ExtractGradient.m

%% gradMetricSub1.m — gradient concentration of D = moco - noMoco (Subject 1)
noMocoFile = 'I:\yannic.delisle\scripts\sub-09\baseline_nomoco\x_nomoco_1bin_mathilda_manual_finalNu240.mat';
% Add the paths of the best stride per window
mocoFiles = {
  'I:\yannic.delisle\scripts\sub-09\sliding_L5.5_S1.1\x_moco_mathilda_smoothedMotion_from_x_cs_tres1.1s_Nu120x120x120_delta1_sliding.mat'
  'I:\yannic.delisle\scripts\sub-09\sliding_L3.5_S2.1\x_moco_mathilda_smoothedMotion_from_x_cs_tres2.1s_Nu120x120x120_delta2_sliding.mat'   
};

% --- no-moco: load, magnitude, normalize by its own 99th percentile ---
S = load(noMocoFile,'x_nomoco');   A = abs(double(S.x_nomoco));
A = A / prctile(A(:),99);
zc  = round(size(A,3)/2);          % central axial slice (matches the heatmap figure)
ref = A(:,:,zc);

% --- brain mask + interior / boundary bands (needs Image Processing Toolbox) ---
mask     = imfill(ref > 0.3, 'holes');        % tune 0.12 if the mask looks wrong
interior = imerode(mask, strel('disk',6));
boundary = mask & ~interior;

figure; imagesc(mask); axis image;           % <-- uncomment to sanity-check the mask

for k = 1:numel(mocoFiles)
    T = load(mocoFiles{k},'x_moco');   B = abs(double(T.x_moco));
    B = B / prctile(B(:),99);
    D  = B(:,:,zc) - ref;                       % same D as the heatmap
    gx = (D([2:end end],:) - D([1 1:end-1],:))/2;
    gy = (D(:,[2:end end]) - D(:,[1 1:end-1]))/2;
    g  = sqrt(gx.^2 + gy.^2);                    % |grad D|
    ri = mean(g(interior));  rb = mean(g(boundary));
    fprintf('%s\n   interior=%.4g   boundary=%.4g   ratio=%.2f\n\n', ...
            mocoFiles{k}, ri, rb, rb/ri);
end


% Subject 6 results:
% I:\yannic.delisle\scripts\sub-06\sliding_L5.5_S5.5\x_moco_mathilda_smoothedMotion_from_x_cs_tres5.5s_Nu120x120x120_delta1_sliding.mat
%    interior=0.03341   boundary=0.03815   ratio=1.14
% 
% I:\yannic.delisle\scripts\sub-06\sliding_L3.5_S2.8\x_moco_mathilda_smoothedMotion_from_x_cs_tres2.8s_Nu120x120x120_delta2_sliding.mat
%    interior=0.03238   boundary=0.03799   ratio=1.17