--- a
+++ b/utils/elastix.py
@@ -0,0 +1,156 @@
+import subprocess
+import os
+
+
+def excute_cmd(command):
+    '''
+    Execute a command and check for success.
+
+    Args:
+        command ('str'): Command to execute.
+    
+    Returns:
+        result ('str'): Output of the command if successful.
+    '''
+    # excute the command
+    result = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True, shell=True)
+
+    # Check the return code to see if the command was successful
+    if result.returncode == 0:
+        # print("Command executed successfully.")
+        # print("Output:")
+        return result.stdout
+    else:
+        print(f"Command failed with an error: {command}")
+        print(result.stderr)
+        return result.stderr
+
+# Perform registration and label propagation
+def register_elastix(fixed_path, 
+                    moving_path, 
+                    reg_params, 
+                    reg_params_key,
+                    create_dir_callback, 
+                    excute_cmd_callback,
+                    fMask = None,
+                    mMask = None):
+    '''
+    Perform image registration using elastix.
+
+    Args:
+        fixed_path ('str'): Path to the fixed image.
+        moving_path ('str'): Path to the moving image.
+        reg_params ('str'): Registration parameters for elastix.
+        reg_params_key ('str'): Key to identify the registration parameters output folder.
+        create_dir_callback ('function'): Callback function to create directories.
+        excute_cmd_callback ('function'): Callback function to execute commands.
+        fMask ('str'): Optional path to a mask file.
+        mMask ('str'): Optional path to a mask file.
+
+    Returns:
+        None
+    '''
+    # Get the names of the fixed and moving images for the output directory, names without the file extensions
+    reg_fixed_name  = fixed_path.replace("\\", "/").split("/")[-1].split(".")[0] # \\
+    reg_moving_name = moving_path.replace("\\", "/").split("/")[-1].split(".")[0]
+
+    # create output dir
+    output_dir = f'output/{reg_params_key}/images/output_{reg_fixed_name}/{reg_moving_name}'
+    create_dir_callback(output_dir)
+
+    # create elastix command line
+    if fMask and not mMask:
+        command_line = f'elastix -f "{fixed_path}" -m "{moving_path}" -fMask {fMask} {reg_params} -out "{output_dir}"'
+    elif mMask and not fMask:
+        command_line = f'elastix -f "{fixed_path}" -m "{moving_path}" -mMask {mMask} {reg_params} -out "{output_dir}"'
+    elif mMask and fMask:
+        command_line = f'elastix -f "{fixed_path}" -m "{moving_path}" -fMask {fMask} -mMask {mMask} {reg_params} -out "{output_dir}"'
+    else:
+        command_line = f'elastix -f "{fixed_path}" -m "{moving_path}" {reg_params} -out "{output_dir}"'
+    print("Excuting command: ", command_line)
+
+    # call elastix command
+    excute_cmd_callback(command_line)
+
+def label_propagation_transformix(
+    fixed_path, 
+    moving_path, 
+    input_label, 
+    transform_path, 
+    replace_text_in_file_callback, 
+    create_dir_callback, 
+    excute_cmd_callback):
+    '''
+    Apply label propagation using transformix.
+
+    Args:
+        fixed_path ('str'): Path to the fixed image.
+        moving_path ('str'): Path to the moving image.
+        input_label ('str'): Path to the input label image.
+        transform_path ('str'): Path to the transformation parameters.
+        replace_text_in_file_callback ('function'): Callback function to replace text in a file.
+        create_dir_callback ('function'): Callback function to create directories.
+        excute_cmd_callback ('function'): Callback function to execute commands.
+
+    Returns:
+        None
+    '''
+    replace_text_in_file_callback(
+        transform_path, 
+        search_text = '(FinalBSplineInterpolationOrder 3)', 
+        replacement_text =  '(FinalBSplineInterpolationOrder 0)')
+
+    # Get the names of the fixed and moving images for the output directory, names without the file extensions
+    reg_fixed_name  = fixed_path.replace("\\", "/").split("/")[-1].split(".")[0] 
+    reg_moving_name = os.path.join(moving_path.replace("\\", "/").split("/")[0], moving_path.replace("\\", "/").split("/")[-1].split(".")[0])
+        
+    # create an output directory for the labels
+    output_dir = f'output/labels/output_{reg_fixed_name}/{reg_moving_name}' # rem _float64
+
+    # creates the output directory
+    create_dir_callback(output_dir)
+    
+    # create transformix command line
+    command_line = f'transformix -in "{input_label}" -tp "{transform_path}"  -out "{output_dir}"'
+    
+    # run transformix on all combinations
+    excute_cmd_callback(command_line)
+
+def control_points_transformix(
+    fixed_path, 
+    moving_path, 
+    reg_params_key,
+    input_points,
+    transform_path,
+    replace_text_in_file_callback,
+    create_dir_callback, 
+    excute_cmd_callback
+):
+    replace_text_in_file_callback(
+        transform_path, 
+        search_text = '(FinalBSplineInterpolationOrder 3)', 
+        replacement_text =  '(FinalBSplineInterpolationOrder 0)')
+    
+    replace_text_in_file_callback(
+            transform_path, 
+            search_text = '(ResultImagePixelType "short")', 
+            replacement_text =  '(ResultImagePixelType "float")')
+        
+    # Get the names of the fixed and moving images for the output directory, names without the file extensions
+    reg_fixed_name  = fixed_path.replace("\\", "/").split("/")[-1].split(".")[0] 
+    reg_moving_name = moving_path.replace("\\", "/").split("/")[-1].split(".")[0]
+
+    # create an output directory for the labels
+    output_dir = f'output/{reg_params_key}/points/output_{reg_fixed_name}/{reg_moving_name}' # rem _float64
+
+    # creates the output directory
+    create_dir_callback(output_dir)
+
+    # create transformix command line
+    command_line = f'transformix -def "{input_points}" -tp "{transform_path}"  -out "{output_dir}"'
+
+    # run transformix on all combinations
+    excute_cmd_callback(command_line)
+
+    return output_dir
+