DCAN-Labs / DCAN-Labs/dcan_bold_processing

Modular processing reintroducing artifacts

Open
#38 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
MATLAB
Stars
9
Forks
8
PR merge metrics
No merged PRs in 30d

Description

I think [dcan_signal_processing.m](https://github.com/DCAN-Labs/dcan_bold_processing/blob/main/matlab_code/dcan_signal_processing.m) suffers from the issues described by [Lindquist et al. 2019](https://doi.org/10.1002/hbm.24528). Motion (and other confounds) are regressed from the data, and then the data are subjected to band-pass filtering. If the filters are not orthogonal to the confounds, they will re-introduce confounding. So, for example, the data after band-pass filtering may still have confounds with motion.

```matlab

rng(0)

% number of time points
N = 1000;
bp_order = 2;
lp_hz = 0.009;
hp_hz = 0.080;
F = 0.7;

% true signal, with autocorrelation
a = 0; b = .4; sigma = 1;
y0 = a / (1 - b); %eg initialize to unconditional mean of stationary time series

x = zeros(N,1);
x(1) = a + b * y0 + randn() * sigma;
for t = 2:N
x(t) = a + b * x(t-1) + randn() * sigma;
end

% can also experiment with signal that has no autocorrelation
% x = randn(N, 1);

% confounds correlated with true signal
r = x + randn(N, 1);

% observed signal
y = x + r + randn(N, 1);

% y is correlated with r (by design)
orig_cor = corr(y,r);
fprintf('original correlation: %.5f\n', orig_cor);

b = regress(y, r);
y_clean = y - r*b;

% regression has removed correlation
clean_cor = corr(y_clean, r);
fprintf('clean correlation: %.5f\n', clean_cor);

% now, apply band-pass filter
Ny = F / 2;
BW_Hz = [lp_hz hp_hz];
BW_N = BW_Hz / Ny;
[b, a] = butter(ceil(bp_order/2), BW_N);
% zero-pad the data for filtering by concatenating rows of zeros on either side of the data
padding = zeros(size(y_clean));
pad_amt = size(padding, 1);
temp = cat(1, padding, y_clean, padding);
y_clean_filtered = filtfilt(b, a, temp);
y_clean_filtered = y_clean_filtered((pad_amt + 1):(end-pad_amt), :);

% but now it's back!
filtered_cor = corr(y_clean_filtered, r);
fprintf('correlation after filtering: %.5f\n', filtered_cor);
```

```matlab
% original correlation: 0.88504
% clean correlation: -0.00005
% correlation after filtering: 0.13719
```

Fixes are straightforward. One approach would be to ensure that the band-pass filter is applied to the confounds before regression (though, be careful with the polynomial detrending).

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.