Below (indented) is a straightforward MATLAB/SPM/Marsbar script for generating separate Marsbar ROI and Nifti ROI spheres (user-defined radius) from a set of user-defined MNI coordinates stored in a text file (‘spherelist.txt’ saved in the same directory as the script).  ROI files are saved to mat and img directories that the script creates.
I use this script to generate *.mat files as seeds for resting connectivity analyses.  Once a *.mat ROI is generated, Marsbar can be used to extract raw timecourses from this region to feed into connectivity analysis as the regressor of interest.  Because MRIcron doesn’t read *.mat Marsbar ROI files, I render the equivalent *.img seed regions on a canonical brain when I need to present them graphically.

% This script loads MNI coordinates specified in a user-created file,
% spherelist.txt, and generates .mat and .img ROI files for use with
% Marsbar, MRIcron etc.  spherelist.txt should list the centres of
% desired spheres, one-per-row, with coordinates in the format:
% X1 Y1 Z1
% X2 Y2 Z2 etc
% .mat sphere ROIs will be saved in the script-created mat directory.
% .img sphere ROIs will be saved in the script-created img directory.
% SPM Toolbox Marsbar should be installed and started before running script.

% specify radius of spheres to build in mm
radiusmm = 4;

% Specify Output Folders for two sets of images (.img format and .mat format)
roi_dir_img = ‘img’;
roi_dir_mat = ‘mat’;
% Make an img and an mat directory to save resulting ROIs
% Go through each set of coordinates from the specified file (line 2)
spherelistrows = length(spherelist(:,1));
for spherenumbers = 1:spherelistrows
% maximum is specified as the centre of the sphere in mm in MNI space
maximum = spherelist(spherenumbers,1:3);
sphere_centre = maximum;
sphere_radius = radiusmm;
sphere_roi = maroi_sphere(struct(‘centre’, sphere_centre, …
‘radius’, sphere_radius));

% Define sphere name using coordinates
coordsx = num2str(maximum(1));
coordsy = num2str(maximum(2));
coordsz = num2str(maximum(3));
spherelabel = sprintf(‘%s_%s_%s’, coordsx, coordsy, coordsz);
sphere_roi = label(sphere_roi, spherelabel);

% save ROI as MarsBaR ROI file
saveroi(sphere_roi, fullfile(roi_dir_mat, sprintf(‘%dmmsphere_%s_roi.mat’,…
radiusmm, spherelabel)));
% Save as image
save_as_image(sphere_roi, fullfile(roi_dir_img, sprintf(‘%dmmsphere_%s_roi.img’,…
radiusmm, spherelabel)));

UPDATE: WordPress messed with the characters in the above script, so here is a link to the script file and an example spherelist.txt file.