diff --git a/setup.m b/setup.m
index 7cc7371..f9d7091 100644
--- a/setup.m
+++ b/setup.m
@@ -1,19 +1,42 @@
 function setup()
     % to execute once after cloning the repo.
     createDefaultConfigFile();
 
     addpath(genpath(pwd));
 end
 
 
 
 function createDefaultConfigFile()
     defaultConfig.maxSCaseIDDigits = 3;
     defaultConfig.SCaseIDValidTypes = ["N", "P"];
     defaultConfig.pythonDir = "/shoulder/methods/python/rcseg";
     defaultConfig.dataDir = "/shoulder/dataDev";
+    
+    defaultConfig.shouldersToMeasure.rightAuto = true;
+    defaultConfig.shouldersToMeasure.rightManual = true;
+    defaultConfig.shouldersToMeasure.leftAuto = true;
+    defaultConfig.shouldersToMeasure.leftManual = true;
+    
+    defaultConfig.standardMeasurementsToRun.loadData = true;
+    defaultConfig.standardMeasurementsToRun.morphology = true;
+    defaultConfig.standardMeasurementsToRun.measureFirst = true;
+    defaultConfig.standardMeasurementsToRun.measureSecond = true;
+    defaultConfig.standardMeasurementsToRun.measureThird = true;
+
+    defaultConfig.specialMeasurementsToRun.sliceAndSegment = false;
+    defaultConfig.specialMeasurementsToRun.measureDegenerations = false;
+    defaultConfig.specialMeasurementsToRun.calcDensity = false;
+
+    defaultConfig.specialMeasurementsArguments.sliceAndSegment = [];
+    defaultConfig.specialMeasurementsArguments.measureDegenerations =...
+        ["rotatorCuffMatthieu", "autoMatthieu"];
+    defaultConfig.specialMeasurementsArguments.calcDensity = [];
+
+    defaultConfig.overwriteMeasurements = false;
+    defaultConfig.saveMeasurements = false;
 
     fid = fopen('config.json','w');
     fprintf(fid, replace(jsonencode(defaultConfig), ",", ",\n"));
     fclose(fid);
 end
\ No newline at end of file