2023_Blaschke_Stroke_tDCS_rsfMRI/scripts/addendum/calculateFD.m

function FD_measures = calculateFD(MP, r, FD_threshold)
% Function to calculate framewise displacement (FD) and related measures.
%
% INPUT:
% MP                 - movement parameter matrix (Nt x 6)
% r                  - radius to use for displacement derived from
%                      rotational movement parameters
% FD_threshold       - threshold (in mm) that defines outlier volumes 
% 
% OUTPUT: 
% FD_measures        - structure with filenames and data
%__________________________________________________________________________
% Copyright (C) Stephan Heunis 2018

% Define variables
FD_measures = struct;
[Nt, p] = size(MP);

% First demean and detrend the movement parameters
MP2 = MP - repmat(mean(MP, 1), Nt,1);
X = (1:Nt)';
X2 = X - mean(X);
X3 = [ones(Nt,1) X2];
b = X3\MP2;
MP_corrected = MP2 - X3(:, 2)*b(2,:);

% Then transform rotational parameters to linear translations (small angle assumption)
MP_mm = MP_corrected; 
MP_mm(:,4:6) = MP_mm(:,4:6)*r; % 50mm from Power 2017; 80 mm from QAP

% Calculate FD and related measures
MP_diff = [zeros(1, 6); diff(MP_mm)];
FD_measures.FD = sum(abs(MP_diff),2);
FD_measures.FD_outliers_regr = FD_measures.FD>=FD_threshold;
FD_measures.FD_outliers_ind = find(FD_measures.FD_outliers_regr);
FD_measures.FD_sum = sum(FD_measures.FD);
FD_measures.FD_mean = FD_measures.FD_sum/Nt;