--- a
+++ b/AutoSegmentationGUI.py
@@ -0,0 +1,198 @@
+import tkinter as tk
+from tkinter import messagebox
+from tkinter import ttk
+import os
+import sys
+
+sys.path.append(os.path.join(os.getcwd(), 'Preprocessing Medical Data Pipeline'))
+import main
+
+def create_subtitle(text):
+    subtitle_label = tk.Label(root, text=text, font=("Helvetica", 12, "bold"), pady=5)
+    subtitle_label.pack()
+
+
+def run_script_preprocessing():
+    ScanDirectory = entry_scan_directory.get("1.0", "end-1c")
+    # runTask = parameter0_combobox.get()
+    scan_folder_name = entry_parameter5.get("1.0", "end-1c")
+    # mask_file_name = entry_parameter6.get("1.0", "end-1c")
+    resizing = parameter2_combobox.get()
+
+    main.Preprocessing(ScanDirectory, scan_folder_name, resizing)
+
+# def run_script_data_aug():
+#     aug_fname = entry_parameter14.get("1.0", "end-1c")
+#     num_augs = entry_parameter4.get()
+#     ScanDirectory = entry_scan_directory.get("1.0", "end-1c")
+
+#     main.DataAug(ScanDirectory, aug_fname, num_augs)
+
+def run_script_prep_test_scan():
+    # runTask = parameter9_combobox.get()
+    cutoffSlice = entry_parameter8.get()
+    ScanDirectory = entry_scan_directory.get("1.0", "end-1c")
+    folders = entry_parameter7.get("1.0", "end-1c")
+
+    main.preprocessTestScansMain(cutoffSlice, ScanDirectory, folders)
+
+def run_script_visualise():
+    # runTask = parameter9_combobox.get()
+    cutoffSlice = entry_parameter12.get()
+    mask_file_name = entry_parameter13.get("1.0", "end-1c")
+    ScanDirectory = entry_scan_directory.get("1.0", "end-1c")
+    main.VisualiseSlice(ScanDirectory, mask_file_name, cutoffSlice)
+
+def run_script_model():
+    # runTask = parameter9_combobox.get()
+    subjectfname = entry_parameter21.get("1.0", "end-1c")
+    ScanDirectory = entry_scan_directory.get("1.0", "end-1c")
+    main.AutoSegModel(ScanDirectory, subjectfname)
+
+
+# Create the main window
+root = tk.Tk()
+root.title("Lower Limb Musculoskeletal Automatic Segmentation Tool")
+
+
+label_scan_directory = tk.Label(root, text="Base Directory (Example: D:/MRI - Tairawhiti):", font=("Helvetica", 12, "bold"))  # Changed label text
+label_scan_directory.pack()
+entry_scan_directory = tk.Text(root, height=1, width=100)
+entry_scan_directory.pack()
+# entry_scan_directory = tk.Entry(root)  # Changed variable name
+# entry_scan_directory.pack()
+
+create_subtitle('-'*160)
+create_subtitle("Preprocessing Training Data (DICOM MRI Scans + NIFITI Binary Segmentation Masks)")
+create_subtitle('-'*160)
+
+# Create input fields
+# label_parameter0 = tk.Label(root, text="Run Preprocessing Raw DICOM MRI Scans & Raw NIFITI Segmentation Masks Task:")
+# label_parameter0.pack()
+# parameter0_values = ["True", "False"]
+# parameter0_combobox = ttk.Combobox(root, values=parameter0_values)
+# parameter0_combobox.pack()
+
+
+label_parameter5 = tk.Label(root, text="Scan Folder Name (Example: 6_AutoBindWATER_650_9B):") 
+label_parameter5.pack()
+entry_parameter5 = tk.Text(root, height=1, width=40)
+entry_parameter5.pack()
+
+# label_parameter6 = tk.Label(root, text="Mask File Name (File Type: _.nii) (Example: 6_RR_fibula_9B) (Note: if Multi-Class, set to 'multi'!):") 
+# label_parameter6.pack()
+# entry_parameter6 = tk.Text(root, height=1, width=40)
+# entry_parameter6.pack()
+
+label_parameter2 = tk.Label(root, text="Select Image Data Size: ")
+label_parameter2.pack()
+parameter2_values = ["512x512", "256x256"]
+parameter2_combobox = ttk.Combobox(root, values=parameter2_values)
+parameter2_combobox.pack()
+
+# label_parameter3 = tk.Label(root, text="Apply Image Preprocessing Techniques:")
+# label_parameter3.pack()
+# parameter3_values = ["True", "False"]
+# parameter3_combobox = ttk.Combobox(root, values=parameter3_values)
+# parameter3_combobox.pack()
+
+# label_parameter4 = tk.Label(root, text="Cropping Dimensions (If Apply_Image_Preprocessing_Techniques = True) (Format: [top,bottom,left,right]):") 
+# label_parameter4.pack()
+# entry_parameter4 = tk.Entry(root)
+# entry_parameter4.pack()
+
+# Create run button
+create_subtitle('-'*80)
+run_button = tk.Button(root, text="Run Preprocessing Layer (Scan Stack & Segmentation Masks)", command=run_script_preprocessing)
+run_button.pack()
+
+create_subtitle('-'*160)
+create_subtitle("Preprocessing Inference/Test Data (Raw DICOM MRI Scans)")
+create_subtitle('-'*160)
+
+# label_parameter9 = tk.Label(root, text="Run Preprocessing Patient Scans For Automatic Segmentation Task:")
+# label_parameter9.pack()
+# parameter9_values = ["True", "False"]
+# parameter9_combobox = ttk.Combobox(root, values=parameter3_values)
+# parameter9_combobox.pack()
+
+
+label_parameter7 = tk.Label(root, text="Scan Folder Name (Example: 6_AutoBindWATER_650_9B):") 
+label_parameter7.pack()
+entry_parameter7 = tk.Text(root, height=1, width=40)
+entry_parameter7.pack()
+
+
+label_parameter8 = tk.Label(root, text="Approximate Slice Index of Pelvis (Lowest Slice Index of Any Region of Interest Being Segmented):") 
+label_parameter8.pack()
+entry_parameter8 = tk.Entry(root)
+entry_parameter8.pack()
+
+create_subtitle('-'*80)
+run_button = tk.Button(root, text="Generate Preprocessed Inference/Prediction (Scan Stack)", command=run_script_prep_test_scan)
+run_button.pack()
+
+
+create_subtitle('-'*160)
+create_subtitle("Run Automatic Segmentation Model (Pre-trained resnet34 U-Net)")
+create_subtitle('-'*160)
+
+# label_parameter9 = tk.Label(root, text="Run Preprocessing Patient Scans For Automatic Segmentation Task:")
+# label_parameter9.pack()
+# parameter9_values = ["True", "False"]
+# parameter9_combobox = ttk.Combobox(root, values=parameter3_values)
+# parameter9_combobox.pack()
+
+
+label_parameter21 = tk.Label(root, text="Subject Scan File Name (Example: msk_006):") 
+label_parameter21.pack()
+entry_parameter21 = tk.Text(root, height=1, width=40)
+entry_parameter21.pack()
+
+create_subtitle('-'*80)
+run_button = tk.Button(root, text="Generate Segmentation Output", command=run_script_model)
+run_button.pack()
+
+# create_subtitle('-'*160)
+# create_subtitle("Data Augmentation")
+# create_subtitle('-'*160)
+
+
+# label_parameter14 = tk.Label(root, text="Preprocessed Data File Name (Example: msk_006):") 
+# label_parameter14.pack()
+# entry_parameter14 = tk.Text(root, height=1, width=40)
+# entry_parameter14.pack()
+
+# label_parameter4 = tk.Label(root, text="Number of Augmentations Per Image:") 
+# label_parameter4.pack()
+# entry_parameter4 = tk.Entry(root)
+# entry_parameter4.pack()
+
+
+# create_subtitle('-'*80)
+# run_button = tk.Button(root, text="Augment Training Data", command=run_script_data_aug)
+# run_button.pack()
+
+
+
+create_subtitle('-'*160)
+create_subtitle("Visualisations of 2D Scans & Masks")
+create_subtitle('-'*160)
+
+label_parameter12 = tk.Label(root, text="Slice Number:") 
+label_parameter12.pack()
+entry_parameter12 = tk.Entry(root)
+entry_parameter12.pack()
+
+label_parameter13 = tk.Label(root, text="Mask File Name (Example: 4_R_tibia_5A, Example(Multi): msk_006) (Requires the preprocessed data!):") 
+label_parameter13.pack()
+entry_parameter13 = tk.Text(root, height=1, width=40)
+entry_parameter13.pack()
+
+create_subtitle('-'*80)
+run_button = tk.Button(root, text="Generate Data Visualisations", command=run_script_visualise)
+run_button.pack()
+create_subtitle('-'*160)
+
+# Start the main loop
+root.mainloop()