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prevent systematic physiological noise bias (phase jitter + demeaning) #101

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prevent systematic physiological noise bias (phase jitter + demeaning) #101

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18 changes: 12 additions & 6 deletions classdefs/@pmNoise/pmNoise.m
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Original file line number Diff line number Diff line change
Expand Up @@ -334,11 +334,13 @@ function compute(noise)
% Frequency [Hz]
fNoise = noise.cardiac_frequency*(1 + noise.jitter(1)*randn(1,1));
% Amplitude
aNoise = noise.cardiac_amplitude*(1 + noise.jitter(2)*randn(1,1));
aNoise = noise.cardiac_amplitude * abs(1 + noise.jitter(2)*randn(1,1));
% Time points
t = noise.PM.timePointsSeries;
% Calculate the noise
tmpNoise{2} = aNoise * sin(2 * pi .* t .* fNoise);
phi = 2*pi*rand(1,1);
tmp = aNoise * sin(2*pi.*t.*fNoise + phi);
tmpNoise{2} = tmp - mean(tmp);
end

% RESPIRATORY
Expand All @@ -349,11 +351,13 @@ function compute(noise)
% Frequency [Hz]
fNoise = noise.respiratory_frequency*(1 + noise.jitter(1)*randn(1,1));
% Amplitude
aNoise = noise.respiratory_amplitude * (1 + noise.jitter(2)*randn(1,1));
aNoise = noise.respiratory_amplitude * abs(1 + noise.jitter(2)*randn(1,1));
% Time points
t = noise.PM.timePointsSeries;
% Calculate the noise
tmpNoise{3} = aNoise * sin(2 * pi .* t .* fNoise);
phi = 2*pi*rand(1,1);
tmp = aNoise * sin(2*pi.*t.*fNoise + phi);
tmpNoise{3} = tmp - mean(tmp);
end

% LOW FREQU DRIFT
Expand All @@ -370,7 +374,7 @@ function compute(noise)

% Jitter: see cardiac and respiratory
fNoise = noise.lowfrequ_frequ * (1 + noise.jitter(1)*randn(1,1));
aNoise = noise.lowfrequ_amplitude * (1 + noise.jitter(2)*randn(1,1));
aNoise = noise.lowfrequ_amplitude * abs(1 + noise.jitter(2)*randn(1,1));

n = floor(2 * (noise.PM.timePointsN * noise.PM.TR)/fNoise + 1);
if (n < 3)
Expand All @@ -380,7 +384,8 @@ function compute(noise)
driftbase = spmdrift(:,2:end); % Eliminate the DC term
driftbase = sum(driftbase,2)';
% Now we need to scale this noise to the actual noise values
tmpNoise{4} = aNoise * driftbase;
tmp = aNoise * driftbase;
tmpNoise{4} = tmp - mean(tmp);
end


Expand All @@ -393,6 +398,7 @@ function compute(noise)
end

% RETURN VALUES
vals = vals - mean(vals);
noise.values = vals;

end
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