https://github.com/CNG-LAB/cngopen
Tip revision: 07d4a1a03267dac12ac8bfbccc8e09049cac9f31 authored by Bin Wan on 09 August 2022, 14:58:28 UTC
Update readme.md
Update readme.md
Tip revision: 07d4a1a
load_data.m
%% Made by Sofie Louise Valk between 2014 and 2021
%% s.valk@fz-juelich.de / valk@cbs.mpg.de
% Dependencies used:
% brainspace: download here: https://brainspace.readthedocs.io/en/latest/pages/install.html
% surfstat: https://mica-mni.github.io/surfstat/
% scientific colourmaps: https://www.fabiocrameri.ch/colourmaps/
% raincloudplots: https://github.com/RainCloudPlots/RainCloudPlots
% canlab-core: https://github.com/canlab/CanlabCore for prediction
% load brain surface
% SN = brain surface to project results on (fsaverage 5)
% mask = no regions in mid-surface cut
% keepallrest = %movement data + bad quality
% load the gradients
% [closed_data] unfortunately data cannot be shared, please contact Sofie Valk
% for details.
%
% Basically, vertex-level functional connectivity matrices are created for each
% individual at each time-point, using functional data that is projected on
% fsaverage5 surfaces. Following, gradients are constructed using
% brainspace (https://brainspace.readthedocs.io/en/latest/) and aligned
% using procrustes alignment to a template functional connectivity matrix
% based on the HCP S1200 young adult sample (van Essen, 2013).
% Following the next analysis are performed, similar to this work:
% https://elifesciences.org/articles/64694. We reran analysis using a
% parcellation framework (e.g. summarized the data within the Schaefer 400
% parcels (Schaefer, 2018) which gave comparable results- but made
% computations faster- and also reran analysis using the BCT toolbox to
% generate alternative measures of integration and segregation: clustering coefficient
% and path length (https://sites.google.com/site/bctnet/).
% vertex level eccentricity for participants across timepoints
for i = 1:992
GGG(i,:) = sqrt((G1(i,:).^2)+(G2(i,:).^2)+(G3(i,:).^2));
end
% make difference score for eccentricity
for difference_score = 1
keep1 = find(~isnan(GGG(:,2))); % remove those without scanning data
keep3 = mintersect(keep1, find(keepallrest2==1)); % remove outliers with 0.3 mm/degree movement
keep_bv = keep3;
keeptest = zeros(length(id),1);
keeptest(keep3) = 1;
eZ = zeros(992,20484);
eZ(:,mask==1) = GGG(1:992,mask==1);
eZ(isnan(eZ)) = 0;
%remove outliers based on correlation with mean eccentrcity (motivated by Hong, 2020)
r = corr(mean(eZ)',eZ');
outliers_ggg = (r>0.5)';
keep = find(keeptest==1);
minit = zeros(size(id));
tp_t0_there = minit;
tp_t1_there = minit;
tp_t2_there = minit;
tp_t3_there = minit;
daysfrombl = minit;
daysfromt1 = minit;
daysfromt2 = minit;
eChange_bl = zeros(size(eZ))-666; % -666 operation is chosen to exclude 0 data otherwise unnoticed by the substraction procedure
eChange_t1 = zeros(size(eZ))-666;
eChange_t2 = zeros(size(eZ))-666;
% who have data there?
for i = 1:length(id) %id is participant id per timepoint
if keeptest(i,:).*outliers_ggg(i,:) == 1
i
inter0 = intersect(find(tpnum==0),find(idnum==idnum(i)));
inter1 = intersect(find(tpnum==1),find(idnum==idnum(i)));
inter2 = intersect(find(tpnum==2),find(idnum==idnum(i)));
inter3 = intersect(find(tpnum==3),find(idnum==idnum(i)));
tp_t0_there(i,1) = ~isempty(inter0) .* keeptest(i)==1;
if ~isempty(inter0)
tp_t0_there(i,1) = tp_t0_there(i,1) .* keeptest(inter0);
end
tp_t1_there(i,1) = ~isempty(inter1) .* keeptest(i)==1;
if ~isempty(inter1)
tp_t1_there(i,1) = tp_t1_there(i,1) .* keeptest(inter1);
end
tp_t2_there(i,1) = ~isempty(inter2) .* keeptest(i)==1;
if ~isempty(inter2)
tp_t2_there(i,1) = tp_t2_there(i,1) .* keeptest(inter2);
end
tp_t3_there(i,1) = ~isempty(inter3) .* keeptest(i)==1;
if ~isempty(inter3)
tp_t3_there(i,1) = tp_t3_there(i,1) .* keeptest(inter3);
end
if keeptest(inter0)~=0
daysfrombl(i,1) = days(i)-days(inter0);
eChange_bl(i,:,:) = (eZ(i,:,:) - eZ(inter0,:,:));
end
if keeptest(inter1)~=0
daysfromt1(i,1) = days(i)-days(inter1);
eChange_t1(i,:,:) = (eZ(i,:,:) - eZ(inter1,:,:));
end
if keeptest(inter2)~=0
daysfromt2(i,1) = days(i)-days(inter2);
eChange_t2(i,:,:) = (eZ(i,:,:) - eZ(inter2,:,:));
end
else
end
end
ZChange_last = zeros(size(GGG));
ZChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:,:);
ZChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:,:);
ZChange_last(strcmp(group4,'Group3') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Group3') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Group3') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Group3') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Group3') & strcmp(tp,'T3'),:,:);
ZChange_last(strcmp(group4,'Control') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Control') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Control') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Control') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Control') & strcmp(tp,'T3'),:,:);
Z_last = ZChange_last;
end
% make difference score for G1
for difference_score = 1
keep1 = find(~isnan(GGG(:,2)));
keep3 = mintersect(keep1, find(keepallrest2==1));
keep_bv = keep3;
keeptest = zeros(length(id),1);
keeptest(keep3) = 1;
eZ = zeros(992,20484);
eZ(:,mask==1) = G1all(1:992,mask==1);
eZ(isnan(eZ)) = 0;
%remove outliers
r = corr(mean(eZ)',eZ');
outliers_g1 = (r>0.5)';
keep = find(keeptest==1);
minit = zeros(size(id));
tp_t0_there = minit;
tp_t1_there = minit;
tp_t2_there = minit;
tp_t3_there = minit;
daysfrombl = minit;
daysfromt1 = minit;
daysfromt2 = minit;
eChange_bl = zeros(size(eZ))-666;
eChange_t1 = zeros(size(eZ))-666;
eChange_t2 = zeros(size(eZ))-666;
% who have data there?
for i = 1:length(id)
if keeptest(i,:).*outliers_g1(i,:) == 1
i
inter0 = intersect(find(tpnum==0),find(idnum==idnum(i)));
inter1 = intersect(find(tpnum==1),find(idnum==idnum(i)));
inter2 = intersect(find(tpnum==2),find(idnum==idnum(i)));
inter3 = intersect(find(tpnum==3),find(idnum==idnum(i)));
tp_t0_there(i,1) = ~isempty(inter0) .* keeptest(i)==1;
if ~isempty(inter0)
tp_t0_there(i,1) = tp_t0_there(i,1) .* keeptest(inter0);
end
tp_t1_there(i,1) = ~isempty(inter1) .* keeptest(i)==1;
if ~isempty(inter1)
tp_t1_there(i,1) = tp_t1_there(i,1) .* keeptest(inter1);
end
tp_t2_there(i,1) = ~isempty(inter2) .* keeptest(i)==1;
if ~isempty(inter2)
tp_t2_there(i,1) = tp_t2_there(i,1) .* keeptest(inter2);
end
tp_t3_there(i,1) = ~isempty(inter3) .* keeptest(i)==1;
if ~isempty(inter3)
tp_t3_there(i,1) = tp_t3_there(i,1) .* keeptest(inter3);
end
if keeptest(inter0)~=0
daysfrombl(i,1) = days(i)-days(inter0);
eChange_bl(i,:,:) = (eZ(i,:,:) - eZ(inter0,:,:));
end
if keeptest(inter1)~=0
daysfromt1(i,1) = days(i)-days(inter1);
eChange_t1(i,:,:) = (eZ(i,:,:) - eZ(inter1,:,:));
end
if keeptest(inter2)~=0
daysfromt2(i,1) = days(i)-days(inter2);
eChange_t2(i,:,:) = (eZ(i,:,:) - eZ(inter2,:,:));
end
else
end
end
ZChange_last = zeros(size(GGG));
ZChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:,:);
ZChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:,:);
ZChange_last(strcmp(group4,'Group3') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Group3') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Group3') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Group3') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Group3') & strcmp(tp,'T3'),:,:);
ZChange_last(strcmp(group4,'Control') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Control') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Control') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Control') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Control') & strcmp(tp,'T3'),:,:);
G1_last = ZChange_last;
end
% make difference score for G2
for difference_score = 1
keep1 = find(~isnan(GGG(:,2)));
keep3 = mintersect(keep1, find(keepallrest2==1));
keep_bv = keep3;
keeptest = zeros(length(id),1);
keeptest(keep3) = 1;
eZ = zeros(992,20484);
eZ(:,mask==1) = G2all(1:992,mask==1);
eZ(isnan(eZ)) = 0;
r = corr(mean(eZ)',eZ');
outliers_g2 = (r>0.5)';
keep = find(keeptest==1);
minit = zeros(size(id));
tp_t0_there = minit;
tp_t1_there = minit;
tp_t2_there = minit;
tp_t3_there = minit;
daysfrombl = minit;
daysfromt1 = minit;
daysfromt2 = minit;
eChange_bl = zeros(size(eZ))-666;
eChange_t1 = zeros(size(eZ))-666;
eChange_t2 = zeros(size(eZ))-666;
% who have data there?
for i = 1:length(id)
if keeptest(i,:).*outliers_g2(i,:) == 1
i
inter0 = intersect(find(tpnum==0),find(idnum==idnum(i)));
inter1 = intersect(find(tpnum==1),find(idnum==idnum(i)));
inter2 = intersect(find(tpnum==2),find(idnum==idnum(i)));
inter3 = intersect(find(tpnum==3),find(idnum==idnum(i)));
tp_t0_there(i,1) = ~isempty(inter0) .* keeptest(i)==1;
if ~isempty(inter0)
tp_t0_there(i,1) = tp_t0_there(i,1) .* keeptest(inter0);
end
tp_t1_there(i,1) = ~isempty(inter1) .* keeptest(i)==1;
if ~isempty(inter1)
tp_t1_there(i,1) = tp_t1_there(i,1) .* keeptest(inter1);
end
tp_t2_there(i,1) = ~isempty(inter2) .* keeptest(i)==1;
if ~isempty(inter2)
tp_t2_there(i,1) = tp_t2_there(i,1) .* keeptest(inter2);
end
tp_t3_there(i,1) = ~isempty(inter3) .* keeptest(i)==1;
if ~isempty(inter3)
tp_t3_there(i,1) = tp_t3_there(i,1) .* keeptest(inter3);
end
if keeptest(inter0)~=0
daysfrombl(i,1) = days(i)-days(inter0);
eChange_bl(i,:,:) = (eZ(i,:,:) - eZ(inter0,:,:));
end
if keeptest(inter1)~=0
daysfromt1(i,1) = days(i)-days(inter1);
eChange_t1(i,:,:) = (eZ(i,:,:) - eZ(inter1,:,:));
end
if keeptest(inter2)~=0
daysfromt2(i,1) = days(i)-days(inter2);
eChange_t2(i,:,:) = (eZ(i,:,:) - eZ(inter2,:,:));
end
else
end
end
ZChange_last = zeros(size(GGG));
ZChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:,:);
ZChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:,:);
ZChange_last(strcmp(group4,'Group3') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Group3') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Group3') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Group3') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Group3') & strcmp(tp,'T3'),:,:);
ZChange_last(strcmp(group4,'Control') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Control') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Control') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Control') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Control') & strcmp(tp,'T3'),:,:);
G2_last = ZChange_last;
end
% make difference score for G3
for difference_score = 1
keep1 = find(~isnan(GGG(:,2)));
keep3 = mintersect(keep1, find(keepallrest2==1));
keep_bv = keep3;
keeptest = zeros(length(id),1);
keeptest(keep3) = 1;
eZ = zeros(992,20484);
eZ(:,mask==1) = G3all(1:992,mask==1);
eZ(isnan(eZ)) = 0;
r = corr(mean(eZ)',eZ');
outliers_g3 = (r>0.5)';
keep = find(keeptest==1);
minit = zeros(size(id));
tp_t0_there = minit;
tp_t1_there = minit;
tp_t2_there = minit;
tp_t3_there = minit;
daysfrombl = minit;
daysfromt1 = minit;
daysfromt2 = minit;
eChange_bl = zeros(size(eZ))-666;
eChange_t1 = zeros(size(eZ))-666;
eChange_t2 = zeros(size(eZ))-666;
% who have data there?
for i = 1:length(id)
if keeptest(i,:).*outliers_g3(i,:) == 1
i
inter0 = intersect(find(tpnum==0),find(idnum==idnum(i)));
inter1 = intersect(find(tpnum==1),find(idnum==idnum(i)));
inter2 = intersect(find(tpnum==2),find(idnum==idnum(i)));
inter3 = intersect(find(tpnum==3),find(idnum==idnum(i)));
tp_t0_there(i,1) = ~isempty(inter0) .* keeptest(i)==1;
if ~isempty(inter0)
tp_t0_there(i,1) = tp_t0_there(i,1) .* keeptest(inter0);
end
tp_t1_there(i,1) = ~isempty(inter1) .* keeptest(i)==1;
if ~isempty(inter1)
tp_t1_there(i,1) = tp_t1_there(i,1) .* keeptest(inter1);
end
tp_t2_there(i,1) = ~isempty(inter2) .* keeptest(i)==1;
if ~isempty(inter2)
tp_t2_there(i,1) = tp_t2_there(i,1) .* keeptest(inter2);
end
tp_t3_there(i,1) = ~isempty(inter3) .* keeptest(i)==1;
if ~isempty(inter3)
tp_t3_there(i,1) = tp_t3_there(i,1) .* keeptest(inter3);
end
if keeptest(inter0)~=0
daysfrombl(i,1) = days(i)-days(inter0);
eChange_bl(i,:,:) = (eZ(i,:,:) - eZ(inter0,:,:));
end
if keeptest(inter1)~=0
daysfromt1(i,1) = days(i)-days(inter1);
eChange_t1(i,:,:) = (eZ(i,:,:) - eZ(inter1,:,:));
end
if keeptest(inter2)~=0
daysfromt2(i,1) = days(i)-days(inter2);
eChange_t2(i,:,:) = (eZ(i,:,:) - eZ(inter2,:,:));
end
else
end
end
ZChange_last = zeros(size(GGG));
ZChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:,:);
ZChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:,:);
ZChange_last(strcmp(group4,'Group3') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Group3') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Group3') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Group3') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Group3') & strcmp(tp,'T3'),:,:);
ZChange_last(strcmp(group4,'Control') & strcmp(tp,'T1'),:,:) = eChange_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),:,:);
ZChange_last(strcmp(group4,'Control') & strcmp(tp,'T2'),:,:) = eChange_t1(strcmp(group4,'Control') & strcmp(tp,'T2'),:,:);
ZChange_last(strcmp(group4,'Control') & strcmp(tp,'T3'),:,:) = eChange_t2(strcmp(group4,'Control') & strcmp(tp,'T3'),:,:);
G3_last = ZChange_last;
end
