make_BIDS.m

function BIDS = make_BIDS(input_dir)
%function BIDS = make_BIDS(input_dir, output_dir)
% 
% Prepare datasets for BIDS format
%
% Required fields of make_BIDS:
%
% input_dir  -  location of the GE data
%
%               data must have passed consistency checks using
%               consistency.m in MICHA_TEST/FA_consistency
%               the script is expecting a file named
%               "biomax_out_*_VERIFIED*.txt" or
%               "biomax_out_*_MODIFIED*.txt" 
%               to be present in the subjects main directory
% 
% output_dir  -  location of the final BIDS data
%
%
% structure BIDS
% input.dir     - directory with verified data
%           e.g. BIDS.input.dir = '/run/media/spectro/DATAPART1/MICHA_TEST/FOR0015'
% input.biomax  - biomax_out filename
%
% file history:
% created M. Czisch & F. Binder 7.11.2017
% last modified 31.1.2018 M. Czisch

clear BIDS
BIDS.input.dir = input_dir;
BIDS.output.dir = '';

% have the data being for consistency checked already?

BIDS = check_BIOMAX(BIDS);


% check and prepare temporary BIDS directory structure

pathInfo = what(BIDS.input.dir);
current_dir = pathInfo.path;

BIDS.output.dir = [current_dir,'/BIDS'];

check_BIDS(BIDS.input.dir);
mkdir_BIDS(BIDS.output.dir);
%cd(BIDS.input.dir);


% load and format biomax_out info

biomax = load(BIDS.input.biomax);

biomax_table = array2table(biomax,...
    'VariableNames',{'Ser','Log','EDF','PPG','Analyzer','Blood'},...
    'RowNames',{'Loc';'T1w';'Cal';'rest1';...
                'EPI1';'TET';'FLAIR';'Reward';...
                'DTI';'Pepolar';'nback';'Loc2';...
                'Cal2';'faces';'EPI2';'rest2';...
                'IST';'Loc3';'rest3'});
            
% read content of GE EXAM and SERIES files

BIDS = read_GE_BIDS(BIDS);

% do the conversion to BIDS format

%convert_GE_BIDS(BIDS, biomax_table);
%cd([BIDS.input.dir]);

% do the conversion of logfiles to BIDS format

convert_LOG_BIDS(BIDS,biomax_table);
%cd([BIDS.input.dir]);

% do tsv conversion of logfiles

Hariri_logfile_bids(BIDS);
NBack_logfile_bids(BIDS);
TET_logfile_bids(BIDS);

% for the IST, this is a bit more tricky due to 2 different versions
% this differentiation is based on Anne Kuehnels script
% 24.1.2018
IST_logfile_bids(BIDS)

cd([BIDS.input.dir]);