diff --git a/functions/04_Regression/getTemporalCharacteristics.m b/functions/04_Regression/getTemporalCharacteristics.m
deleted file mode 100755
index 3a9c659..0000000
--- a/functions/04_Regression/getTemporalCharacteristics.m
+++ /dev/null
@@ -1,157 +0,0 @@
-%% This function computes the temporal characteristics (duration, occurences, etc.)
-% given a set of time courses
-%
-% Inputs:
-% - TC: cell array with iCAPs time courses for every subject
-% - clusteringResults: structure containing clustering results, fields:
-% .subject_labels
-% .time_labels
-% [.scrub_labels]
-% - param: structure with input parameters
-% .TR: TR
-%
-% Outputs:
-% - out: structure containing all computed characteristics:
-% .durations_total_n_subs: total number of frames an iCAP is active
-% in every subject
-% .durations_total_s_subs: total time (in seconds) an iCAP is active
-% in every subject
-%
-% .durations_avg(_n/_s): average duration of an iCAPs activity
-
-function [tempChar] = getTemporalCharacteristics(TC,clusteringResults,param)
-
- nSub=length(TC);
- for iS=1:nSub
- nTP_sub(iS)=nnz(clusteringResults.AI_subject_labels==iS);
- end
- subject_labels=clusteringResults.subject_labels;
- IDX=clusteringResults.IDX;
-
- % adding option of scrubbed time courses
- if isfield(param,'excludeMotionFrames') && param.excludeMotionFrames
- scrub_labels=iCAPsResults.scrub_labels;
- else
- scrub_labels=ones(nTP_sub*nSub,1);
- end
-
-
- tempChar = computeTemporalCharacteristics(iCAPsResults.Time_Courses,1,param,scrub_labels,subject_labels,IDX);
-% plotTCandInnov(iCAPsResults,param);
-
-
-end
-
-
-%%
-function plotTCandInnov(iCAPsResults,param)
- %% constants
- nSub=length(iCAPsResults.Time_Courses);
- nClus=size(iCAPsResults.Time_Courses{1},1);
- nTP_sub=size(iCAPsResults.Time_Courses{1},2);
-
- % adding option of scrubbed time courses
- if isfield(param,'excludeMotionFrames') && param.excludeMotionFrames
- scrub_labels=iCAPsResults.scrub_labels;
- else
- scrub_labels=ones(nTP_sub*nSub,1);
- end
-
- for iS=1:nSub
- vols_iS=(iS-1)*nTP_sub+1:iS*nTP_sub;
- nTP_sub_scrub(iS,1) = nnz(scrub_labels(vols_iS));
- TemporalMask{iS}=scrub_labels(vols_iS);
- end
-
-
- %% get data and iCAPs output directories
- if isfield(param,'data_title') % in case of new data saving structure (clustering in subfolders)
- % there is a main folder according to data+thresholding
- % and a separate one for clustering
- outDir_main=fullfile(param.PathData,'iCAPs_results',[param.data_title,'_',param.thresh_title]);
- outDir_iCAPs=fullfile(param.PathData,'iCAPs_results',[param.data_title,'_',param.thresh_title],param.iCAPs_title);
- else
- % before, there was a separate folder for
- % thresholding/data/clustering parameters
- outDir_main=fullfile(param.PathData,'iCAPs_results',[param.thresh_title,'_',param.iCAPs_title]);
- outDir_iCAPs=fullfile(param.PathData,'iCAPs_results',[param.thresh_title,'_',param.iCAPs_title]);
- end
-
-
- %% plotting time courses and innovation indices
- if ~exist(fullfile(outDir_iCAPs,'Time_Courses_and_Innovations'),'dir'); mkdir(fullfile(outDir_iCAPs,'Time_Courses_and_Innovations'));end;
- if ~exist(fullfile(outDir_iCAPs,'Time_Courses'),'dir'); mkdir(fullfile(outDir_iCAPs,'Time_Courses'));end;
-
- iCAPsResults.time_labels(iCAPsResults.time_labels>195)=-(iCAPsResults.time_labels(iCAPsResults.time_labels>195)-195);
-
- for iS = 1:nSub
- % normalize time courses
- iCAPsResults.Time_Courses_plot{iS,1}=reshape(zscore(iCAPsResults.Time_Courses{iS}(:)),size(iCAPsResults.Time_Courses{iS},1),size(iCAPsResults.Time_Courses{iS},2));
- end
-
-
- colors = cbrewer('div', 'Spectral', 10);
- cmap=cbrewer('div', 'RdYlBu',100);
- cmap=cmap(100:-1:1,:);
- % colors = [colors;colors([11:-1:1],:)];
- set(groot,'defaultAxesColorOrder',colors);
- set(groot,'defaultAxesFontSize',15);
-
- clims=[-3,3];
-
- for iS=1:10:nSub
- figure('position',[440 378 515 420]);
- imagesc(iCAPsResults.Time_Courses_plot{iS},clims);
- title(['subject ' num2str(iS)])
- colormap(cmap)
- c=colorbar;
- c.Label.String='amplitude';
- xlabel('time [frames]');
- % ylabel('iCAP');
- print(fullfile(outDir_iCAPs,'Time_Courses',['SUB' num2str(iS)]),'-dpng','-painters');
-
-
- for iC=1:nClus
- fig=figure('Position',[440 573 560 167]);
- hold on;
- grid on
- stemAmp=max(abs(iCAPsResults.Time_Courses_plot{iS,1}(iC,:)))/2;
- stemAmp=2;
- patch('Vertices',[0 -1; nTP_sub -1; nTP_sub 1; 0 1],'Faces',[1 2 3 4],'facecolor',0.5*[1 1 1],'edgeColor',0.5*[1 1 1],'FaceAlpha',0.3,'EdgeAlpha',0.3);
- pl(1)=stem(abs(iCAPsResults.time_labels(iCAPsResults.subject_labels==iS&iCAPsResults.IDX==iC)),...
- stemAmp*sign(iCAPsResults.time_labels(iCAPsResults.subject_labels==iS&iCAPsResults.IDX==iC)),'k')
- plot([0 200],[0 0],'k-')
- pl(2)=plot(iCAPsResults.Time_Courses_plot{iS}(iC,:),'linewidth',1.5,'color',colors(3,:));
- % title(['subject ' num2str(iS)])
- xlabel('time [frames]')
- % ylabel('amplitude')
- % set(gca,'ylim',2.5*[-stemAmp stemAmp]);
- set(gca,'ytick',[-20:2:20],'ylim',[min(-4,1.1*min(iCAPsResults.Time_Courses_plot{iS,1}(iC,:))) max(4,1.1*max(iCAPsResults.Time_Courses_plot{iS,1}(iC,:)))]);
- if ~exist(fullfile(outDir_iCAPs,'Time_Courses_and_Innovations'),'dir'); mkdir(fullfile(outDir,'Time_Courses_and_Innovations'));end;
- outFileName=fullfile(outDir_iCAPs,'Time_Courses_and_Innovations',['SUB' num2str(iS) ' - iCAP' num2str(iC)]);
- % figure(fig);
- % legend(pl,{'',''},'location','eastoutside');
- set(gca,'xlim',[1 195])
- print(outFileName,'-depsc2','-painters');
- close gcf
-
-
-
-% stemAmp=max(abs(iCAPsResults.Time_Courses_plot{iS}(iC,:)))/2;
-% fig=figure('position',[440 662 560 136]);
-% imagesc([1 nTP_sub]+1,[-5 5],TemporalMask{iS}','alphadata',0.1,[0,1]);colormap('gray');
-% hold on;
-% stem(abs(iCAPsResults.time_labels(iCAPsResults.subject_labels==iS&iCAPsResults.IDX==iC)),...
-% stemAmp*sign(iCAPsResults.time_labels(iCAPsResults.subject_labels==iS&iCAPsResults.IDX==iC)))
-% stairs(iCAPsResults.Time_Courses_plot{iS}(iC,:),'linewidth',1.5);
-% title(['SUB' num2str(iS) ' - iCAP' num2str(iC)])
-% xlabel('frame')
-% % ylabel('amplitude')
-% set(gca,'ylim',2.5*[-stemAmp stemAmp]);
-% outFileName=fullfile(outDir_iCAPs,'Time_Courses_and_Innovations',['SUB' num2str(iS) ' - iCAP' num2str(iC)]);
-% figure(fig);
-% print(outFileName,'-depsc2','-painters');
-% close gcf
- end
- end
-end