CopBET_CarhartHarris_2016_data.m

%% Function to load CH2016 data structured according to the specifications 
% in the README file
% 
% Copyright (C) 2023 Anders Stevnhoved Olsen & Drummond E-Wen McCulloch
%
%    This program is free software: you can redistribute it and/or modify
%    it under the terms of the GNU General Public License as published by
%    the Free Software Foundation, either version 3 of the License, or
%    (at your option) any later version.
%
%    This program is distributed in the hope that it will be useful,
%    but WITHOUT ANY WARRANTY; without even the implied warranty of
%    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%    GNU General Public License for more details.
%
%    You should have received a copy of the GNU General Public License
%    along with this program.  If not, see http://www.gnu.org/licenses/.
function [tbl,data,opts] = CopBET_CarhartHarris_2016_data(atlas,ts_ROI2ROI,type)
if type=='example'
    topfolder = [pwd,'/LSDdata/exampledata/'];
elseif type == 'full'
    topfolder = [pwd,'/LSDdata/'];
else
    error('Please specify whether to load the full dataset (''full'') (needs to be downloaded from OpenNeuro and processed using the function LSDdata/LSDdata_ROI.m first) or ''example'' with the first placebo and first LSD scan from subject 1')
end

if nargin==0||isempty(atlas)
%     error('An atlas needs to be specified')
    atlas = 'yeo7';
else
    %%%%%%%%%%%%%% function-wide settings and import stuff
    possible_atlases = {'AAL90','Craddock200','HarvardOxford_cort_subcort',...
        'Lausanne463','Schaefer1000','Shen268','yeo17','smith20','SchaeferTian232'};
    
    if all(~strcmpi(atlas,possible_atlases))
        disp(possible_atlases)
        error('Please input a different atlas name. Possible options above')
    end
end

subs = dir([topfolder,'sub-*']);
if isempty(subs)
    error('Please make sure you''re standing in the right directory')
end
nummats = numel(dir([topfolder,'ROIdata/AAL90/*.mat']));
conditions = {'ses-PLCB','ses-LSD'};

opts.subjects = {subs(:).name};

tblvarnames = [{'data','rp','subject', 'condition','session','num_vols','entropy'}];
tblvartypes = [{'cell','cell','cell','cell','double','double','cell'}];
tbl  = table('Size',[nummats,numel(tblvartypes)],...
    'VariableNames', tblvarnames,...
    'VariableTypes',tblvartypes);

tblcount = 1;

for sub = 1:numel(opts.subjects) %loop through subjects
    for cond = 1:numel(conditions)
        for ses = [1,3]
            % Fill tbl
            if strcmp(ts_ROI2ROI,'denoised_volumes')
                if exist([subs(sub).folder,'/',subs(sub).name,'/',...
                conditions{cond},'/func/',subs(sub).name,'_',conditions{cond},...
                '_task-rest_run-0',num2str(ses),'_bold.nii.gz'])
                tbl.data{tblcount} = [subs(sub).folder,'/',subs(sub).name,'/',...
                conditions{cond},'/func/',subs(sub).name,'_',conditions{cond},...
                '_task-rest_run-0',num2str(ses),'_bold.nii.gz'];
                else
                    tbl.data{tblcount} = [subs(sub).folder,'/',subs(sub).name,'/',...
                conditions{cond},'/func/',subs(sub).name,'_',conditions{cond},...
                '_task-rest_run-0',num2str(ses),'_bold_shortened.nii.gz'];
                end
            else
            load([topfolder,'ROIdata/',...
                atlas,'/',subs(sub).name,'_',conditions{cond},...
                '_task-rest_run-0',num2str(ses),'_bold']);
            tbl.data{tblcount} = V_roi;
            tbl.num_vols(tblcount) = size(tbl.data{tblcount},1);
            end
            tbl.subject{tblcount} = subs(sub).name;
            tbl.condition{tblcount} = conditions{cond};
            tbl.session(tblcount) = ses;
            
            tblcount = tblcount + 1;
        end
    end
end

% check?
if ~strcmp(ts_ROI2ROI,'denoised_volumes')
for h = 1:height(tbl)
    for h2 = h+1:height(tbl)
        if size(tbl.data{h},1)==size(tbl.data{h2},1)
            if norm(tbl.data{h}-tbl.data{h2},'fro')<1
                error(['equality problem for ',num2str(h),'-',num2str(h2)])
            end
        end
    end
end
end
data=[];
opts = [];
end