changed the flip in the anat step of the registration, changed it back to before

code/register_masks.py

@@ -56,35 +56,6 @@ def main():
                 print(f"An error occurred: {e}")
                 
             progress_bar.update(1)
-    
-    registered_masks_path = os.path.join(args.input,"**","RegisteredTractMasks", "*.nii.gz")
-    registered_masks_files = glob.glob(registered_masks_path, recursive=True)
-
-    total_iterations = len(registered_masks_files)
-    progress_bar = tqdm(total=total_iterations, desc='Flipping Masks', unit='files')
-
-    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=0), axis=1)
-        flipped_mask = np.flip(mask_data, axis=0)
-        
-
-        # 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, "RegisteredTractMasks")
-
-
-
-        # Define the new file name and save the flipped mask
-        if "anat" in mask_file:
-            adjusted_mask_file = os.path.join(adjusted_masks_dir, os.path.basename(mask_file).replace(".nii.gz",".nii.gz"))
-            nib.save(nib.Nifti1Image(flipped_mask, mask_nifti.affine), adjusted_mask_file)
-
-        progress_bar.update(1)
 
     progress_bar.close()
     print("Flipping of RegisteredTractMasks and saving to RegisteredTractMasks_adjusted: DONE\n")