diff --git a/CBCTCardiacSegmentation/CreateCBCTSegmentations.py b/CBCTCardiacSegmentation/CreateCBCTSegmentations.py
index c206960..8fe741d 100644
--- a/CBCTCardiacSegmentation/CreateCBCTSegmentations.py
+++ b/CBCTCardiacSegmentation/CreateCBCTSegmentations.py
@@ -27,6 +27,7 @@
 
 
 def CreateCBCTSegmentations(CBCTDir,OutputDir='./CBCTSegmentations',SegmentationMethod='Synthetic',PlanningCTDir='',ElastixParamDir='',StructFile='',
+                            ElastixRunDir = '',
                             HeartPadDistance=30,
                             KeepTempFiles=False):
     
@@ -68,7 +69,8 @@ def CreateCBCTSegmentations(CBCTDir,OutputDir='./CBCTSegmentations',Segmentation
     Register Images to prepare for Segmentation
     """
     if not(SegmentationMethod == 'Direct'):        
-        VolReg = VolumeRegistration(RegOutputDir=TempDir,ParamDir=ElastixParamDir)
+        VolReg = VolumeRegistration(RegOutputDir=TempDir,ParamDir=ElastixParamDir,
+                                    ElastixDir=ElastixRunDir)
     
         #Align PlanningCT Volume to CBCT Volume
         print('Initial Alignment of Planning CT File to CBCT File')
@@ -179,6 +181,7 @@ def CreateCBCTSegmentations(CBCTDir,OutputDir='./CBCTSegmentations',Segmentation
     parser.add_argument('--SegmentationMethod',default='Synthetic',type=str,help='The method used to segment the CBCT image {Synthetic|Transform|Direct}. Default is Synthetic')
     parser.add_argument('--PlanningCTDir',type=str, default='',help='Location of the Planning CT that is to be segmented. Can be a Dicom Series or Volume file. Default is None')
     parser.add_argument('--ElastixParamDir',type=str,default='',help='Location of the elastix parameter files used for the registrations. Default is the parameters is the provided ElastixParameterFiles')
+    parser.add_argument('--ElastixRunDir',type=str,default='',help='Location of the bin and lib directories from the installed/downaloded version of elastix to be used. Needed for linux implementations')
     parser.add_argument('--StructFile',type=str,default='',help='Location of the structures contoured from the planning CT File. Default is None')
     parser.add_argument('--KeepTempFiles',action='store_true',help='If true the temporary files and directories created will not be deleted. If False these files will be deleted.')
     
diff --git a/CBCTCardiacSegmentation/Registration.py b/CBCTCardiacSegmentation/Registration.py
index 25bc3be..a6ef674 100644
--- a/CBCTCardiacSegmentation/Registration.py
+++ b/CBCTCardiacSegmentation/Registration.py
@@ -14,7 +14,7 @@
 class VolumeRegistration:
 
     def __init__(self, RegOutputDir='', ParamDir='', RigidParamFile='', NonRigidParamFile='', InverseParamFile='',
-                 RigidNonRigidParamFile='',TranslationParamFile='',GPUEnabled=False):
+                 RigidNonRigidParamFile='',TranslationParamFile='',ElastixDir='',GPUEnabled=False):
 
         if not ParamDir:
             #If no elastix parameter directory defined then get the one
@@ -26,6 +26,11 @@ def __init__(self, RegOutputDir='', ParamDir='', RigidParamFile='', NonRigidPara
 
         self.RegOutputDir = RegOutputDir
 
+        if platform.system() == 'Linux':
+            assert not(not ElastixDir),'Directory to elastix bin/lib files needs to be added for linux'
+
+        self.ElastixDir = ElastixDir
+
         if not ParamDir:
             self.RigidParamFile = RigidParamFile
             self.NonRigidParamFile = NonRigidParamFile
@@ -157,7 +162,7 @@ def TransformVolume(self, ParamFile, OutputFile, FixedVolume):
     def CallFunctionFromCmdLine(self,CmdStr):
         # Run command from terminal
         if platform.system() == 'Linux':
-            run(CmdStr, shell=True, env={"PATH": '/home/mark/elastix/bin', "LD_LIBRARY_PATH": '/home/mark/elastix/lib'})
+            run(CmdStr, shell=True, env={"PATH": os.path.join(self.ElastixDir,'bin'), "LD_LIBRARY_PATH": os.path.join(self.ElastixDir,'lib')})
         else:
             run(CmdStr)
 
diff --git a/tests/test_CBCT_Segmentation.py b/tests/test_CBCT_Segmentation.py
index 9d33d33..25b320f 100644
--- a/tests/test_CBCT_Segmentation.py
+++ b/tests/test_CBCT_Segmentation.py
@@ -113,7 +113,7 @@ def test_BadSegMethodInput():
     
     rmtree(data_path) 
     rmtree(OutputDir) 
-    
+
 def test_NiftiCBCTSegmentationGeneration():
     
     # Download the test data
@@ -131,6 +131,10 @@ def test_NiftiCBCTSegmentationGeneration():
     ElastixParamDir = ''
     StructFile = ''
     
+    #Define Elastix directories
+    home_dir = Path(os.path.expanduser('~'))  # may have to update for github system
+    elastix_dir = home_dir / 'ElastixDownload' / 'elastix-5.0.1-linux'
+    
     for SegMethod in SegmentationMethods:
         print(SegMethod)
         OutputDir = './CBCTSegmentations'    
@@ -139,7 +143,8 @@ def test_NiftiCBCTSegmentationGeneration():
                                 SegmentationMethod=SegMethod,
                                 PlanningCTDir=PlanningCTDir,
                                 ElastixParamDir=ElastixParamDir,
-                                StructFile=StructFile)
+                                StructFile=StructFile,
+                                ElastixRunDir=elastix_dir)
     
         CardiacSegList = ['Heart','A_Aorta','A_Cflx','A_Coronary_L','A_Coronary_R','A_LAD','A_Pulmonary','Atrium_L',
                           'Atrium_R','CN_Atrioventricular','CN_Sinoatrial','V_Venacava_S','Valve_Aortic','Valve_Mitral',
@@ -210,4 +215,4 @@ def test_NiftiToDicomStruct():
     assert Path(OutputStructFile).exists(),'Output Struct {} was not created successfully'.format(OutputStructFile)
     
     rmtree(data_path) 
-    rmtree(OutputDir)
\ No newline at end of file
+    rmtree(OutputDir)