ImaGIN_AverageTF.m
11 KB
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function D = ImaGIN_AverageTF(S)
% Average TF in a given frequency band (from 3D to 2D data)
% -=============================================================================
% This function is part of the ImaGIN software:
% https://f-tract.eu/
%
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
%
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE AUTHORS
% DO NOT ASSUME ANY LIABILITY OR RESPONSIBILITY FOR ITS USE IN ANY CONTEXT.
%
% Copyright (c) 2000-2018 Inserm U1216
% =============================================================================-
%
% Authors: Olivier David
[Finter,Fgraph,CmdLine] = spm('FnUIsetup','TF',0);
try
D = S.D;
catch
D = spm_select(inf, '\.mat$', 'Select EEG mat file');
end
P = spm_str_manip(D, 'H');
try
if size(D,1)==1
D = spm_eeg_load(D);
else
DD=D;
clear D
for i1=1:size(DD,1)
D{i1}= spm_eeg_load(deblank(DD(i1,:)));
end
end
catch
error(sprintf('Trouble reading file %s', D));
end
if iscell(D)
try
Method = S.Method;
catch
Ctype = {
'Mean',...
'Median',...
'ITC'};
str = 'Type of averaging ';
Sel = spm_input(str, 2, 'm', Ctype);
Method = Ctype{Sel};
end
DD=D;clear D
switch Method
case 'Mean'
data=zeros([size(DD{1}) length(DD)]);
for i1=1:length(DD)
D =DD{i1};
if length(size(data))==4
data(:,:,:,i1)=double(D(:,:,:));
else
data(:,:,:,:,i1)=double(D(:,:,:,:));
end
end
data=jg_nanmean(data,length(size(data)));
case 'ITC'
data=0;
for i1=1:length(DD)
data=data+exp(1i*double(DD{i1}(:,:,:)));
end
data=abs(data./length(DD));
case 'Median'
data=zeros([size(DD{1}) length(DD)]);
for i1=1:length(DD)
D =DD{i1};
if length(size(data))==4
data(:,:,:,i1)=double(D(:,:,:));
else
data(:,:,:,:,i1)=double(D(:,:,:,:));
end
end
data=nanmedian(data,length(size(data)));
end
try
Name=S.NewName;
catch
Name=spm_input('Name of new file', '+1', 's');
end
D=DD{1};
if isempty(Name)%Assume namefiles are numbered, have the same events
for i1=1:length(D.fnamedat)
if ~strcmp(DD{1}.fnamedat(i1),DD{2}.fnamedat(i1))
fn=D.fnamedat;
i2=find(fn(i1+1:end)=='_');
fnamedat=[fn(1:i1-1) 'Mean_' fn(i1+i2(1)+1:end)];
break
end
end
else
fnamedat=[Name '.dat'];
end
D=clone(D,fnamedat,[D.nchannels D.Nfrequencies size(D,3) 1]);
D(:,:,:)=data;
save(D);
else
if isfield(D, 'Nfrequencies');
try
fmt = S.fmt;
catch
spm_input('average over ...', 1, 'd')
Ctype = {
'electrodes',...
'events',...
'frequency'};
str = 'Average over which dimension';
Sel = spm_input(str, 2, 'm', Ctype);
fmt = Ctype{Sel};
end
switch fmt
case {'electrodes'}
Ctype = {
'Dat',...
'Img'};
str = 'Generate ';
Sel = spm_input(str, 2, 'm', Ctype);
fmt2 = Ctype{Sel};
switch fmt2
case {'Dat'}
data=(sum(D(1:round(D.nchannels/2),:,:,:),1)+sum(D(round(D.nchannels/2)+1:end,:,:,:),1))./D.nchannels;
D=clone(D,['e' D.fnamedat], [1 size(D,2) size(D,3)]);
D.tf.channels=1;
D(:,:,:)=data;
save(D);
case {'Img'}
try
D.electrodes_of_interest = S.thresholds.elecs;
catch
str = 'electrodes[s]';
Ypos = -1;
while 1
if Ypos == -1
[D.electrodes_of_interest, Ypos] = spm_input(str, '+1', 'r', [], [1 Inf]);
else
D.electrodes_of_interest = spm_input(str, Ypos, 'r', [], [1 Inf]);
end
t=1:D.nchannels;
tmp=[];
for en=D.electrodes_of_interest;
if isempty(find(t==en))
tmp=[tmp,en];
end
end
if isempty(tmp) break, end
end
end
try
D.Nregion = S.region_no;
catch
str = 'region number';
Ypos = -1;
while 1
if Ypos == -1
[D.Nregion, Ypos] = spm_input(str, '+1', 'r', [], [1 Inf]);
else
D.Nregion = spm_input(str, Ypos, 'r', [], [1 Inf]);
end
if ~isempty(D.Nregion) break, end
str = 'No data';
end
end
%number the different types
Events=events(D);
if(~isempty(Events))
try
Events(1).type;
catch
Events=Events{1};
end
end
Types={};
for i1=1:length(Events)
trouve=0;
for i2=1:length(Types)
if ~strcmp(Types{i2},Events(i1).type) && i2==length(Types) && ~trouve
Types{end+1}=Events(i1).type;
elseif strcmp(Types{i2},Events(i1).type)
trouve=1;
end
end
if isempty(Types)
Types{1}=Events(1).type;
end
end
for i = 1 : length(Types)
Itrials = find(Events.type == Events(i).type);
cd(D.path)
dname = sprintf('%dROI_TF_trialtype%d', D.Nregion, Events(i).types);
[m, sta] = mkdir(dname);
cd(dname);
for l = Itrials
% if single trial data make new directory for single trials,
% otherwise just write images to trialtype directory
if D.ntrials~= Types
% single trial data
dname = sprintf('trial%d.img', l);
fname = dname;
[m, sta] = mkdir(dname);
cd(dname);
else
fname = 'average.img';
end
data=squeeze(mean(D(D.electrodes_of_interest,:,:,i),1));
V.fname = fname;
V.dim = [D.Nfrequencies D.nsamples 1 ];
V.dt=[spm_type('float64') 0]; %%%check later with john
V.mat = eye(4);
V.pinfo = [1 0 0]';
spm_write_vol(V, data); % d is data
end
end
end
case {'frequency'}
try
D.Frequency_window = S.freqs;
Ypos = -1;
while 1
if Ypos == -1
Ypos = '+1';
end
inds=find(D.tf.frequencies>=D.Frequency_window(1) & D.tf.frequencies<=D.Frequency_window(2));
if ~isempty(inds) break, end
str = 'No data in range';
end
catch
str = 'Frequency window';
Ypos = -1;
while 1
if Ypos == -1
Ypos = '+1';
end
[D.Frequency_window, Ypos] = spm_input(str, Ypos, 'r', [], 2);
inds = find(D.tf.frequencies>=D.Frequency_window(1) & D.tf.frequencies<=D.Frequency_window(2));
if ~isempty(inds) break, end
str = 'No data in range';
end
end
data=squeeze(mean(D(:,inds,:,:),2));
D=clone(D,['F' num2str(D.Frequency_window(1)) '_' num2str(D.Frequency_window(2)) '_' D.fnamedat], [size(D,1) size(D,3) 1]);
D(:,:)=data;
D=rmfield(D,'Nfrequencies');
D=rmfield(D,'tf');
save(D);
case {'events'}
%number the different types
Events=events(D);
if(~isempty(Events))
try
Events(1).type;
catch
Events=Events{1};
end
end
Types={};
for i1=1:length(Events)
trouve=0;
for i2=1:length(Types)
if ~strcmp(Types{i2},Events(i1).type) && i2==length(Types) && ~trouve
Types{end+1}=Events(i1).type;
elseif strcmp(Types{i2},Events(i1).type)
trouve=1;
end
end
if isempty(Types)
Types{1}=Events(1).type;
end
end
data=squeeze(mean(D(:,:,:,:),4));
D=clone(D,['m_' D.fnamedat], [D.nchannels D.Nfrequencies D.nsamples 1]);
D=events(D,1,Events);
D(:,:,:)=data;
save(D);
end
else
error('No time frequency data');
end
end