--- a
+++ b/combinedDeepLearningActiveContour/functions/save_contours.m
@@ -0,0 +1,36 @@
+% save contours into txt files
+function output=save_contours(masks,t_cont_names,slice_per_patient)
+
+% get number of studies
+num_studies=length(slice_per_patient);
+
+
+for k=1:num_studies
+    
+    % get number of slices per patient
+    spp=slice_per_patient(k);
+
+    % make a new directory
+    dirn=['matFiles/auto_contours/auto',num2str(k)];
+    mkdir(dirn);
+    
+    for k2=1:spp
+        
+         % get manual contour file name
+         ind=k2+sum(slice_per_patient(1:k-1));
+         origStr=t_cont_names(ind).name;
+
+         % replace manual with auto in the name
+         modifiedStr = strrep(origStr, 'manual', 'auto');
+
+         % convert mask to contours
+         temp=(contourc(masks(:,:,ind),[0 0]))';
+         auto_contour=temp(2:end,:);
+         
+         % save contours into txt files         
+         filename=[dirn,'/',modifiedStr];
+         save (filename,'auto_contour','-ASCII');
+    end  
+end
+
+output='done'