adjusted code to also save masks for dsistudio folder for fa map etc

bin/register_masks.py

@@ -11,7 +11,8 @@
 import os
 import glob
 import csv
-
+import nibabel as nib
+import numpy as np
 def main():
     parser = argparse.ArgumentParser(description="Image Registration and Resampling")
 
@@ -89,6 +90,35 @@ def main():
                 print(f"Errors:\n{result.stderr.decode()}")
             except Exception as e:
                 print(f"An error occurred: {e}")
+
+    # Adjust by flipping for the fa0 and ad files
+    # Locate all files in the "RegisteredTractMasks" folder
+    registered_masks_path = os.path.join(args.input,"**","RegisteredTractMasks", "*.nii.gz")
+    registered_masks_files = glob.glob(registered_masks_path, recursive=True)
+
+    for mask_file in registered_masks_files:
+        # Load the mask file
+        mask_nifti = nib.load(mask_file)
+        mask_data = mask_nifti.get_fdata()
+
+        # Flip the mask along the Y and Z axes
+        #flipped_mask = np.flip(np.flip(mask_data, axis=1), axis=2)
+        flipped_mask = np.flip(mask_data, axis=2)
+
+
+        # Determine the directory to save the adjusted mask
+        mask_dir = os.path.dirname(os.path.dirname(mask_file))
+        adjusted_masks_dir = os.path.join(mask_dir, "DSI_studio", "RegisteredTractMasks_adjusted")
+
+        # Create the directory if it doesn't exist
+        if not os.path.exists(adjusted_masks_dir):
+            os.makedirs(adjusted_masks_dir)
+
+        # Define the new file name and save the flipped mask
+        adjusted_mask_file = os.path.join(adjusted_masks_dir, os.path.basename(mask_file).replace(".nii.gz","_flipped.nii.gz"))
+        nib.save(nib.Nifti1Image(flipped_mask, mask_nifti.affine), adjusted_mask_file)
+
+        print("Flipping of RegisteredTractMasks and saving to RegisteredTractMasks_adjusted: DONE\n")
 
     # Save the missing matrix paths to a CSV file
     missing_matrix_csv_path = os.path.join(args.input, "missing_matrix_paths.csv")
@@ -104,4 +134,4 @@ def main():
 
 
 if __name__ == "__main__":
-    main()
+    main()