--- a
+++ b/create_script.py
@@ -0,0 +1,145 @@
+import sys
+import argparse
+import os
+
+from utils.logger import logger
+from utils.filemanager import create_directory_if_not_exists, get_paths, check_paths, extract_parameter
+
+if __name__ == "__main__":
+    # optional arguments from the command line 
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument('--dataset_path', type=str, default='dataset/train', help='root dir for nifti data')
+    parser.add_argument('--experiment_name', type=str, default='elastix_01', help='experiment name')
+    parser.add_argument('--parameters_path', type=str, default='elastix-parameters/Par0003', help='root dir for elastix parameters. The script will use all the parameters in this directory. A single .txt file can also be used.')
+    parser.add_argument('--output_path', type=str, default='output', help='root dir for output scripts')
+    parser.add_argument("--use_masks", action='store_true', help='if True, segmentation masks will be used during the registration.')
+
+    # parse the arguments
+    args = parser.parse_args()
+
+    # check if parameters_path is .txt file
+    if os.path.isfile(args.parameters_path):
+        parameters      = args.parameters_path
+
+        # cteate params key folder name
+        reg_params      = '-p "{}"'.format(parameters).replace('\\', '/')
+        reg_params_key  = parameters.split('/')[-1].replace('.txt', '')
+        transform_idx   = 0
+
+    elif os.path.isdir(args.parameters_path):
+        # get the parameters from the parameters_path
+        parameters = os.listdir(args.parameters_path)
+
+        if len(parameters) == 0:
+            logger.error(f"No parameters found in {args.parameters_path} directory.")
+            sys.exit(1)
+    
+        # cteate params key folder name
+        reg_params      = ' '.join(['-p "{}"'.format(os.path.join(args.parameters_path, param)) for param in parameters]).replace('\\', '/')    
+        reg_params_key  = '+'.join(['{}'.format(param.replace('.txt', '')) for param in parameters])
+        transform_idx   = len(parameters) - 1
+
+    # get the name of the parameters folder
+    params_folder_name = extract_parameter(args.parameters_path) # Par0003, Par0004, ...
+
+    # create experiment output
+    # args.experiment_name is useful to distinguish between different experiments (e.g. with or without preprocessing, etc.)
+    # reg_params_key is useful to distinguish between different registration parameters (e.g. Par0003, Par0004, etc.)
+    args.exp_output = os.path.join(args.output_path, args.experiment_name, reg_params_key)
+    create_directory_if_not_exists(args.exp_output)
+
+    # get the exhale and inhale volumes and segmentations
+    exhale_volumes = get_paths(args, "eBHCT")
+    inhale_volumes = get_paths(args, "iBHCT")
+
+    check_paths(args, exhale_volumes, "exhale volumes")
+    check_paths(args, inhale_volumes, "inhale volumes")
+
+    # get the exhale and inhale segmentations if args.use_masks is True
+    exhale_seg = get_paths(args, "eBHCT_lung") if args.use_masks else [0 for _ in range(len(exhale_volumes))] # the list has to have values for the zip(*) to return the values inside
+    inhale_seg = get_paths(args, "iBHCT_lung") if args.use_masks else [0 for _ in range(len(inhale_volumes))]
+
+    if args.use_masks:
+        check_paths(args, exhale_seg, "exhale segmentations")
+        check_paths(args, inhale_seg, "inhale segmentations")
+
+    logger.info(f"Creating .bat file in {args.exp_output} output directory for {args.experiment_name} experiment.")
+    logger.info(f"Experimenting using {reg_params} params command...")
+    logger.info(f"Key for the experiment: {reg_params_key}...")
+
+    # creating the .bat file
+    with open(os.path.join(args.exp_output, 'elastix_transformix.bat'), 'w') as file:
+        file.write("@echo on\n")
+        file.write(f"echo To execute this file, use: call {os.path.join(args.exp_output, 'elastix_transformix.bat')} \n")
+
+        for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):
+            # Append commands to the .bat file
+            file.write(f"\nREM Processing {e_path} and {i_path}\n")
+
+            # defining the sample name and the file names
+            sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...
+            e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..
+            i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..
+
+            # defining fixed and moving paths
+            fixed_path = i_path
+            fMask = i_seg_path
+
+            moving_path = e_path
+            mMask = e_seg_path
+
+            # defining the control point to be transformed abd transform file paths
+            input_points = os.path.join(args.dataset_path ,f'{sample_name}/{sample_name}_300_iBH_xyz_r1.txt') # i_cntl_pt
+            transform_path = f'{args.exp_output}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{transform_idx}.txt'
+
+            # 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]
+
+            elastix_output_dir = f'{args.exp_output}/images/output_{reg_fixed_name}/{reg_moving_name}'
+            transformix_output_dir = f'{args.exp_output}/points/output_{reg_fixed_name}/{reg_moving_name}'
+
+            create_directory_if_not_exists(elastix_output_dir)
+            create_directory_if_not_exists(transformix_output_dir)
+
+            if params_folder_name == 'Par0003':
+                # elastix version: 3.9 -- fails to allocate memory to register; also can't -def point transformation
+                # elastix_v_path      = '.\\elastix-versions\\elastix_windows32_v3.9\\elastix'
+                # transformix_v_path  = '.\\elastix-versions\\elastix_windows32_v3.9\\transformix'
+                
+                # using default is 4.7
+                elastix_v_path      = '.\\elastix-versions\\elastix_windows64_v4.7\\elastix'
+                transformix_v_path  = '.\\elastix-versions\\elastix_windows64_v4.7\\transformix'
+            
+            elif params_folder_name == 'Par0007':
+                # elastix version: 4.0 -- fails to allocate memory to register; also can't -def point transformation
+                # elastix_v_path      = '.\\elastix-versions\\elastix_windows32_v4.0\\elastix'
+                # transformix_v_path  = '.\\elastix-versions\\elastix_windows32_v4.0\\transformix'
+
+                # using default is 4.7
+                elastix_v_path      = '.\\elastix-versions\\elastix_windows64_v4.7\\elastix'
+                transformix_v_path  = '.\\elastix-versions\\elastix_windows64_v4.7\\transformix'
+
+            elif params_folder_name == 'Par0011':
+                # elastix version: 4.301
+                elastix_v_path      = '.\\elastix-versions\\elastix_windows64_v4.3\\elastix'
+                transformix_v_path  = '.\\elastix-versions\\elastix_windows64_v4.3\\transformix'
+            else:
+                # default is 4.7
+                elastix_v_path      = '.\\elastix-versions\\elastix_windows64_v4.7\\elastix'
+                transformix_v_path  = '.\\elastix-versions\\elastix_windows64_v4.7\\transformix'
+
+
+            # create elastix command line
+            if args.use_masks:
+                elastix_command_line = f'{elastix_v_path} -f "{fixed_path}" -m "{moving_path}" -fMask "{fMask}" -mMask "{mMask}" {reg_params} -out "{elastix_output_dir}"'
+            else:
+                elastix_command_line = f'{elastix_v_path} -f "{fixed_path}" -m "{moving_path}" {reg_params} -out "{elastix_output_dir}"'
+
+            # create transformix command line
+            trasformix_command_line = f'{transformix_v_path} -def "{input_points}" -tp "{transform_path}"  -out "{transformix_output_dir}"'
+
+            file.write(f"{elastix_command_line}\n")
+            file.write(f"{trasformix_command_line}\n")
+            
\ No newline at end of file