The problem comes from the closerequestfcn property of the graphic object. The currently distributed art.m script contains this line:
set(handles.figure1,'closerequestfcn',['try,if isunix,txt=''rm ''; else txt=''del ''; end; [nill,ok]=system([txt,''',fullfile(output_dir,art_mask_temporalfile),''']);catch;end;close(gcbf);']);
This is a very elegant way to remove temporary files when the ART window is closed, but on my linux station, I have an alias for interactively remove the files or the directories (alias rm 'rm -i') ... So when the Art tool is running on an linux station with this configuration, the close(gcf) command awaits for an interactive action ... So, If you encounter this symptom, changing the previous line by the following should fix:
set(handles.figure1,'closerequestfcn',['try,if isunix,txt=''rm -f ''; else txt=''del ''; end; [nill,ok]=system([txt,''',fullfile(output_dir,art_mask_temporalfile),''']);catch;end;close(gcbf);']);
It could be a good idea that the next version of ART tool include this very minor change ...