% J Grahn
% MarsBaR batch script to convert roi format to image format
%% See http://marsbar.sourceforge.net
%
roi_dir = '/imaging/jessica/anatomy toolboxes/rois/MNItemplateROIs'; %Directory with ROIs to convert

% MarsBaR version check
if isempty(which('marsbar'))
  error('Need MarsBaR on the path');
end
v = str2num(marsbar('ver'));
if v < 0.35
  error('Batch script only works for MarsBaR >= 0.35');
end
marsbar('on');  % needed to set paths etc

% %For a single, named ROI
% roi_name = fullfile(roi_dir, 'MNI_Putamen_L_roi.mat');
% roi_array{1} = maroi(roi_name);
% 
% for roi_no = 1:length(roi_array)
%    roi = roi_array{roi_no};
% save_as_image(roi, fullfile(roi_dir, 'test.nii'))
% end

%For batch converting the contents of a directory of ROIs
roi_namearray = dir(fullfile(roi_dir, '*_roi.mat'))
for roi_no = 1:length(roi_namearray)
    roi_array{roi_no} = maroi(fullfile(roi_dir, roi_namearray(roi_no).name));
    roi = roi_array{roi_no};
    name = strtok(roi_namearray(roi_no).name, '.')
    save_as_image(roi, fullfile(roi_dir, [name '.nii']))
end