From d5508deadc0a0520578b7f4a231ca3386236cb29 Mon Sep 17 00:00:00 2001
From: Marcel Rosier <marcel.rosier@gmx.de>
Date: Thu, 4 Sep 2025 13:52:49 +0200
Subject: [PATCH 1/2] Change to use new AtlasCentricPreprocessor

Fix typing and logic issues
---
 brainles_preprocessing/cli.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/brainles_preprocessing/cli.py b/brainles_preprocessing/cli.py
index 547ece6..af826e0 100644
--- a/brainles_preprocessing/cli.py
+++ b/brainles_preprocessing/cli.py
@@ -9,7 +9,7 @@
 from brainles_preprocessing.normalization.percentile_normalizer import (
     PercentileNormalizer,
 )
-from brainles_preprocessing.preprocessor import Preprocessor
+from brainles_preprocessing.preprocessor import AtlasCentricPreprocessor
 
 
 def version_callback(value: bool):
@@ -59,7 +59,7 @@ def main(
         ),
     ],
     output_dir: Annotated[
-        str,
+        str | Path,
         typer.Option(
             "-o",
             "--output_dir",
@@ -117,8 +117,9 @@ def main(
         defacing_mask_output_path=output_dir / "t1c_defacing_mask.nii.gz",
     )
 
+    moving_modalities = []
     for modality in ["t1", "t2", "fla"]:
-        moving_modalities = [
+        moving_modalities.append(
             Modality(
                 modality_name=modality,
                 input_path=eval(f"input_{modality}"),
@@ -134,18 +135,18 @@ def main(
                 normalized_defaced_output_path=output_dir
                 / f"{modality}_defaced_normalized.nii.gz",
             )
-        ]
+        )
 
-    # if the input atlas is the SRI24 BraTS atlas, set it to None, because it will be picked up through the package
-    if input_atlas == "SRI24 BraTS atlas":
-        input_atlas = None
+    optional_kwargs = {}
+    if input_atlas is not None:
+        optional_kwargs["atlas_image_path"] = input_atlas
 
     # instantiate and run the preprocessor using defaults for registration/ brain extraction/ defacing backends
-    preprocessor = Preprocessor(
+    preprocessor = AtlasCentricPreprocessor(
         center_modality=center,
         moving_modalities=moving_modalities,
         temp_folder=output_dir / "temp",
-        input_atlas=input_atlas,
+        **optional_kwargs,
     )
 
     preprocessor.run()

From 756f4de254cbdc825566dcde49b79be301eda5f1 Mon Sep 17 00:00:00 2001
From: Marcel Rosier <marcel.rosier@gmx.de>
Date: Thu, 4 Sep 2025 13:58:54 +0200
Subject: [PATCH 2/2] Fix eval security issue

---
 brainles_preprocessing/cli.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/brainles_preprocessing/cli.py b/brainles_preprocessing/cli.py
index af826e0..5490d51 100644
--- a/brainles_preprocessing/cli.py
+++ b/brainles_preprocessing/cli.py
@@ -118,11 +118,13 @@ def main(
     )
 
     moving_modalities = []
-    for modality in ["t1", "t2", "fla"]:
+    for input_path, modality in zip(
+        [input_t1, input_t2, input_fla], ["t1", "t2", "fla"]
+    ):
         moving_modalities.append(
             Modality(
                 modality_name=modality,
-                input_path=eval(f"input_{modality}"),
+                input_path=input_path,
                 normalizer=percentile_normalizer,
                 # specify the output paths for the raw and normalized images of each step - here only for atlas registered and brain extraction
                 raw_skull_output_path=output_dir / f"{modality}_skull_raw.nii.gz",