Codigo Matlab

% fmrib_fastr() - Remove FMRI gradient artifacts from EEG data using
% FMRI artifact Slice Template Removal (FASTR) [Niazy06] and uses optimal
% basis sets (OBS) to reduce the residuals.
%
% This subtraction algorithm is based on the principles outlined by
% [Niazy06] with few improvements and modifications. This program
% constructs a unique artifact template for each slice then subtracts the
% artifact. Residual artifacts are removed by constructing a matrix of
% the residuals, doing a PCA then fitting the first 4 PCs (Optimal basis
% set - OBS)to the residuals in each slice. This procedure should not be
% applied for non-EEG channels (e.g. ECG) as it can remove some high frequency
% details from a signal (e.g. QRS complex). Adaptive noise cancellation
% (ANC) [Allen00] is then used.
%
%
% USAGE:
% EEG=fmrib_fastr(EEG,lpf,L,window,Trigs,strig,anc_chk,tc_chk,Volumes,Slices,v
arargin);
% EEG: EEGLAB data structure
% lpf: low-pass filter cutoff
% L: Interpolation folds
% window: length of averaging window in number of artifacts
% Trigs: An array of slice triggers locations.
% strig: 1 for slice triggers, 0 for volume / section triggers.
% anc_chk: 1 to do Adaptive noise cancellation
%
0 to not.
% tc_chk: 1 to correct for missing triggers, 0 for not
% Volumes: FMRI volumes for use in trigger correction
% Slices: FMRI Slices / Volume for use in trigger correction
% varargin{1}: relative position of slice trigger from beginning of
%
slice acquisition: 0 for exact start -> 1 for exact end
%
default=0.03;
% varargin{2}: Channels not to perform OBS on.
% varargin{3}: Numer of PCs to use in OBS. use 0 to skip this step.
%
'auto' or empty for auto order selection.
%
% [Niazy06] R.K. Niazy, C.F. Beckmann, G.D. Iannetti, J.M. Brady, and
% S.M. Smith (2005) Removal of FMRI environment artifacts from EEG data
% using optimal basis sets. NeuroImage 28 (3), pages 720-737.
%
%
% [Allen00] A Method for Removing Imaging Artifact from Continuous EEG
% Recording during Functional MRI, P.J. Allen, O. Josephs, R. Turner.
% NeuroImage 12, 230-239 (2000).
%
%
%
%
% Author: Rami K. Niazy, FMRIB Centre, Univ. of Oxford.
%
% Copyright (c) 2006 University of Oxford
%
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%
Copyright (C) 2006 University of Oxford

Author: Rami K. Niazy, FMRIB Centre
rami@fmrib.ox.ac.uk
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
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(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 31 MAR 2006
% PCA of residual now done on HPF data at 70Hz. This resolved overfitting
% issues, which sometimes caused removal of data.
% 10 MAR 2006
% Fixed potentially sereous bug related to command line input order of varargin
% 13 JAN 2006
% ECG Channel Artifact now not least-square fitted
% 13 JAN 2006
% Fixed Section Marker Limit for s=sections case
% 16 SEP 2005
% Fixed bug when processing non-eeg channels
% 15 SEP 2005
% Added code to lengthen the section to insure enough triggers are
% contained.
% 13 SEP 2005
% Edited use of 'find' to be backward compatible with MATLAB 6
% 02 SEP 2005
% Fixed typo bug when interpolation = 1;
% Fixed problem when using '/' with single precision numbers.
% 01 SEP 2005
% Commented out test code causing problems when not in 'auto' mode.
% 09 AUG 2005
% Automatic order selection of residual PCs added.
%
%
%
%
05 AUG 2005
search window for max correlation now determined by original fs.
Fixed Misc bugs for volume/section triggers
ANC made optional.
% 12 MAR 2005
% Program made to work for interleaved recording / Volume triggers
% Fixed various bugs
% 23 JAN 2005
% Fixed rounding of Filter Order
% 14 JAN 2005
% Updated Help
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%
23 DEC 2004
Added use of binary
adaptive noise cancellation
binary corr (pcorr2)
Updated (c) info
%
%
%
%
21 DEC 2004
Fixed bug for
sections==1
made ANC called from file
%
%
%
%
17 DEC 2004
Use CORRCOEF instead of
CORR2 to eliminate need for
image porc toolbox
% 14 DEC 2004
% Major Updates:
% Added RAPCO.
% Input for trig events replaced with an array of Trigs instead
% to simplify scripting.
% Other misc bugs fixed.
% 06 OCT 2004
% Edited for possibility of L=1
% i.e. no interpolation / decimation
function EEG=fmrib_fastr(EEG,lpf,L,Window,Trigs,strig,anc_chk,tc_chk,Volumes,Sli
ces,varargin)
EEG.data = double(EEG.data);
tic;
% Check Input & Intialize Params
% -----------------------------if nargin < 8
error('Incorrect number of input arguments.','fmrib_fastr() error!');
end
if tc_chk==1
if nargin < 10
error('Volumes and Slices must be included in input arguments - See help
.','fmrib_fastr() error!');
end
end
if nargin > 13
error('Incorrect number of input arguments.','fmrib_fastr() error!');
end
pre_frac=0.03;
npc='auto';
exc=[];
hpf=70;
fs=EEG.srate;
SecT=60;
if isempty(lpf)
lpf=0;
end
if anc_chk==1 & lpf==0
lpf=70;
end
if rem(Window,2)~=0
Window=Window+1;
end
if strig==1
hwinl=Window;
else
hwinl=Window/2;
end
scount=0;
[m n]=size(EEG.data);
minorder=15;
minfac=3;
STARTFLAG=0;
LASTFLAG=0;
TH_SLOPE=2;
TH_CUMVAR=80;
TH_VAREXP=5;
if nargin>10
pre_frac=varargin{1};
end
if nargin>11
exc=varargin{2};
if ~isempty(exc)
exc=sort(exc);
if exc(end)>m | exc(1)<1
error('Channel to exclude from OBS out of range',...
'fmrib_fastr() error!');
end
end
end
if nargin>12
if ischar(npc)
if ~strcmp(lower(npc),'auto')
error('unknown PC option: %s\n',npc);
end
end
npc=varargin{3};
end
% check for DSP Toolbox
%---------------------if ~exist('firls')
error('FASTR requires the signal processing toolbox.','fmrib_fastr() error!')
;
end
% Extract triggers from Event field and correct triggers if needed
% ---------------------------------------------------------------markerch(Trigs)=-1;
markerch(n)=0;
if tc_chk==1
if length(Trigs)~=(Slices*Volumes)
fprintf('correcting slice triggers...\n')
markerch=trigcorrect(markerch,Slices,Volumes,1);
Trigs=[];
Trigs=find(markerch==-1);
end
end
ml=length(Trigs);
if strig==1
if Window>floor((ml-3)/2)
Window=floor((ml-3)/2);
if rem(Window,2)~=0
Window=Window-1;
end
hwinl=Window;
warning('For %d slice triggers, the maximum averaging\nwindow length all
owed is %d. Window length set to %d.\n',...
ml, Window,Window);
end
elseif strig==0
if Window>(ml-2)
Window=ml-2;
if rem(Window,2)~=0
Window=Window-1;
end
hwinl=Window/2;
warning('For %d volume triggers, the maximum averaging\nwindow length al
lowed is %d. Window length set to %d.\n',...
ml, Window,Window);
end
end
% Calculate artifact dimentions

%------------------------------clear marker markerch peaks ;
marker=Trigs*L;
clear dmarker;
dmarker=diff(marker);
min_isi=ceil(median(dmarker));
max_isi=ceil(1.01*min_isi);
end_artlength=max_isi-min_isi;
pre_peak=round(min_isi*pre_frac+end_artlength);
post_peak=round((1-pre_frac)*min_isi);
max_postpeak=round(post_peak+end_artlength);
art_length=pre_peak+post_peak+1;
max_artlength=art_length+end_artlength;
searchw=round(3*L);
pad_sec=ceil((art_length/L)*(hwinl/2+1)/fs)*fs;
% calculating lpf filter weights
% ------------------------------
trans=0.15;
nyq=0.5*fs;
if lpf>0
if (1+trans)*lpf/nyq > 1
error('LPF cutoff frequency to close to Nyquist frequency.',...
'fmrib_fastr() error!');
end
filtorder=round(minfac*fix(fs/lpf));
if filtorder < minorder
filtorder=minorder;
end
if rem(filtorder,2)~=0
filtorder=filtorder+1;
end
f=[0 lpf/nyq lpf*(1+trans)/nyq 1];
a=[1 1 0 0];
lpfwts=firls(filtorder,f,a);
end
% calculating hpf filter weights for template formation
% ----------------------------------------------------filtorder=round(1.2*fs*L/(hpf-10));
end
f=[0 (hpf-10)/(nyq*L) (hpf+10)/(nyq*L) 1];
a=[0 0 1 1];
hpfwts=firls(filtorder,f,a);
% calculating hpf of ANC
% ---------------------if strig==1
Tr=1;
while Tr<=length(Trigs)
Trtime=Trigs(Tr+1)-Trigs(1);
if Trtime>=fs
break
end
Tr=Tr+1;
end
ANCf=0.75*Tr;
else
ANCf=2;
end
filtorder=round(1.2*fs/(ANCf*(1-trans)));
end
f=[0 ANCf*(1-trans)/nyq ANCf/nyq 1];
ANCfwts=firls(filtorder,f,a);
% Other & ANC settings

%---------------------peaks=zeros(1,n);
peaks(Trigs)=1;
c=1;
tcount=0;
secmarker=[];
SCount=1;
sec=1;
d1=Trigs(1)-ceil(1.25*art_length/L);
if d1 <= 0
d1=1;
end
d2=Trigs(end)+ceil(2.25*art_length/L);
if d2 > length(EEG.data)
d2=length(EEG.data);
end
N=double(ceil(max_artlength/L));
mANC=d2-d1+1;
sections=floor(mANC/(floor(fs*SecT)))+1;
N=double(N);
% Validate section length has enough triggers and adjust
% -----------------------------------------------------SecTFlag=0;
SecTENDFlag=0;
if sections>1
while SecTFlag==0
if (d1-1)+floor(SecT*fs)+pad_sec > EEG.pnts
sections=1;
SecTENDFlag=1;
break;
end
secpeaks=peaks(d1:(d1-1)+floor(SecT*fs)+pad_sec);
tmpmarker=find(secpeaks==1)*L;
if strig==1
if round(length(tmpmarker)/2)<1.5*Window
SecT=SecT+0.1;
else
SecTFlag=1;
end
elseif strig==0
if length(tmpmarker)<1.5*Window
SecT=SecT+0.1;
else
SecTFlag=1;
end
end
end
if SecTENDFlag==0;
sections=floor(mANC/(floor(fs*SecT)))+1;
end
end
% Allocate Memory
% --------------fprintf('Allocating memory...\n');
if strig==1
slice_art1=zeros(hwinl+1,art_length);
slice_art2=zeros(hwinl+1,art_length);
else
slice_art1=zeros(2*hwinl+1,art_length);
end
avg_art=zeros(1,art_length);
Idata=zeros(1,(floor(fs*SecT)+2*pad_sec)*L);
Iorig=zeros(1,(floor(fs*SecT)+2*pad_sec)*L);
INoise=zeros(1,(floor(fs*SecT)+2*pad_sec)*L);
fNoise=zeros(1,(floor(fs*SecT)+2*pad_sec));
Noise=zeros(1,n);
fcleanEEG=zeros(1,(floor(fs*SecT)+2*pad_sec));
cleanEEG=zeros(1,n);
tmpd=zeros(n,1);
d=zeros(mANC,1);
refs=zeros(mANC,1);
out=zeros(mANC,1);
y=zeros(mANC,1);
W=zeros(N+1,1);
% Align Slice triggers according to first channel
% ----------------------------------------------while sec<=sections
if sec==1 & sections > 1
rempeaks=peaks((d1-1)+sec*floor(fs*SecT)+1:d2);
remmarker=find(rempeaks==1);
if length(remmarker) > 3*hwinl
secpeaks=peaks(d1:(d1-1)+sec*floor(fs*SecT)+pad_sec);
else
secpeaks=peaks(d1:d2);
sec=sections;
end
elseif sec==1 & sections==1
secpeaks=peaks(d1:d2);
elseif sec==sections
secpeaks=peaks((d1-1)+(sec-1)*floor(fs*SecT)+1-pad_sec:d2);
else
rempeaks=peaks((d1-1)+sec*floor(fs*SecT)+1-pad_sec:d2);
remmarker=find(rempeaks==1);
if length(remmarker) > 3*hwinl
secpeaks=peaks((d1-1)+(sec-1)*floor(fs*SecT)+1-pad_sec:...
(d1-1)+sec*floor(fs*SecT)+pad_sec);
else
secpeaks=peaks((d1-1)+(sec-1)*floor(fs*SecT)+1-pad_sec:d2);
sec=sections;
end
end
tmpmarker=find(secpeaks==1)*L;
markerl(SCount)=length(tmpmarker);
if sec==1 | sec==sections
secl(SCount)=length(secpeaks)-pad_sec;
else
secl(SCount)=length(secpeaks)-2*pad_sec;
end
secmarker=[secmarker tmpmarker];
SCount=SCount+1;
sec=sec+1;
end
%---------------SCount=1;
sections=length(secl);
steps=(sections+1)*m;
pcamat=zeros(floor(max(markerl)/2),pre_peak+max_postpeak+1);
for sec=1:sections
if sec==1
barth=5;
barth_step=barth;
Flag25=0;
Flag50=0;
Flag75=0;
fprintf('\nStage 1 of 2: Slice Alignment\n')
end
if L > 1
Idata=interp(EEG.data(c,d1:(d1-1)+secl(sec)+pad_sec),L,4,1);
Idata=interp(EEG.data(c,d1:d2),L,4,1);
Idata=interp(EEG.data(c,(d1-1)+sum(secl(1:sec-1))+1-pad_sec:...
d2),L,4,1);
else
Idata=interp(EEG.data(c,(d1-1)+sum(secl(1:sec-1))+1-pad_sec:...
(d1-1)+sum(secl(1:sec))+pad_sec),L,4,1);
end
else
Idata=EEG.data(c,d1:(d1-1)+secl(sec)+pad_sec);
Idata=EEG.data(c,d1:d2);
Idata=EEG.data(c,(d1-1)+sum(secl(1:sec-1))+1-pad_sec:d2);
else
Idata=EEG.data(c,(d1-1)+sum(secl(1:sec-1))+1-pad_sec:...
(d1-1)+sum(secl(1:sec))+pad_sec);
end
end
if sec==1
ml=0;
if sections>1
for nsec=2:sections
if nsec==sections
starts=sum(markerl(1:nsec-1))+1;
lasts=sum(markerl(1:nsec));
else
starts=sum(markerl(1:nsec-1))+2;
lasts=sum(markerl(1:nsec))-2;
end
ml=ml+(lasts-starts+1);
end
end
starts=1;
if sections>1
lasts=markerl(SCount)-2;
else
lasts=markerl(SCount);
end
ml=ml+(lasts-starts+1);
starts=sum(markerl(1:SCount-1))+1;
lasts=sum(markerl(1:SCount));
else
starts=sum(markerl(1:SCount-1))+2;
lasts=sum(markerl(1:SCount))-2;
end
for s=starts:lasts
if s==starts & sec==1
try
slice_art(1,:)=...
Idata(secmarker(s)-pre_peak:secmarker(s)+post_peak);
catch
slice_art(1,:)=...
Idata(secmarker(s+1)-pre_peak:secmarker(s+1)+post_peak);
end
end
if sec==sections & s==lasts
try
ppn=1;
for pp=secmarker(s)-searchw:secmarker(s)+searchw
match(ppn)=prcorr2(slice_art(1,:),...
Idata(pp-pre_peak:pp+post_peak));
ppn=ppn+1;
end
[CV,CP]=max(match);
adjust=CP-(searchw+1);
secmarker(s)=secmarker(s)+adjust;
catch
end
elseif s>=starts+1;
ppn=1;
for pp=secmarker(s)-searchw:secmarker(s)+searchw
match(ppn)=prcorr2(slice_art(1,:),...
Idata(pp-pre_peak:pp+post_peak));
ppn=ppn+1;
end
[CV,CP]=max(match);
adjust=CP-(searchw+1);
secmarker(s)=secmarker(s)+adjust;
end
tcount=tcount+1;
percentdone=floor(tcount*100/ml);
if floor(percentdone)>=barth
if percentdone>=25 & Flag25==0
fprintf('25%% ')
Flag25=1;
elseif percentdone>=50 & Flag50==0
fprintf('50%% ')
Flag50=1;
fprintf('75%% ')
Flag75=1;
elseif percentdone==100
fprintf('100%%\n')
else
fprintf('.')
end
while barth<=percentdone
barth=barth+barth_step;
end
if barth>100
barth=100;
end
end
end
SCount=SCount+1;
end
secmarker2=secmarker;
% Construct Artifacts and Subtract
% --------------------------------for c=1:m
% Progress bar Init
if c==1
barth=5;
barth_step=barth;
Flag25=0;
Flag50=0;
Flag75=0;
fprintf('\nStage 2 of 2: Artifact Subtraction\n');
end
tmpdata=EEG.data(c,:)-mean(EEG.data(c,:));
cleanEEG=EEG.data(c,:);
% Process in sections of SecT seconds for memory concerns
for sec=1:sections
if L > 1
Idata=interp(tmpdata(d1:(d1-1)+secl(sec)+pad_sec),L,4,1);
Iorig=interp(EEG.data(c,d1:(d1-1)+secl(sec)+pad_sec),L,4,1);
Idata=interp(tmpdata(d1:d2),L,4,1);
Iorig=interp(EEG.data(c,d1:d2),L,4,1);
Idata=interp(tmpdata((d1-1)+...
sum(secl(1:sec-1))+1-pad_sec:d2),L,4,1);
Iorig=interp(EEG.data(c,(d1-1)+...
sum(secl(1:sec-1))+1-pad_sec:d2),L,4,1);
else
Idata=interp(tmpdata((d1-1)+sum(secl(1:sec-1))+...
1-pad_sec:(d1-1)+sum(secl(1:sec))+pad_sec),L,4,1);
Iorig=interp(EEG.data(c,(d1-1)+sum(secl(1:sec-1))+...
1-pad_sec:(d1-1)+sum(secl(1:sec))+pad_sec),L,4,1);
end
else
Idata=tmpdata(d1:(d1-1)+secl(sec)+pad_sec);
Iorig=EEG.data(c,d1:(d1-1)+secl(sec)+pad_sec);
Idata=tmpdata(d1:d2);
Iorig=EEG.data(c,d1:d2);
Idata=tmpdata((d1-1)+sum(secl(1:sec-1))+1-pad_sec:d2);
Iorig=EEG.data(c,(d1-1)+sum(secl(1:sec-1))+1-pad_sec:d2);
else
Idata=tmpdata((d1-1)+sum(secl(1:sec-1))+1-pad_sec:...
Iorig=EEG.data(c,(d1-1)+sum(secl(1:sec-1))+1-pad_sec:...
end
end
INoise=zeros(1,length(Idata));
%Average Artifacts & Subtract
if sections==1
starts=1;
lasts=markerl(sec);
elseif sec==1
starts=1;
lasts=markerl(sec)-2;
starts=sum(markerl(1:sec-1))+2;
lasts=sum(markerl(1:sec));
else
starts=sum(markerl(1:sec-1))+2;
lasts=sum(markerl(1:sec))-2;
end
for s=starts:lasts
if strig==1 % Slice Triggers
if s==starts
art=1;
ssc=1;
for ss=starts+1:2:starts+2*hwinl+1
slice_art1(ssc,:)=...
Idata(secmarker(ss)-pre_peak:...
secmarker(ss)+post_peak);
ssc=ssc+1;
end
avg_art=mean(slice_art1,1);
elseif s==starts+1
ssc=1;
for ss=starts+2:2:starts+2*hwinl+2
ssc=ssc+1;
end
elseif ((s>(starts+hwinl+2)) & (s<=(lasts-(hwinl+2))))
ss=s+hwinl;
switch art
case 1
slice_art1=[slice_art1(2:end,:);...
secmarker(ss)+post_peak)];
art=2;
case 2
art=1;
end
end
elseif strig==0 % Volume/Section Triggers
if s==starts
art=1;
ssc=1;
for ss=starts+1:starts+2*hwinl+1
ssc=ssc+1;
end
elseif ((s>(starts+hwinl+2)) & (s<=(lasts-(hwinl+2))))
ss=s+hwinl;
end
end
% For first channel, find shift in artifact position to minimise
% sum of squared error between data and artifact template
% - Assume same shift applies for all channels% Also calculate Scale factor 'Alpha' to minimize sum of
% squared error
ppn=1;
if s==1
try
if c==1
for B=secmarker(s)-searchw:secmarker(s)+searchw
C(ppn)=prcorr2(Idata(B-pre_peak:B+post_peak),...
avg_art);
ppn=ppn+1;
end
[CV,CP]=max(C);
Beta=CP-(searchw+1);
secmarker2(s)=secmarker(s)+Beta;
end
if isempty(intersect(exc,c))
Alpha=sum(Idata(secmarker2(s)-pre_peak:secmarker2(s)+...
post_peak).*avg_art)/sum(avg_art.*avg_art);
else
Alpha=1;
end
INoise(secmarker2(s)-pre_peak:secmarker2(s)+...
post_peak)=Alpha*avg_art;
catch
if c==1
if sec==1
warning...
('Not enough data to remove first artifact segment')
;
STARTFLAG=1;
end
end
end
elseif sec==sections & s==lasts
try
if c==1
avg_art);
ppn=ppn+1;
end
[CV,CP]=max(C);
end
Alpha=...
sum(Idata(secmarker2(s)-pre_peak:...
secmarker2(s)+post_peak).*avg_art)/...
sum(avg_art.*avg_art);
else
Alpha=1;
end
INoise(secmarker2(s)-pre_peak:secmarker2(s)+post_peak)...
=Alpha*avg_art;
catch
if c==1
warning('Not enough data to remove last artifact segment');
LASTFLAG=1;
end
end
else
if c==1
avg_art);
ppn=ppn+1;
end
[CV,CP]=max(C);
end
Alpha=sum(Idata(secmarker2(s)-pre_peak:...
secmarker2(s)+post_peak).*avg_art)/...
sum(avg_art.*avg_art);
else
Alpha=1;
end
INoise(secmarker2(s)-pre_peak:secmarker2(s)+post_peak)=...
Alpha*avg_art;
end
if s==starts+1
c;
end
end
%----------PCA of residuals------------------fitted_res=zeros(length(INoise),1);
if isempty(intersect(exc,c)) & npc~=0
Ipca=filtfilt(hpfwts,1,double(Idata-INoise));
pccount=1;
skcount=1;
pick=cumsum(ones(markerl(sec),1)*2+round(rand(markerl(sec),1)));
if strig~=1
pick=[pick(1):pick(end)];
end
for s=starts+1:lasts-1
% construct PCAMAT
if skcount==pick(pccount)
pcamat(pccount,:)=...
Ipca(secmarker(s)-pre_peak:...
secmarker(s)+max_postpeak);
pccount=pccount+1;
end
skcount=skcount+1;
end
pcamat=detrend(pcamat','constant')';
[apc,ascore,asvar]=pca_calc(pcamat(1:(pccount-1),:)');
oev=100*asvar/sum(asvar);
if sec==1
if ischar(npc)
d_oev=find(abs(diff(oev))<TH_SLOPE);
dd_oev=diff(d_oev);
for I=1:length(dd_oev)-3
if [dd_oev(I) dd_oev(I+1) dd_oev(I+2)]==[1 1 1]
break
end
end
SLOPETH_PC=d_oev(I)-1;
TMPTH=find(cumsum(oev)>TH_CUMVAR);
CUMVARTH_PC=TMPTH(1);
TMPTH=find(oev<TH_VAREXP);
VAREXPTH_PC=TMPTH(1)-1;
pcs=floor(mean([SLOPETH_PC CUMVARTH_PC VAREXPTH_PC]));
fprintf('\n%d residual PCs will be removed from channel %d\n
. If you get an error "line 746 of fmrib_fastr: index exceeds matrix dimensions
" it means there is an inconsistency in your TR triggers, either the TR length o
r the number of markers',pcs,c);
else
pcs=npc;
end
end
% TEST CODE
%
%
%
%
SPCS(c)=SLOPETH_PC;
CPCS(c)=CUMVARTH_PC;
VPCS(c)=VAREXPTH_PC;
PCS(c)=pcs;
if strig==0
papc=double([ascore(:,1:pcs) ones(pre_peak+max_postpeak+1,1)]);
else
papc=double([ascore(:,1:pcs)]);
end
minmax1=max(papc(:,1))-min(papc(:,1));
for apc=2:pcs
papc(:,apc)=papc(:,apc)*minmax1/...
(max(papc(:,apc))-min(papc(:,apc)));
end
for s=starts:lasts
if s==1
if ~STARTFLAG
fitted_res(secmarker(s)-pre_peak:secmarker(s)+max_postpea
k)=...
papc*(papc\...
double(Ipca(secmarker(s)-pre_peak:...
secmarker(s)+max_postpeak))');
end
elseif s==lasts & sec==sections
if ~LASTFLAG
fitted_res(secmarker(s)-pre_peak:secmarker(s)+max_postpe
ak)=...
papc*(papc\...
end
else
fitted_res(secmarker(s)-pre_peak:secmarker(s)+max_postpeak)=
...
papc*(papc\...
end
end
elseif strig==0 % not doing OBS and using volume triggers
Ipca=Idata-INoise;
papc=double(ones(pre_peak+max_postpeak+1,1));
for s=starts:lasts
if s==1
if ~STARTFLAG
fitted_res(secmarker(s)-pre_peak:secmarker(s)+max_postpea
k)=...
papc*(papc\...
end
elseif s==lasts & sec==sections
if ~LASTFLAG
fitted_res(secmarker(s)-pre_peak:secmarker(s)+max_postpe
ak)=...
papc*(papc\...
end
else
fitted_res(secmarker(s)-pre_peak:secmarker(s)+max_postpeak)=
...
papc*(papc\...
end
end
end
%-----------------end PCA Section-----------------Idata=Iorig-INoise-fitted_res';
if L > 1
fcleanEEG=decimate2(Idata,L);
fNoise=decimate2(INoise+fitted_res',L);
else
fcleanEEG=Idata;
fNoise=INoise+fitted_res';
end
if sec==1
if sections==1
cleanEEG(d1:d2)=fcleanEEG;
Noise(d1:d2)=fNoise;
else
cleanEEG(d1:(d1-1)+secl(sec))=fcleanEEG(1:end-pad_sec);
Noise(d1:(d1-1)+secl(sec))=fNoise(1:end-pad_sec);
end
cleanEEG((d1-1)+sum(secl(1:sec-1))+1:d2)=...
fcleanEEG(pad_sec+1:end);
Noise((d1-1)+sum(secl(1:sec-1))+1:d2)=fNoise(pad_sec+1:end);
else
cleanEEG((d1-1)+sum(secl(1:sec-1))+1:(d1-1)+sum(secl(1:sec)))=...
fcleanEEG(pad_sec+1:end-pad_sec);
Noise((d1-1)+sum(secl(1:sec-1))+1:(d1-1)+sum(secl(1:sec)))=...
fNoise(pad_sec+1:end-pad_sec);
end
%Update progress bar
scount=scount+1;
percentdone=floor(scount*100/steps);
fprintf('25%% ')
Flag25=1;
fprintf('50%% ')
Flag50=1;
fprintf('75%% ')
Flag75=1;
fprintf('100%%\n')
else
fprintf('.')
end
end
if barth>100
barth=100;
end
end
end
if lpf>0
cleanEEG=filtfilt(lpfwts,1,double(cleanEEG));
Noise=filtfilt(lpfwts,1,double(Noise));
end
if anc_chk==1
% Adaptive Noise cancellation
% --------------------------refs=Noise(d1:d2)';
tmpd=filtfilt(ANCfwts,1,double(cleanEEG))';
d=double(tmpd(d1:d2));
Alpha=sum(d.*refs)/sum(refs.*refs);
refs=double(Alpha*refs);
mu=double(0.05/(N*var(refs)));
[out,y]=fastranc(refs,d,N,mu);
if isinf(max(y))
wst=sprintf('ANC Failed for channel number %d. Skipping ANC.',c);
warning(wst);
EEG.data(c,d1:d2)=cleanEEG(d1:d2);
else
EEG.data(c,d1:d2)=cleanEEG(d1:d2)-y';
end
else
EEG.data(c,d1:d2)=cleanEEG(d1:d2);
end
scount=scount+1;
percentdone=floor(scount*100/steps);
fprintf('25%% ')
Flag25=1;
fprintf('50%% ')
Flag50=1;
fprintf('75%% ')
Flag75=1;
fprintf('100%%\n')
else
fprintf('.')
end
end
if barth>100
barth=100;
end
end
end
% Calculate processing time
% -------------------------mttoc=floor(toc/60);
sttoc=round(toc-mttoc*60);
if mttoc < 60
fprintf('FASTR Finished in %d min %d sec.\n',mttoc,sttoc);
else
httoc=floor(mttoc/60);
mttoc=round(mttoc-httoc*60);
fprintf('FASTR Finished in %d hrs %d min %d sec.\n',httoc,mttoc,sttoc);
end
return;

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% fmrib_fastr() - Remove FMRI gradient artifacts from EEG data using

Copyright (C) 2006 University of Oxford

(at your option) any later version.

% Calculate artifact dimentions

% Other & ANC settings

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