ds003216/code/add_volume_timing.m

% Adds a volume timing metadata to the json for each vaso file
%
% requires bids-matlab: https://github.com/bids-standard/bids-matlab
%

% The 5.16 for the repetition time in the JSON file refers to the average.
% The TRs from the oscilloscope were 5.1002 and 5.1999 respectively.

% NOTE:
% For the first 10 TRs, the scanner was a bit slower (0.0025s).
% But I think we can ignore that. One would think that a "realtime system" is more accurate

clear;

root_dir = fullfile(fileparts(mfilename('fullpath')), '..');

% this is hard coded here
% but obviously would have to be adapted dynamically to each file
TRs = [5.1002; 5.1999];
nb_volumes = 200;

%%
BIDS = bids.layout(root_dir, 'use_schema', false);
all_files = bids.query(BIDS, 'data', 'suffix', 'vaso');
all_metadata = bids.query(BIDS, 'metadata', 'suffix', 'vaso');

for i = 1:numel(all_files)

    bf = bids.File(all_files{i});

    if numel(all_metadata) > 1
        metadata = all_metadata{i};
    else
        metadata = all_metadata;
    end
    
    AcquisitionDuration = repmat(TRs, nb_volumes / numel(TRs), 1);
    metadata.VolumeTiming = cumsum([0 ; AcquisitionDuration(1:end-1)]);
    metadata.AcquisitionDuration = AcquisitionDuration;

    output_file = fullfile(BIDS.pth, ...
                           bf.bids_path, ...
                           'func', ...
                           bf.json_filename);

    bids.util.jsonencode(output_file, metadata);

end