# Visualization#
!
J+5*!$*j;*!5-./0'*8!-0&!5-++*5'1;1'=!*4'1.%'*46!%+8!/-'*+'1%22=!5-./0'*8!4-.*!4'%'14'1546!
$*! $122! $%+'! '-! ;140%21(*! '[*! &*402'4@!#7VH! 50&&*+'2=! /&-;18*4! '[&**! .%1+! ;140%21(%'1-+!
/&-:&%.4!,-&!*f/2-&1+:!&*402'4!,-&!%! 41+:2*!8%'%4*'!-&!%!5-[-&'!-,! 8%'%4*'4Z!! %+!7+'*&%5'1;*!
H1.*KV&*e0*+5=!F&186!%+!7+'*&%5'1;*!L&%1+G-;1*C96!%+8!)%04%2!M&-c*5'1-+!O'-!a*!&*2*%4*8!1+!
#7VH! "@?a*'%P@!V-&! '[*! +*f'! 4*;*&%2! 4*5'1-+46! 2*'j4! 4'%&'! a=! ;140%21(1+:! '[*! &*402'4! ,-&! *%5[!
5-+81'1-+! 4*/%&%'*2=@! Q*'j4! a*:1+! a=! 4*2*5'1+:! -+2=! '[*! U&67L0#"() 8%'%4*'! %4! 4[-$+! 1+!
V1:0&*!B?@!
!
!
B#]&W(!*E+!:('(ZT!U)'\!T_(!RespWrong!XQTQS(T!TU!ZU)T#)&(+!
!
6.9.1.# Interactive#Time?Frequency#Grid#
!
L&1+:! 0/! '[*! 7+'*&%5'1;*! H1.*KV&*e0*+5=! F&18! J/'1-+4! F<7! a=! 4*2*5'1+:!
:,B"!6#S&Q'#aQT#U)!!"#$(@BW(e&()Z\! 9W#X@! H[14! 5%+! %24-! a*! %5[1*;*8! ,&-.! '[*!
5-..%+8K21+*Z!
>> pop_vis_TimeFrequencyGrid(EEG);
#
H[14! 4[-028! :*+*&%'*! '[*! F<7! 4**+! 1+! V1:0&*! B"@! H[14! F<7! [%4! 40a4'%+'1%22=! .-&*! -/'1-+4!
'[%+!$*j;*!/&*;1-042=!4**+6!%+8!$*!$122!-+2=!a&1*,2=!1+'&-805*!'[*.
!
A?!
$[15[!BW(e&()Z#(S"UC'UT@!<40%22=!$*!$%+'!'-!;140%21(*!%!40a4*'!-,!%22!,&*e0*+51*46!'-!.%b*!
1+'*&*4'1+:!8*'%124!.-&*!4%21*+'@!U*!5%+!%24-!5-+'&-2![-$!'[*!5-2-&!.%/!14!4%'0&%'*86!041+:!.)
701#01)5-2-&!21.1'4!-&!%8%/'1;*!-+*4!a%4*8!-+!/*&5*+'12*4!-,!'[*!8%'%@!!M15b1+:!%!:--8!5-2-&!
45%21+:! 14! 1./-&'%+'! ,-&! ;140%2! 1+4/*5'1-+! -,! '[*! 8%'%@! 7,! 4-0&5*! 2-5%21(%'1-+! [%4! a**+!
/*&,-&.*8!$*!5%+!4*'!:U&WZ(%QW]#)C'UT!'-!dipole!'-!/2-'!'[*!%+%'-.15%2!2-5%'1-+4!-,!'[*!
4-0&5*4!-+!'[*!5-20.+!%+8!&-$!.%&:1+4@!7,!4-0&5*!2-5%'1-+4!%&*!+-'!%;%12%a2*6!a0'!7)I![%4!
a**+!/*&,-&.*86!$*!5%+!4*'!'[14!/&-/*&'=!'-!topoplot!'-!1+4'*%8!/2-'!'[*!45%2/!.%/4!-,!'[*!
7)4!-+!'[*!.%&:1+4@!U*!5%+!/&-;18*!%!>QS('#)(!$1+8-$!O1+!4*5-+84P!,-&!5-./0'1+:!*;*+'K
&*2%'*8!.*%40&*4@!U*!5%+!%24-!/*&,-&.!4'%'14'15%2!"_W(S_U'X#)]!-&!04*!41./2*!/*&5*+'12*!-&!
%a4-20'*! '[&*4[-284! '-! *4'%a214[! 41:+1,15%+5*@! 7,! '[*! '[&*4[-28! 14! 5-+4'%+'6! 5-+'-0&4! 5%+! a*!
/2-''*8! %&-0+8! 41:+1,15%+'! &*:1-+4! a=! *+%a21+:! C'UT2U)TU&W@! V1+%22=6! $*! 5%+! 504'-.1(*! %!
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6.10.2.# Bayesian#Mixture#Model#
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7.# Conclusions#and#Future#Work#
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8.# Acknowledgements#
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10.# References#
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