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2016.Valk.ReSource.FN.m
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2016.Valk.ReSource.FN.m
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%% ReSource Matlab Cortical Thickness DBM
% January 2016
%
%
%
% author: [email protected], [email protected],de
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% settings
% -----------------
% paths, toolboxes, colormaps
% -----------------
close all
clear all;
for load_data = 1
P = ['/scr/elbe10/boris/Resting_sofie/matlab_sofie/Project3/Boris'];
%P = '/Users/boris/Downloads/Boris'
addpath([P '/toolboxes/2012-08-14_BCT/'])
addpath([P '/toolboxes/useful/'])
addpath([P '/toolboxes/surfstat_chicago'])
addpath([P '/toolboxes/gretna/'])
addpath([P '/toolboxes/NIFTI_20110921/'])
addpath([P '/toolboxes/boris_noelsoft/boris'])
addpath([P '/toolboxes/matlab-tools'])
addpath([P '/toolboxes/Functions'])
ico = '5';
kernel = '20';
RPATHO = [P '/results_' kernel '/'];
SPATH = [P '/toolboxes/surf_fsa5'];
mkdir(RPATHO)
blackblue = [zeros(1,3)*0.8;
zeros(127,1) (0:126)'/127 ones(127,1)];
mycol.blackblue = flipud(blackblue);
blue = [ones(1,3)*0.8;
zeros(127,1) (0:126)'/127 ones(127,1)];
mycol.blue = flipud(blue);
mycol.red = [ones(1,3)*0.8; ...
ones(64,1) linspace(0,253,64)'/254 zeros(64,1);...
ones(64,1) ones(64,1) linspace(0,253,64)'/254];
buckner = ([102 51 51; 51 51 102; 102 102 153; 153 153 204; 153 255 51; ...
102 204 51; 255 255 51; 255 153 51; 255 102 51; 204 51 0])./255;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% read surface data
% -----------------
% mesh, parcels,
% -----------------
% load: mesh
% -----------------
cd(SPATH)
SPHERE = SurfStatReadSurf({'lh.sphere','rh.sphere'});
S = SurfStatReadSurf({'lh.inflated','rh.inflated'});
SW = SurfStatReadSurf({'lh.white','rh.white'});
SP = SurfStatReadSurf({'lh.pial','rh.pial'});
SM.tri = SW.tri;
SM.coord = (SW.coord + SP.coord)./2;
SInf = SW;ls
SInf.coord = 0.2 *SW.coord + 0.8* S.coord;
% load: Destrieux atlas
% -----------------
[vertices, label, colortable] = ...
fs_read_annotation([SPATH 'lh.aparc.a2009s.annot']);
aparcleft = label;
for i = 1:size(colortable.table,1)
mycode = colortable.table(i,5);
aparcleft(find(aparcleft == mycode)) = i;
end
[vertices, label, colortable] = ...
fs_read_annotation([SPATH 'rh.aparc.a2009s.annot']);
aparcright = label;
for i = 1:size(colortable.table,1)
mycode = colortable.table(i,5);
aparcright(find(aparcright == mycode)) = i;
end
aparc = [aparcleft;aparcright+100];
aparc = aparc';
% load: curvature
% -----------------
CURV = SurfStatReadData({'fsaverage_curv_lh.asc','fsaverage_curv_rh.asc'});
end
%% read csv
% -----------------
for readcsv = 1
fid = fopen([P '/time_points_scan_NOV2015_4.csv']);
C = textscan(fid,'%s%s%n%s%s%s%s%s%n%n%n%n%n','Delimiter',',','CollectOutput',1,'Headerlines',1);
fclose(fid);
dropout = C{4}(:,4);
bad = C{4}(:,5);
tphelp = C{3}(:,5);
keep = mintersect(find(~dropout), ...
find(~bad), ...
find(~strcmp(tphelp,'-666')), ...
find(~strcmp(tphelp,'T4')));
code = C{1}(keep,1);
age = C{2}(keep,1);
sex = C{3}(keep,1);
site = C{3}(keep,2);
group = C{3}(keep,3);
id = C{3}(keep,4);
tp = C{3}(keep,5);
year = C{4}(keep,1);
month = C{4}(keep,2);
day = C{4}(keep,3);
days = datenum(year,month,day);
dayssince_first = days - min(days(days>0));
monthssince_first = dayssince_first/30;
group4 = group;
group4(strcmp(group4,'Retest_Control')) = {'Control'};
group4(strcmp(group4,'Active_Control_Abends')) = {'Group3'};
group4(strcmp(group4,'Active_Control_Morgens')) = {'Group3'};
idnum = zeros(size(id));
tpnum = idnum;
for i = 1:length(id)
idnum(i) = str2num(id{i});
if strcmp(tp{i},'T0')
tpnum(i) = 0;
elseif strcmp(tp{i},'T1')
tpnum(i) = 1;
elseif strcmp(tp{i},'T2')
tpnum(i) = 2;
elseif strcmp(tp{i},'T3')
tpnum(i) = 3;
end
end
%% retreat data (Appendix A) (to calculate not days between measurement but days between training
% TC1:
TC1_R1 = datenum(2013,6,21);
TC1_R2 = datenum(2013,9,20);
TC1_R3 = datenum(2014,1,3);
% TC2:
TC2_R1 = datenum(2013,8,9);
TC2_R2 = datenum(2013,11,8);
TC2_R3 = datenum(2014,2,21);
cd([P '/data/'])
load('CT.mat')
load('isthere-ct.mat')
load('isthere-dbm.mat')
load('myDBMsurf.mat')
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% generate change brain
% ---------------
zmap = load('zmyDBMsurf.mat')
end
for change_brain = 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;
daysfromr1 = minit;
daysfromr2 = minit;
daysfromr3 = minit;
CTChange_bl = zeros(size(CT))-666;
CTChange_t1 = zeros(size(CT))-666;
CTChange_t2 = zeros(size(CT))-666;
CTChange_blN = zeros(size(CT))-666;
CTChange_T1N = zeros(size(CT))-666;
CTChange_T2N = zeros(size(CT))-666;
CTbl = zeros(size(CT))-666;
DBMchange_bl = zeros(size(zmap.zdbm_map))-666;
DBMchange_t1 = zeros(size(zmap.zdbm_map))-666;
DBMchange_t2 = zeros(size(zmap.zdbm_map))-666;
for i = 1:length(id)
%% TC1
this = find(strcmp(group{i},'Group_1'));
if ~isempty(this)
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) .* isthere_ct(i)==1;
if ~isempty(inter0)
tp_t0_there(i,1) = tp_t0_there(i,1) .* isthere_ct(inter0);
end
tp_t1_there(i,1) = ~isempty(inter1) .* isthere_ct(i)==1;
if ~isempty(inter1)
tp_t1_there(i,1) = tp_t1_there(i,1) .* isthere_ct(inter1);
end
tp_t2_there(i,1) = ~isempty(inter2) .* isthere_ct(i)==1;
if ~isempty(inter2)
tp_t2_there(i,1) = tp_t2_there(i,1) .* isthere_ct(inter2);
end
tp_t3_there(i,1) = ~isempty(inter3) .* isthere_ct(i)==1;
if ~isempty(inter3)
tp_t3_there(i,1) = tp_t3_there(i,1) .* isthere_ct(inter3);
end
try
CTbl(i,:) = CT(inter0,:);
daysfrombl(i,1) = days(i)-days(inter0);
daysfromr1(i,1) = days(i)- TC1_R1;
CTChange_bl(i,:) = CT(i,:) - CT(inter0,:);
CTChange_blN(i,:) = (CT(i,:) - CT(inter0,:))./CT(inter0,:);
DBMchange_bl(i,:) = zmap.zdbm_map(i,:) - zmap.zdbm_map(inter0,:);
catch
%
end
try
daysfromt1(i,1) = days(i)-days(inter1);
daysfromr2(i,1) = days(i)-TC1_R2;
CTChange_t1(i,:) = CT(i,:) - CT(inter1,:);
CTChange_t1N(i,:) = (CT(i,:) - CT(inter1,:))./CT(inter1,:);
DBMchange_t1(i,:) = zmap.zdbm_map(i,:) - zmap.zdbm_map(inter1,:);
catch
%
end
try
daysfromt2(i,1) = days(i)-days(inter2);
daysfromr3(i,1) = days(i)-TC1_R3;
CTChange_t2(i,:) = CT(i,:) - CT(inter2,:);
CTChange_t2N(i,:) = (CT(i,:) - CT(inter2,:))./CT(inter2,:);
DBMchange_t2(i,:) = zmap.zdbm_map(i,:) - zmap.zdbm_map(inter2,:);
catch
%
end
else
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) .* isthere_ct(i)==1;
if ~isempty(inter0)
tp_t0_there(i,1) = tp_t0_there(i,1) .* isthere_ct(inter0);
end
tp_t1_there(i,1) = ~isempty(inter1) .* isthere_ct(i)==1;
if ~isempty(inter1)
tp_t1_there(i,1) = tp_t1_there(i,1) .* isthere_ct(inter1);
end
tp_t2_there(i,1) = ~isempty(inter2) .* isthere_ct(i)==1;
if ~isempty(inter2)
tp_t2_there(i,1) = tp_t2_there(i,1) .* isthere_ct(inter2);
end
tp_t3_there(i,1) = ~isempty(inter3) .* isthere_ct(i)==1;
if ~isempty(inter3)
tp_t3_there(i,1) = tp_t3_there(i,1) .* isthere_ct(inter3);
end
try
CTbl(i,:) = CT(inter0,:);
daysfrombl(i,1) = days(i)-days(inter0);
daysfromr1(i,1) = days(i)- TC2_R1;
CTChange_bl(i,:) = CT(i,:) - CT(inter0,:);
CTChange_blN(i,:) = (CT(i,:) - CT(inter0,:))./CT(inter0,:);
DBMchange_bl(i,:) = zmap.zdbm_map(i,:) - zmap.zdbm_map(inter0,:);
catch
%
end
try
daysfromt1(i,1) = days(i)-days(inter1);
daysfromr2(i,1) = days(i)-TC2_R2;
CTChange_t1(i,:) = CT(i,:) - CT(inter1,:);
CTChange_t1N(i,:) = (CT(i,:) - CT(inter1,:))./CT(inter1,:);
DBMchange_t1(i,:) = zmap.zdbm_map(i,:) - zmap.zdbm_map(inter1,:);
catch
%
end
try
daysfromt2(i,1) = days(i)-days(inter2);
daysfromr3(i,1) = days(i)-TC2_R3;
CTChange_t2(i,:) = CT(i,:) - CT(inter2,:);
CTChange_t2N(i,:) = (CT(i,:) - CT(inter2,:))./CT(inter2,:);
DBMchange_t2(i,:) = zmap.zdbm_map(i,:) - zmap.zdbm_map(inter2,:);
catch
%
end
end
end
% dat = [ idnum/10000 tpnum isthere_ct tp_t0_there tp_t1_there tp_t2_there ...
% daysfrombl./max(abs(daysfrombl)) daysfromt1./max(abs(daysfromt1)) ...
% daysfromt2./max(abs(daysfromt2))];
% f=figure, imagesc(dat)
mask = mean(CT,1)>0.9;
end
for load_behav = 1
cd([P '/data/'])
load('P_body.mat')
load('P_breath.mat')
load('A_hearth.mat')
load('A_adyad.mat')
load('Pe_thought.mat')
load('Pe_pdyad.mat')
load('tom.mat')
load('compassion.mat')
load('attention_c.mat')
load('attention.mat')
% not all subjects are there for the resting!!
load('rp_arest.mat')
load('FD_Power_RS.mat')
end
for initi = 1
minit = zeros(size(id))-666;
com_bl = minit;
com_bl2 = minit;
com_bl3 = minit;
comChange_bl = minit;
comChange_t1 = minit;
comChange_t2 = minit;
comChange_blN = minit;
comChange_t1N = minit;
comChange_t2N = minit;
att_bl = minit;
att_bl2 = minit;
att_bl3 = minit;
attChange_bl = minit;
attChange_t1 = minit;
attChange_t2 = minit;
attChange_blN = minit;
attChange_t1N = minit;
attChange_t2N = minit;
att_bl_c = minit;
attChange_bl_c = minit;
attChange_t1_c = minit;
attChange_t2_c = minit;
tom_bl = minit;
tom_bl2 = minit;
tom_bl3 = minit;
tomChange_bl = minit;
tomChange_t1 = minit;
tomChange_t2 = minit;
tomChange_blN = minit;
tomChange_t1N = minit;
tomChange_t2N = minit;
hearChange_bl = minit;
hearChange_t1 = minit;
hearChange_t2 = minit;
rp_arestChange_bl = zeros(size(FD_Power_RS))-666;
rp_arestChange_t1 = zeros(size(FD_Power_RS))-666;
rp_arestChange_t2 = zeros(size(FD_Power_RS))-666;
end
%% attention
for i = 1: length(id)
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)));
attention2 = (attention);
if ~isempty(inter1) & attention(inter1)> -500
if ~isempty(inter0) & attention(inter0)> -500
att_bl(i) = (attention(inter0,1));
attChange_bl(i) = (attention2(i)-attention2(inter0));
attChange_blN(i) = (attention(i)-attention(inter0))./attention(inter0);
attChange_bf(i) = attention(inter0);
attChange_bl_c(i) = (attention_c(i)-attention_c(inter0));
attChange_blN_c(i) = (attention_c(i)-attention_c(inter0))./attention_c(inter0);
end
end
if ~isempty(inter2) & attention(inter2)> -500
if ~isempty(inter1) & attention(inter1)> -500
att_bl2(i) = (attention(inter1,1));
attChange_t1(i) = (attention2(i)-attention2(inter1));
attChange_t1N(i) = (attention(i)-attention(inter1))./attention(inter1);
attChange_t1_c(i) = (attention_c(i)-attention_c(inter1));
attChange_t1N_c(i) = (attention_c(i)-attention_c(inter1))./attention_c(inter1);
end
end
if ~isempty(inter3) & attention(inter3)> -500
if ~isempty(inter2) & attention(inter2)> -500
att_bl3(i) = (attention(inter2,1));
attChange_t2(i) = (attention2(i)-attention2(inter2));
attChange_t2N(i) = (attention(i)-attention(inter2))./attention(inter2);
attChange_t2_c(i) = (attention_c(i)-attention_c(inter2));
attChange_t2N_c(i) = (attention_c(i)-attention_c(inter2))./attention_c(inter2);
end
end
end
%% tom
for i = 1: length(id)
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)));
if ~isempty(inter1) & tom(inter1)> -500
if ~isempty(inter0) & tom(inter0)> -500
tom_bl(i) = tom(inter0);
tomChange_bl(i) = (tom(i)-tom(inter0));
tomChange_blN(i) = (tom(i)-tom(inter0))./tom(inter0);
hearChange_bl(i) = (hearing(i)-hearing(inter0));
end
end
if ~isempty(inter2) & tom(inter2)> -500
if ~isempty(inter1) & tom(inter1)> -500
tom_bl2(i) = tom(inter1);
tomChange_t1(i) = (tom(i)-tom(inter1));
tomChange_t1N(i) = (tom(i)-tom(inter1))./tom(inter1);
tomChange_t1b(i) = tom(inter1);
hearChange_t1(i) = (hearing(i)-hearing(inter1));
end
end
if ~isempty(inter3) & tom(inter3)> -500
if ~isempty(inter2) & tom(inter2)> -500
tom_bl3(i) = tom(inter2);
tomChange_t2(i) = (tom(i)-tom(inter2));
tomChange_t2N(i) = (tom(i)-tom(inter2))./tom(inter2);
hearChange_t2(i) = (hearing(i)-hearing(inter2));
end
end
end
%% compassion
for i = 1: length(id)
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)));
compassion2 = (compassion);
if ~isempty(inter1) & compassion(inter1)> -500
if ~isempty(inter0) & compassion(inter0)> -500
com_bl(i) = compassion(inter0);
comChange_bl(i) = (compassion2(i)-compassion2(inter0));
comChange_blN(i) = (compassion(i)-compassion(inter0))./compassion(inter0);
comChange_bf(i) = compassion(inter0);
end
end
if ~isempty(inter2) & compassion(inter2)> -500
if ~isempty(inter1) & compassion(inter1)> -500
com_bl2(i) = compassion(inter1);
comChange_t1(i) = (compassion2(i)-compassion2(inter1));
comChange_t1N(i) = (compassion(i)-compassion(inter1))./compassion(inter1);
end
end
if ~isempty(inter3) & compassion(inter3)> -500
if ~isempty(inter2) & compassion(inter2)> -500
com_bl3(i) = compassion(inter2);
comChange_t2(i) = (compassion2(i)-compassion2(inter2));
comChange_t2N(i) = (compassion(i)-compassion(inter2))./compassion(inter2);
end
end
end
%% resting-move
for i = 1: length(id)
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)));
if ~isempty(inter1) & FD_Power_RS(inter1,1)~=0
if ~isempty(inter0) & FD_Power_RS(inter0,1)~=0
rp_arestChange_bl(i,:) = (FD_Power_RS(i,:)-FD_Power_RS(inter0,:));
end
end
if ~isempty(inter2) & FD_Power_RS(inter2,1)~=0
if ~isempty(inter1) & FD_Power_RS(inter1,1)~=0
rp_arestChange_t1(i,:) = (FD_Power_RS(i,:)-FD_Power_RS(inter1,:));
end
end
if ~isempty(inter3) & FD_Power_RS(inter3,1)~=0
if ~isempty(inter2) & FD_Power_RS(inter2,1)~=0
rp_arestChange_t2(i,:) = (FD_Power_RS(i,:)-FD_Power_RS(inter2,:));
end
end
end
%% make behavior and groups re-ordered
% ---------------
% label the training blocks
% ---------------
for reorder = 1
groupN = group4;
groupN(strcmp(group4,'Group_1') & strcmp(tp,'T1')) = {'Presence'};
groupN(strcmp(group4,'Group_1') & strcmp(tp,'T2')) = {'Affect'};
groupN(strcmp(group4,'Group_1') & strcmp(tp,'T3')) = {'Perspective'};
groupN(strcmp(group4,'Group_2') & strcmp(tp,'T1')) = {'Presence'};
groupN(strcmp(group4,'Group_2') & strcmp(tp,'T2')) = {'Perspective'};
groupN(strcmp(group4,'Group_2') & strcmp(tp,'T3')) = {'Affect'};
groupN(strcmp(group4,'Group3') & strcmp(tp,'T1')) = {'Affect'};
groupN(strcmp(group4,'Control') & strcmp(tp,'T1')) = {'Control1'};
groupN(strcmp(group4,'Control') & strcmp(tp,'T2')) = {'Control1'};
groupN(strcmp(group4,'Control') & strcmp(tp,'T3')) = {'Control1'};
%% remodel brain change wrt last time point
% ---------------
% reoder differences in thickness
% ---------------
CTChange_last = zeros(length(id),size(CTChange_bl,2));
CTChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:) = CTChange_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:);
CTChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:) = CTChange_t1(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:);
CTChange_last(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:) = CTChange_t2(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:);
CTChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:) = CTChange_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:);
CTChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:) = CTChange_t1(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:);
CTChange_last(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:) = CTChange_t2(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:);
CTChange_last(strcmp(group4,'Group3') & strcmp(tp,'T1'),:) = CTChange_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),:);
CTChange_last(strcmp(group4,'Group3') & strcmp(tp,'T2'),:) = CTChange_t1(strcmp(group4,'Group3') & strcmp(tp,'T2'),:);
CTChange_last(strcmp(group4,'Group3') & strcmp(tp,'T3'),:) = CTChange_t2(strcmp(group4,'Group3') & strcmp(tp,'T3'),:);
CTChange_last(strcmp(group4,'Control') & strcmp(tp,'T1'),:) = CTChange_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),:);
CTChange_last(strcmp(group4,'Control') & strcmp(tp,'T2'),:) = CTChange_t1(strcmp(group4,'Control') & strcmp(tp,'T2'),:);
CTChange_last(strcmp(group4,'Control') & strcmp(tp,'T3'),:) = CTChange_t2(strcmp(group4,'Control') & strcmp(tp,'T3'),:);
% for T0-T2 differences in thickness...
CTChangeBL = zeros(length(id),size(CTChange_bl,2));
CTChangeBL(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:) = CTChange_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:);
CTChangeBL(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:) = CTChange_bl(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:);
CTChangeBL(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:) = CTChange_bl(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:);
CTChangeBL(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:) = CTChange_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:);
CTChangeBL(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:) = CTChange_bl(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:);
CTChangeBL(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:) = CTChange_bl(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:);
CTChangeBL(strcmp(group4,'Group3') & strcmp(tp,'T1'),:) = CTChange_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),:);
CTChangeBL(strcmp(group4,'Group3') & strcmp(tp,'T2'),:) = CTChange_bl(strcmp(group4,'Group3') & strcmp(tp,'T2'),:);
CTChangeBL(strcmp(group4,'Group3') & strcmp(tp,'T3'),:) = CTChange_bl(strcmp(group4,'Group3') & strcmp(tp,'T3'),:);
CTChangeBL(strcmp(group4,'Control') & strcmp(tp,'T1'),:) = CTChange_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),:);
CTChangeBL(strcmp(group4,'Control') & strcmp(tp,'T2'),:) = CTChange_bl(strcmp(group4,'Control') & strcmp(tp,'T2'),:);
CTChangeBL(strcmp(group4,'Control') & strcmp(tp,'T3'),:) = CTChange_bl(strcmp(group4,'Control') & strcmp(tp,'T3'),:);
% % normalized differences in thickness
% % ---------------
CTChange_lastN = zeros(length(id),size(CTChange_blN,2));
CTChange_lastN(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:) = CTChange_blN(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:);
CTChange_lastN(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:) = CTChange_t1N(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:);
CTChange_lastN(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:) = CTChange_t2N(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:);
CTChange_lastN(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:) = CTChange_blN(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:);
CTChange_lastN(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:) = CTChange_t1N(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:);
CTChange_lastN(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:) = CTChange_t2N(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:);
CTChange_lastN(strcmp(group4,'Group3') & strcmp(tp,'T1'),:) = CTChange_blN(strcmp(group4,'Group3') & strcmp(tp,'T1'),:);
CTChange_lastN(strcmp(group4,'Group3') & strcmp(tp,'T2'),:) = CTChange_t1N(strcmp(group4,'Group3') & strcmp(tp,'T2'),:);
CTChange_lastN(strcmp(group4,'Group3') & strcmp(tp,'T3'),:) = CTChange_t2N(strcmp(group4,'Group3') & strcmp(tp,'T3'),:);
CTChange_lastN(strcmp(group4,'Control') & strcmp(tp,'T1'),:) = CTChange_blN(strcmp(group4,'Control') & strcmp(tp,'T1'),:);
CTChange_lastN(strcmp(group4,'Control') & strcmp(tp,'T2'),:) = CTChange_t1N(strcmp(group4,'Control') & strcmp(tp,'T2'),:);
CTChange_lastN(strcmp(group4,'Control') & strcmp(tp,'T3'),:) = CTChange_t2N(strcmp(group4,'Control') & strcmp(tp,'T3'),:);
%% remodel dbm change wrt last time point
DBMchange_last = zeros(length(id),size(DBMchange_bl,2));
DBMchange_last(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:) = DBMchange_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:);
DBMchange_last(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:) = DBMchange_t1(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:);
DBMchange_last(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:) = DBMchange_t2(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:);
DBMchange_last(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:) = DBMchange_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:);
DBMchange_last(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:) = DBMchange_t1(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:);
DBMchange_last(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:) = DBMchange_t2(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:);
DBMchange_last(strcmp(group4,'Group3') & strcmp(tp,'T1'),:) = DBMchange_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),:);
DBMchange_last(strcmp(group4,'Group3') & strcmp(tp,'T2'),:) = DBMchange_t1(strcmp(group4,'Group3') & strcmp(tp,'T2'),:);
DBMchange_last(strcmp(group4,'Group3') & strcmp(tp,'T3'),:) = DBMchange_t1(strcmp(group4,'Group3') & strcmp(tp,'T3'),:);
DBMchange_last(strcmp(group4,'Control') & strcmp(tp,'T1'),:) = DBMchange_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),:);
DBMchange_last(strcmp(group4,'Control') & strcmp(tp,'T2'),:) = DBMchange_t1(strcmp(group4,'Control') & strcmp(tp,'T2'),:);
DBMchange_last(strcmp(group4,'Control') & strcmp(tp,'T3'),:) = DBMchange_t2(strcmp(group4,'Control') & strcmp(tp,'T3'),:);
%% remodel days wrt last time point
Days_last = zeros(length(id),1);
Days_last(strcmp(group4,'Group_1') & strcmp(tp,'T1')) = daysfrombl(strcmp(group4,'Group_1') & strcmp(tp,'T1'));
Days_last(strcmp(group4,'Group_1') & strcmp(tp,'T2')) = daysfromt1(strcmp(group4,'Group_1') & strcmp(tp,'T2'));
Days_last(strcmp(group4,'Group_1') & strcmp(tp,'T3')) = daysfromt2(strcmp(group4,'Group_1') & strcmp(tp,'T3'));
Days_last(strcmp(group4,'Group_2') & strcmp(tp,'T1')) = daysfrombl(strcmp(group4,'Group_2') & strcmp(tp,'T1'));
Days_last(strcmp(group4,'Group_2') & strcmp(tp,'T2')) = daysfromt1(strcmp(group4,'Group_2') & strcmp(tp,'T2'));
Days_last(strcmp(group4,'Group_2') & strcmp(tp,'T3')) = daysfromt2(strcmp(group4,'Group_2') & strcmp(tp,'T3'));
Days_last(strcmp(group4,'Control') & strcmp(tp,'T1')) = daysfrombl(strcmp(group4,'Control') & strcmp(tp,'T1'));
Days_last(strcmp(group4,'Control') & strcmp(tp,'T2')) = daysfromt1(strcmp(group4,'Control') & strcmp(tp,'T2'));
Days_last(strcmp(group4,'Control') & strcmp(tp,'T3')) = daysfromt2(strcmp(group4,'Control') & strcmp(tp,'T3'));
Days_last(strcmp(group4,'Group3') & strcmp(tp,'T1')) = daysfrombl(strcmp(group4,'Group3') & strcmp(tp,'T1'));
Days_last(strcmp(group4,'Group3') & strcmp(tp,'T2')) = daysfromt1(strcmp(group4,'Group3') & strcmp(tp,'T2'));
Days_last(strcmp(group4,'Group3') & strcmp(tp,'T3')) = daysfromt2(strcmp(group4,'Group3') & strcmp(tp,'T3'));
%% remodel days wrt last time point- retreats
Days_last = zeros(length(id),1);
Days_last(strcmp(group4,'Group_1') & strcmp(tp,'T1')) = daysfromr1(strcmp(group4,'Group_1') & strcmp(tp,'T1'));
Days_last(strcmp(group4,'Group_1') & strcmp(tp,'T2')) = daysfromr2(strcmp(group4,'Group_1') & strcmp(tp,'T2'));
Days_last(strcmp(group4,'Group_1') & strcmp(tp,'T3')) = daysfromr3(strcmp(group4,'Group_1') & strcmp(tp,'T3'));
Days_last(strcmp(group4,'Group_2') & strcmp(tp,'T1')) = daysfromr1(strcmp(group4,'Group_2') & strcmp(tp,'T1'));
Days_last(strcmp(group4,'Group_2') & strcmp(tp,'T2')) = daysfromr2(strcmp(group4,'Group_2') & strcmp(tp,'T2'));
Days_last(strcmp(group4,'Group_2') & strcmp(tp,'T3')) = daysfromr3(strcmp(group4,'Group_2') & strcmp(tp,'T3'));
Days_last(strcmp(group4,'Control') & strcmp(tp,'T1')) = daysfrombl(strcmp(group4,'Control') & strcmp(tp,'T1'));
Days_last(strcmp(group4,'Control') & strcmp(tp,'T2')) = daysfromt1(strcmp(group4,'Control') & strcmp(tp,'T2'));
Days_last(strcmp(group4,'Control') & strcmp(tp,'T3')) = daysfromt2(strcmp(group4,'Control') & strcmp(tp,'T3'));
Days_last(strcmp(group4,'Group3') & strcmp(tp,'T1')) = daysfrombl(strcmp(group4,'Group3') & strcmp(tp,'T1'));
Days_last(strcmp(group4,'Group3') & strcmp(tp,'T2')) = daysfromt1(strcmp(group4,'Group3') & strcmp(tp,'T2'));
Days_last(strcmp(group4,'Group3') & strcmp(tp,'T3')) = daysfromt2(strcmp(group4,'Group3') & strcmp(tp,'T3'));
%% remake behavioral change wrt last time point
%--- attention change % note the slight difference in syntax
chA = zeros(length(id),1);
chA(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:) = attChange_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),1);
chA(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:) = attChange_t1(strcmp(group4,'Group_1') & strcmp(tp,'T2'),1);
chA(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:) = attChange_t2(strcmp(group4,'Group_1') & strcmp(tp,'T3'),1);
chA(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:) = attChange_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),1);
chA(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:) = attChange_t1(strcmp(group4,'Group_2') & strcmp(tp,'T2'),1);
chA(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:) = attChange_t2(strcmp(group4,'Group_2') & strcmp(tp,'T3'),1);
chA(strcmp(group4,'Group3') & strcmp(tp,'T1'),:) = attChange_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),1);
chA(strcmp(group4,'Control') & strcmp(tp,'T1'),:) = attChange_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),1);
chA(strcmp(group4,'Control') & strcmp(tp,'T2'),:) = attChange_t1(strcmp(group4,'Control') & strcmp(tp,'T2'),1);
chA(strcmp(group4,'Control') & strcmp(tp,'T3'),:) = attChange_t2(strcmp(group4,'Control') & strcmp(tp,'T3'),1);
chA_c = zeros(length(id),1);
chA_c(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:) = attChange_bl_c(strcmp(group4,'Group_1') & strcmp(tp,'T1'),1);
chA_c(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:) = attChange_t1_c(strcmp(group4,'Group_1') & strcmp(tp,'T2'),1);
chA_c(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:) = attChange_t2_c(strcmp(group4,'Group_1') & strcmp(tp,'T3'),1);
chA_c(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:) = attChange_bl_c(strcmp(group4,'Group_2') & strcmp(tp,'T1'),1);
chA_c(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:) = attChange_t1_c(strcmp(group4,'Group_2') & strcmp(tp,'T2'),1);
chA_c(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:) = attChange_t2_c(strcmp(group4,'Group_2') & strcmp(tp,'T3'),1);
chA_c(strcmp(group4,'Group3') & strcmp(tp,'T1'),:) = attChange_bl_c(strcmp(group4,'Group3') & strcmp(tp,'T1'),1);
chA_c(strcmp(group4,'Control') & strcmp(tp,'T1'),:) = attChange_bl_c(strcmp(group4,'Control') & strcmp(tp,'T1'),1);
chA_c(strcmp(group4,'Control') & strcmp(tp,'T2'),:) = attChange_t1_c(strcmp(group4,'Control') & strcmp(tp,'T2'),1);
chA_c(strcmp(group4,'Control') & strcmp(tp,'T3'),:) = attChange_t2_c(strcmp(group4,'Control') & strcmp(tp,'T3'),1);
%%baseline
chAbl = zeros(length(id),1);
chAbl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:) = att_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),1);
chAbl(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:) = att_bl2(strcmp(group4,'Group_1') & strcmp(tp,'T2'),1);
chAbl(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:) = att_bl3(strcmp(group4,'Group_1') & strcmp(tp,'T3'),1);
chAbl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:) = att_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),1);
chAbl(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:) = att_bl2(strcmp(group4,'Group_2') & strcmp(tp,'T2'),1);
chAbl(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:) = att_bl3(strcmp(group4,'Group_2') & strcmp(tp,'T3'),1);
chAbl(strcmp(group4,'Group3') & strcmp(tp,'T1'),:) = att_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),1);
chAbl(strcmp(group4,'Control') & strcmp(tp,'T1'),:) = att_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),1);
chAbl(strcmp(group4,'Control') & strcmp(tp,'T2'),:) = att_bl2(strcmp(group4,'Control') & strcmp(tp,'T2'),1);
chAbl(strcmp(group4,'Control') & strcmp(tp,'T3'),:) = att_bl3(strcmp(group4,'Control') & strcmp(tp,'T3'),1);
chc = zeros(length(id),1);
chc(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:) = comChange_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),1);
chc(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:) = comChange_t1(strcmp(group4,'Group_1') & strcmp(tp,'T2'),1);
chc(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:) = comChange_t2(strcmp(group4,'Group_1') & strcmp(tp,'T3'),1);
chc(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:) = comChange_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),1);
chc(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:) = comChange_t1(strcmp(group4,'Group_2') & strcmp(tp,'T2'),1);
chc(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:) = comChange_t2(strcmp(group4,'Group_2') & strcmp(tp,'T3'),1);
chc(strcmp(group4,'Group3') & strcmp(tp,'T1'),:) = comChange_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),1);
chc(strcmp(group4,'Control') & strcmp(tp,'T1'),:) = comChange_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),1);
chc(strcmp(group4,'Control') & strcmp(tp,'T2'),:) = comChange_t1(strcmp(group4,'Control') & strcmp(tp,'T2'),1);
chc(strcmp(group4,'Control') & strcmp(tp,'T3'),:) = comChange_t2(strcmp(group4,'Control') & strcmp(tp,'T3'),1);
% %%baseline
chcbl = zeros(length(id),1);
chcbl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:) = com_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),1);
chcbl(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:) = com_bl2(strcmp(group4,'Group_1') & strcmp(tp,'T2'),1);
chcbl(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:) = com_bl3(strcmp(group4,'Group_1') & strcmp(tp,'T3'),1);
chcbl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:) = com_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),1);
chcbl(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:) = com_bl2(strcmp(group4,'Group_2') & strcmp(tp,'T2'),1);
chcbl(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:) = com_bl3(strcmp(group4,'Group_2') & strcmp(tp,'T3'),1);
chcbl(strcmp(group4,'Group3') & strcmp(tp,'T1'),:) = com_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),1);
chcbl(strcmp(group4,'Control') & strcmp(tp,'T1'),:) = com_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),1);
chcbl(strcmp(group4,'Control') & strcmp(tp,'T2'),:) = com_bl2(strcmp(group4,'Control') & strcmp(tp,'T2'),1);
chcbl(strcmp(group4,'Control') & strcmp(tp,'T3'),:) = com_bl3(strcmp(group4,'Control') & strcmp(tp,'T3'),1);
%--- tom change
cht = zeros(length(id),1);
cht(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:) = tomChange_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),1);
cht(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:) = tomChange_t1(strcmp(group4,'Group_1') & strcmp(tp,'T2'),1);
cht(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:) = tomChange_t2(strcmp(group4,'Group_1') & strcmp(tp,'T3'),1);
cht(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:) = tomChange_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),1);
cht(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:) = tomChange_t1(strcmp(group4,'Group_2') & strcmp(tp,'T2'),1);
cht(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:) = tomChange_t2(strcmp(group4,'Group_2') & strcmp(tp,'T3'),1);
cht(strcmp(group4,'Group3') & strcmp(tp,'T1'),:) = tomChange_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),1);
cht(strcmp(group4,'Control') & strcmp(tp,'T1'),:) = tomChange_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),1);
cht(strcmp(group4,'Control') & strcmp(tp,'T2'),:) = tomChange_t1(strcmp(group4,'Control') & strcmp(tp,'T2'),1);
cht(strcmp(group4,'Control') & strcmp(tp,'T3'),:) = tomChange_t2(strcmp(group4,'Control') & strcmp(tp,'T3'),1);
% %%baseline
chtbl = zeros(length(id),1);
chtbl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:) = tom_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),1);
chtbl(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:) = tom_bl2(strcmp(group4,'Group_1') & strcmp(tp,'T2'),1);
chtbl(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:) = tom_bl3(strcmp(group4,'Group_1') & strcmp(tp,'T3'),1);
chtbl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:) = tom_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),1);
chtbl(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:) = tom_bl2(strcmp(group4,'Group_2') & strcmp(tp,'T2'),1);
chtbl(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:) = tom_bl3(strcmp(group4,'Group_2') & strcmp(tp,'T3'),1);
chtbl(strcmp(group4,'Group3') & strcmp(tp,'T1'),:) = tom_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),1);
chtbl(strcmp(group4,'Control') & strcmp(tp,'T1'),:) = tom_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),1);
chtbl(strcmp(group4,'Control') & strcmp(tp,'T2'),:) = tom_bl2(strcmp(group4,'Control') & strcmp(tp,'T2'),1);
chtbl(strcmp(group4,'Control') & strcmp(tp,'T3'),:) = tom_bl3(strcmp(group4,'Control') & strcmp(tp,'T3'),1);
% %--- movement change
mvt = zeros(length(id),1);
mvt(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:) = rp_arestChange_bl(strcmp(group4,'Group_1') & strcmp(tp,'T1'),:);
mvt(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:) = rp_arestChange_t1(strcmp(group4,'Group_1') & strcmp(tp,'T2'),:);
mvt(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:) = rp_arestChange_t2(strcmp(group4,'Group_1') & strcmp(tp,'T3'),:);
mvt(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:) = rp_arestChange_bl(strcmp(group4,'Group_2') & strcmp(tp,'T1'),:);
mvt(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:) = rp_arestChange_t1(strcmp(group4,'Group_2') & strcmp(tp,'T2'),:);
mvt(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:) = rp_arestChange_t2(strcmp(group4,'Group_2') & strcmp(tp,'T3'),:);
mvt(strcmp(group4,'Group3') & strcmp(tp,'T1'),:) = rp_arestChange_bl(strcmp(group4,'Group3') & strcmp(tp,'T1'),:);
mvt(strcmp(group4,'Control') & strcmp(tp,'T1'),:) = rp_arestChange_bl(strcmp(group4,'Control') & strcmp(tp,'T1'),:);
mvt(strcmp(group4,'Control') & strcmp(tp,'T2'),:) = rp_arestChange_t1(strcmp(group4,'Control') & strcmp(tp,'T2'),:);
mvt(strcmp(group4,'Control') & strcmp(tp,'T3'),:) = rp_arestChange_t2(strcmp(group4,'Control') & strcmp(tp,'T3'),:);
%% data
X = CTChange_last;
X(isnan(X)) = 0;
X(isinf(X)) = 0;
XBL = CTChangeBL;
XBL(isnan(XBL)) = 0;
XBL(isinf(XBL)) = 0;
XB = DBMchange_last;
XB(isnan(XB)) = 0;
XB(isinf(XB)) = 0;
Att = chA;
Att(abs(Att)>100) = -666;
Att_c = chA_c;
Att_c(abs(Att_c)>100) = -666;
Comp = chc;
Comp(abs(chc)>100) = -666;
Tom = cht;
Tom(abs(Tom)>100) = -666;
Move = mvt;
Move(abs(Move)>100) = -666;
end
%% make ct baseline;
%% //Preparestuff ---------------------------------------------------------
%% analysis settings
% -----------------
% these are the analysis settings for the Resource analysis
p_threshs = [0.001 0.005 0.01 0.025 0.03];
lobescheck = [1 2 3 4 5 6 9 10];
pval = 4;
p_thresh = p_threshs(pval); % cluster-level threshold
RPATH = [RPATHO '/APRIL_' num2str(p_thresh) '/'];
mkdir(RPATH)
pwe = 0.025;
%% SUBJECTS INCLUSIONS
for subjects_incl = 1
keep = find(isthere_ct ==1), find(~strcmp(group4,'Group3')))
size(keep) %N=848
size((find(tpnum(keep)==0))) % N = 232
size(intersect(find(tpnum(keep)==0), find(strcmp(group4(keep),'Group_1')))) %77/80
size(intersect(find(tpnum(keep)==0), find(strcmp(group4(keep),'Group_2')))) %74/81
size(intersect(find(tpnum(keep)==0), find(strcmp(group4(keep),'Control')))) %81/90
idk = id(keep)
missing_T0_G1 = idk(intersect(find(tpnum(keep)==0), find(strcmp(group(keep),'Group_2'))))
missing_T0_G2 = idk(intersect(find(tpnum(keep)==0), find(strcmp(group(keep),'Group_2'))))
missing_T0_RCC = idk(intersect(find(tpnum(keep)==0), find(strcmp(group4(keep),'Control'))))
mean(age) %40.52
std(age) %9.3
size((find(tpnum(keep)==1))) % N = 213
size(intersect(find(tpnum(keep)==1), find(strcmp(group4(keep),'Group_1')))) %69/80
size(intersect(find(tpnum(keep)==1), find(strcmp(group4(keep),'Group_2')))) %69/81
size(intersect(find(tpnum(keep)==1), find(strcmp(group4(keep),'Control')))) %75/90
missing_T1_G1 = idk(intersect(find(tpnum(keep)==1), find(strcmp(group(keep),'Group_1'))))
missing_T1_G2 = idk(intersect(find(tpnum(keep)==1), find(strcmp(group(keep),'Group_2'))));
missing_T1_RCC = idk(intersect(find(tpnum(keep)==1), find(strcmp(group4(keep),'Control'))));
size((find(tpnum(keep)==2))) % N = 204
size(intersect(find(tpnum(keep)==2), find(strcmp(group4(keep),'Group_1')))) %65
size(intersect(find(tpnum(keep)==2), find(strcmp(group4(keep),'Group_2')))) %69
size(intersect(find(tpnum(keep)==2), find(strcmp(group4(keep),'Control')))) %70
size((find(tpnum(keep)==3))) % N = 199
size(intersect(find(tpnum(keep)==3), find(strcmp(group4(keep),'Group_1')))) %59
size(intersect(find(tpnum(keep)==3), find(strcmp(group4(keep),'Group_2')))) %68
size(intersect(find(tpnum(keep)==3), find(strcmp(group4(keep),'Control')))) %72
keep = mintersect(find(isthere_ct ==1),...
find(tp_t0_there==1), ...
find(tp_t1_there==1), ...
find(tp_t2_there==1), ...
find(tp_t3_there==1), ...
union(find(tpnum==0), union(find(tpnum==1),union(find(tpnum==3), find(tpnum==2 )))));
size(keep) %N = 716
size((find(tpnum(keep)==0))) % N = 179
size(intersect(find(tpnum(keep)==0), find(strcmp(group4(keep),'Group_1')))) %54
size(intersect(find(tpnum(keep)==0), find(strcmp(group4(keep),'Group_2')))) %59
size(intersect(find(tpnum(keep)==0), find(strcmp(group4(keep),'Control')))) %66
mean(age(keep)) %40.3
std(age(keep)) %9.6
size(intersect(find(tpnum(keep)==0), find(strcmp(sex(keep),'female')))) %96 (81)
end
%% for QC
for QC = 1
istherekeep = find(isthere_ct);
for i= 1:length(istherekeep)
f = figure,
BoSurfStatViewData(CT(istherekeep(i),:), SInf,'')
exportfigbo(f,[RPATH 'sub' num2str(idnum(keep(i))) '_T' num2str(tpnum(keep(i))) 'CT.png'],'png',10);
close(f)
end
keep = mintersect(find(isthere_dbm), ...
find(tp_t3_there==1), ...
find(tp_t1_there==1), ...
find(tp_t2_there==1 ), ...
find(tp_t0_there==1 ), ...
union(find(tpnum==0), union(find(tpnum==1),union(find(tpnum==3), find(tpnum==2 )))));
istherekeep = keep;
for i= 1 :length(istherekeep)
f = figure,
BoSurfStatViewData(zmap.zdbm_map(istherekeep(i),:), SInf,'')
BoSurfStatColLim([-3 3])
exportfigbo(f,[RPATH 'sub' num2str(idnum(istherekeep(i))) '_T' num2str(tpnum(istherekeep(i))) 'DBM.png'],'png',10);
close(f)
end
end
%% load AAL atlas
for aal = 1
cd([P '/data/')
load('aal.mat')
end
%% CT CHANGE FIGURE 2 and 3 | SUPPLEMENTs
for FIG12 = 1
keep = mintersect(find(isthere_ct), ...
find(tp_t0_there==1), ...
find(tp_t3_there==1), ...
find(tp_t1_there==1), ...
find(tp_t2_there==1 ), ...
union(find(tpnum==0), union(find(tpnum==1),union(find(tpnum==3), find(tpnum==2 )))));
keepMAIN = keep;
size(keep) % N = 716
mask = mean(CT,1)>0.4;
Ck = CT(keep,:);
ik = id(keep,:);
ink = idnum(keep);
tk = tpnum(keep,:);
dk = Days_last(keep);
dkfac = tp(keep);
gk = group(keep);
g4k = group4(keep);