By design, when MDS failed at the initial trial, it might be fixed (in the catch blocks) by changing criterion from user-specified criterion to 'stress', or adding 0.2 to distances to avoid colocalization. However, this information is never shown or accessible by users. That is, MDS plot is displayed as normal and users could easily ignore the fact that the MDS criterion might have been changed. Therefore, I edit the codes so that whenever the MDS fails at the initial trial (and is fixed afterwards by the catch blocks), the description of the changes made is visible to the users.

(1)Comment out the saveas() block at the end (line 1044).
"gcf" has already been closed by handleCurrentFigure() (line 942 and 1041), and the plots have already been saved as files.
Thus, any attempt to call saveas(gcf,...) is needless. ( With gcf being closed, this will only save a blank file).

In case if one would like to keep the saveas() block uncommented, there are several bugs to be fixed.
(2)Initiate userOptions.saveFigureFig in the "set default options" block.
Error Message: 
Reference to non-existent field 'saveFigureFig'.
line 1051 in compareRefRDM2candRDMs.m.
Reason:
The field 'userOptions.saveFigureFig' is not initiated at the "set default options" block.

(3)Typo: "userOptions.saveFigureEPS" is mistakenly typed as "userOptions.savesFigurePS". (line 1048)
Old:
if userOptions.saveFiguresPS
    saveas(gcf,[userOptions.analysisName,'_comparingRefRDM2CandRDMs','.eps'],'eps');
end
Fixed:
if userOptions.saveFigureEPS
     saveas(gcf,[userOptions.analysisName,'_comparingRefRDM2CandRDMs','.eps'],'eps');
end