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aggregate_etkinlab_cvb_biomarker.m
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aggregate_etkinlab_cvb_biomarker.m
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function [roi_table results] = aggregate_etkinlab_cvb_biomarker()
roi_table = table();
methodname = 'sn_denoised';
metricname = 'mccc';
studyname = 'best-eegfmri';
resttype = 'rest2';
sessiontype = 'tp1';
sessionlabel = 'within';
runlabel = 'within';
samplesize = 't400';
samplesizename = '5min';
results_name = [studyname '-' resttype sessiontype '-' samplesize];
disp(['Results: ' results_name])
pipeline_name = 'etkinlab_analysis';
resultsdir = fullfile('tmp','15-Oct-2018',results_name,pipeline_name);
ls(resultsdir)
load(fullfile(resultsdir,'trt_best-eegfmri_rfmri.mat'))
metric = results.cpac.(methodname).trt_reliability.(metricname);
metric = round(metric,4);
sm_roi_table = table();
sm_roi_table.(metricname) = reshape(metric,[length(metric) 1]);
sm_roi_table.restName = repmat({resttype},[length(metric) 1]);
sm_roi_table.sessionType = repmat({sessionlabel},[length(metric) 1]);
sm_roi_table.runType = repmat({runlabel},[length(metric) 1]);
sm_roi_table.n_time = repmat({samplesize},[length(metric) 1]);
sm_roi_table.method = repmat({methodname},[length(metric) 1]);
roi_table = vertcat(roi_table,sm_roi_table);
resttype = 'rest1';
sessiontype = 'tp2';
sessionlabel = 'within';
runlabel = 'within';
samplesize = 't400';
samplesizename = '5min';
results_name = [studyname '-' resttype sessiontype '-' samplesize];
disp(['Results: ' results_name])
pipeline_name = 'etkinlab_analysis';
resultsdir = fullfile('tmp','22-Mar-2018',results_name,pipeline_name);
ls(resultsdir)
load(fullfile(resultsdir,'trt_best-eegfmri_rfmri.mat'))
metric = results.cpac.(methodname).trt_reliability.(metricname);
metric = round(metric,4);
sm_roi_table = table();
sm_roi_table.(metricname) = reshape(metric,[length(metric) 1]);
sm_roi_table.restName = repmat({resttype},[length(metric) 1]);
sm_roi_table.sessionType = repmat({sessionlabel},[length(metric) 1]);
sm_roi_table.runType = repmat({runlabel},[length(metric) 1]);
sm_roi_table.n_time = repmat({samplesize},[length(metric) 1]);
sm_roi_table.method = repmat({methodname},[length(metric) 1]);
roi_table = vertcat(roi_table,sm_roi_table);
resttype = 'rest2';
sessiontype = 'tp1';
sessionlabel = 'within';
runlabel = 'within';
samplesize = 't200';
samplesizename = '2min';
results_name = [studyname '-' resttype sessiontype '-' samplesize];
disp(['Results: ' results_name])
pipeline_name = 'etkinlab_analysis';
resultsdir = fullfile('tmp','22-Mar-2018',results_name,pipeline_name);
ls(resultsdir)
load(fullfile(resultsdir,'trt_best-eegfmri_rfmri.mat'))
metric = results.cpac.(methodname).trt_reliability.(metricname);
metric = round(metric,4);
sm_roi_table = table();
sm_roi_table.(metricname) = reshape(metric,[length(metric) 1]);
sm_roi_table.restName = repmat({resttype},[length(metric) 1]);
sm_roi_table.sessionType = repmat({sessionlabel},[length(metric) 1]);
sm_roi_table.runType = repmat({runlabel},[length(metric) 1]);
sm_roi_table.n_time = repmat({samplesize},[length(metric) 1]);
sm_roi_table.method = repmat({methodname},[length(metric) 1]);
roi_table = vertcat(roi_table,sm_roi_table);
resttype = 'rest1';
sessiontype = 'tp2';
sessionlabel = 'within';
runlabel = 'within';
samplesize = 't200';
samplesizename = '5min';
results_name = [studyname '-' resttype sessiontype '-' samplesize];
disp(['Results: ' results_name])
pipeline_name = 'etkinlab_analysis';
resultsdir = fullfile('tmp','22-Mar-2018',results_name,pipeline_name);
ls(resultsdir)
load(fullfile(resultsdir,'trt_best-eegfmri_rfmri.mat'))
metric = results.cpac.(methodname).trt_reliability.(metricname);
metric = round(metric,4);
sm_roi_table = table();
sm_roi_table.(metricname) = reshape(metric,[length(metric) 1]);
sm_roi_table.restName = repmat({resttype},[length(metric) 1]);
sm_roi_table.sessionType = repmat({sessionlabel},[length(metric) 1]);
sm_roi_table.runType = repmat({runlabel},[length(metric) 1]);
sm_roi_table.n_time = repmat({samplesize},[length(metric) 1]);
sm_roi_table.method = repmat({methodname},[length(metric) 1]);
roi_table = vertcat(roi_table,sm_roi_table);
resttype = '';
sessiontype = 'tp1';
sessionlabel = 'within';
runlabel = 'between';
samplesize = 't200';
samplesizename = '2min';
results_name = [studyname '-' resttype sessiontype '-' samplesize];
disp(['Results: ' results_name])
pipeline_name = 'etkinlab_analysis';
resultsdir = fullfile('tmp','22-Mar-2018',results_name,pipeline_name);
ls(resultsdir)
load(fullfile(resultsdir,'trt_best-eegfmri_rfmri.mat'))
metric = results.cpac.(methodname).trt_reliability.(metricname);
metric = round(metric,4);
sm_roi_table = table();
sm_roi_table.(metricname) = reshape(metric,[length(metric) 1]);
sm_roi_table.restName = repmat({resttype},[length(metric) 1]);
sm_roi_table.sessionType = repmat({sessionlabel},[length(metric) 1]);
sm_roi_table.runType = repmat({runlabel},[length(metric) 1]);
sm_roi_table.n_time = repmat({samplesize},[length(metric) 1]);
sm_roi_table.method = repmat({methodname},[length(metric) 1]);
roi_table = vertcat(roi_table,sm_roi_table);
resttype = '';
sessiontype = 'tp1';
sessionlabel = 'within';
runlabel = 'between';
samplesize = 't400';
samplesizename = '5min';
results_name = [studyname '-' resttype sessiontype '-' samplesize];
disp(['Results: ' results_name])
pipeline_name = 'etkinlab_analysis';
resultsdir = fullfile('tmp','22-Mar-2018',results_name,pipeline_name);
ls(resultsdir)
load(fullfile(resultsdir,'trt_best-eegfmri_rfmri.mat'))
metric = results.cpac.(methodname).trt_reliability.(metricname);
metric = round(metric,4);
sm_roi_table = table();
sm_roi_table.(metricname) = reshape(metric,[length(metric) 1]);
sm_roi_table.restName = repmat({resttype},[length(metric) 1]);
sm_roi_table.sessionType = repmat({sessionlabel},[length(metric) 1]);
sm_roi_table.runType = repmat({runlabel},[length(metric) 1]);
sm_roi_table.n_time = repmat({samplesize},[length(metric) 1]);
sm_roi_table.method = repmat({methodname},[length(metric) 1]);
roi_table = vertcat(roi_table,sm_roi_table);
resttype = '';
sessiontype = 'tp1';
sessionlabel = 'within';
runlabel = 'between';
samplesize = 't800';
samplesizename = '10min';
results_name = [studyname '-' resttype sessiontype '-' samplesize];
disp(['Results: ' results_name])
pipeline_name = 'etkinlab_analysis';
resultsdir = fullfile('tmp','22-Mar-2018',results_name,pipeline_name);
ls(resultsdir)
load(fullfile(resultsdir,'trt_best-eegfmri_rfmri.mat'))
metric = results.cpac.(methodname).trt_reliability.(metricname);
metric = round(metric,4);
sm_roi_table = table();
sm_roi_table.(metricname) = reshape(metric,[length(metric) 1]);
sm_roi_table.restName = repmat({resttype},[length(metric) 1]);
sm_roi_table.sessionType = repmat({sessionlabel},[length(metric) 1]);
sm_roi_table.runType = repmat({runlabel},[length(metric) 1]);
sm_roi_table.n_time = repmat({samplesize},[length(metric) 1]);
sm_roi_table.method = repmat({methodname},[length(metric) 1]);
roi_table = vertcat(roi_table,sm_roi_table);
resttype = '';
sessiontype = '';
sessionlabel = 'between';
runlabel = 'between';
samplesize = 't200';
samplesizename = '2min';
results_name = [studyname '-' resttype sessiontype '-' samplesize];
disp(['Results: ' results_name])
pipeline_name = 'etkinlab_analysis';
resultsdir = fullfile('tmp','22-Mar-2018',results_name,pipeline_name);
ls(resultsdir)
load(fullfile(resultsdir,'trt_best-eegfmri_rfmri.mat'))
metric = results.cpac.(methodname).trt_reliability.(metricname);
metric = round(metric,4);
sm_roi_table = table();
sm_roi_table.(metricname) = reshape(metric,[length(metric) 1]);
sm_roi_table.restName = repmat({resttype},[length(metric) 1]);
sm_roi_table.sessionType = repmat({sessionlabel},[length(metric) 1]);
sm_roi_table.runType = repmat({runlabel},[length(metric) 1]);
sm_roi_table.n_time = repmat({samplesize},[length(metric) 1]);
sm_roi_table.method = repmat({methodname},[length(metric) 1]);
roi_table = vertcat(roi_table,sm_roi_table);
resttype = '';
sessiontype = '';
sessionlabel = 'between';
runlabel = 'between';
samplesize = 't400';
samplesizename = '5min';
results_name = [studyname '-' resttype sessiontype '-' samplesize];
disp(['Results: ' results_name])
pipeline_name = 'etkinlab_analysis';
resultsdir = fullfile('tmp','22-Mar-2018',results_name,pipeline_name);
ls(resultsdir)
load(fullfile(resultsdir,'trt_best-eegfmri_rfmri.mat'))
metric = results.cpac.(methodname).trt_reliability.(metricname);
metric = round(metric,4);
sm_roi_table = table();
sm_roi_table.(metricname) = reshape(metric,[length(metric) 1]);
sm_roi_table.restName = repmat({resttype},[length(metric) 1]);
sm_roi_table.sessionType = repmat({sessionlabel},[length(metric) 1]);
sm_roi_table.runType = repmat({runlabel},[length(metric) 1]);
sm_roi_table.n_time = repmat({samplesize},[length(metric) 1]);
sm_roi_table.method = repmat({methodname},[length(metric) 1]);
roi_table = vertcat(roi_table,sm_roi_table);
resttype = '';
sessiontype = '';
sessionlabel = 'between';
runlabel = 'between';
samplesize = 't800';
samplesizename = '10min';
results_name = [studyname '-' resttype sessiontype '-' samplesize];
disp(['Results: ' results_name])
pipeline_name = 'etkinlab_analysis';
resultsdir = fullfile('tmp','22-Mar-2018',results_name,pipeline_name);
ls(resultsdir)
load(fullfile(resultsdir,'trt_best-eegfmri_rfmri.mat'))
metric = results.cpac.(methodname).trt_reliability.(metricname);
metric = round(metric,4);
sm_roi_table = table();
sm_roi_table.(metricname) = reshape(metric,[length(metric) 1]);
sm_roi_table.restName = repmat({resttype},[length(metric) 1]);
sm_roi_table.sessionType = repmat({sessionlabel},[length(metric) 1]);
sm_roi_table.runType = repmat({runlabel},[length(metric) 1]);
sm_roi_table.n_time = repmat({samplesize},[length(metric) 1]);
sm_roi_table.method = repmat({methodname},[length(metric) 1]);
roi_table = vertcat(roi_table,sm_roi_table);
savefilename = ['tmp/22-Mar-2018/all_' metricname ];
writetable(roi_table,savefilename,'WriteVariableNames',1,'Delimiter','\t');
within_run_idx = strcmp(roi_table.sessionType,'within') & ...
strcmp(roi_table.runType,'within');
t400_run_idx = strcmp(roi_table.n_time,'t200');
y_methods = roi_table(within_run_idx,:).(metricname)
x_methods = roi_table(within_run_idx,:).n_time;
% x_methods = roi_table(within_run_idx,:).runType;
[y_mean y_ci] = grpstats(y_methods,x_methods,{'mean','meanci'})
grammobj(1,1) = plot_reliability_dotplot(unique(x_methods),fliplr(y_mean'),...
fliplr(y_ci(:,1)'),fliplr(y_ci(:,2)'),(unique(x_methods)),[]);
within_run_idx = strcmp(roi_table.sessionType,'between') & ...
strcmp(roi_table.runType,'between');
y_methods = roi_table(within_run_idx,:).(metricname)
x_methods = roi_table(within_run_idx,:).n_time;
% x_methods = roi_table(within_run_idx,:).runType;
[y_mean y_ci] = grpstats(y_methods,x_methods,{'mean','meanci'})
grammobj(2,1) = plot_reliability_dotplot(unique(x_methods),(y_mean'),...
(y_ci(:,1)'),(y_ci(:,2)'),(unique(x_methods)),[]);
grammobj.draw()
resultsdir
print('-dpng','-r150', ...
fullfile('tmp','22-Mar-2018','all_mccc_t200_t400_mccc.png')); %grammobj.export('file_name','tmp/22-Mar-2018/between_within_t400_mccc.png');
end
function export_mean_roi_reliability(roi_table)
end
function grammobj = plot_reliability_dotplot(x_methods, y_methods,y_lo,y_hi,methodnames,community)
geom_type = 'geom_point';
color_type = 'common';
ncommunities = 7;
alternate_color = zeros(1,length(y_methods));
switch color_type
case 'odd-even'
alternate_color(1:2:end) = 1;
alternate_color(2:2:end) = 2;
mycolormap = brewermap(length(unique(alternate_color))*...
ncommunities,...
'Paired' ...
);
otherwise
alternate_color = community;
mycolormap = brewermap(ncommunities,'Spectral');
end
grammobj = gramm('x', x_methods,...
'y', y_methods, ...
'ymin', y_lo,...
'ymax', y_hi ...
);
switch geom_type
case 'geom_bar'
grammobj.geom_bar('dodge',0.8,'width',0.6);
case 'geom_point'
grammobj.geom_point();
grammobj.set_point_options('base_size',10);
otherwise
grammobj.geom_point();
end
grammobj.geom_interval('geom','black_errorbar',...
'dodge',0.8,'width',.5);
grammobj.set_color_options('map', mycolormap);
grammobj.set_names( 'x', 'Method',...
'y','Mean Reliability' ...
);
grammobj.set_text_options('base_size',22);
ylim_upper = round(10*max(y_methods(:)))/10;
grammobj.axe_property('ylim',[0 max([.6 ylim_upper])]);
grammobj.no_legend();
end