brainles-preprocessing 0.4.0__tar.gz → 0.5.0__tar.gz

{brainles_preprocessing-0.4.0 → brainles_preprocessing-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: brainles_preprocessing
-Version: 0.4.0
+Version: 0.5.0
 Summary: Tool for preprocessing tasks in biomedical imaging, with a focus on (but not limited to) multi-modal brain MRI
 License: Apache-2.0
 Keywords: brain tumor,glioma,BraTS,skullstripping,brain extraction
@@ -20,17 +20,17 @@ Provides-Extra: all
 Provides-Extra: itk-elastix
 Provides-Extra: picsl-greedy
 Requires-Dist: antspyx (>=0.5.4,<1.0.0)
-Requires-Dist: auxiliary (>=0.0.42)
+Requires-Dist: auxiliary (>=0.3.1)
 Requires-Dist: black (>=22.1.0,<23.0.0)
 Requires-Dist: brainles_hd_bet (>=0.0.10,<1.0.0)
 Requires-Dist: itk-elastix (>=0.20.0,<0.21.0) ; extra == "all" or extra == "itk-elastix"
 Requires-Dist: nibabel (>=3.2.1)
 Requires-Dist: numpy (>=1.23.0,<2.0.0)
-Requires-Dist: path (>=16.10.0,<17.0.0)
 Requires-Dist: pathlib (>=1.0.1,<2.0.0)
 Requires-Dist: picsl_greedy (>=0.0.6,<0.0.7) ; extra == "all" or extra == "picsl-greedy"
 Requires-Dist: rich (>=13.6.0,<14.0.0)
 Requires-Dist: scipy (<1.14)
+Requires-Dist: simpleitk (>=2.2.1)
 Requires-Dist: tqdm (>=4.64.1,<5.0.0)
 Requires-Dist: ttictoc (>=0.5.6,<0.6.0)
 Requires-Dist: typer (>=0.15.0,<0.16.0)
@@ -49,9 +49,10 @@ Description-Content-Type: text/markdown
 
 `BrainLes preprocessing` is a comprehensive tool for preprocessing tasks in biomedical imaging, with a focus on (but not limited to) multi-modal brain MRI. It can be used to build modular preprocessing pipelines:
 
-This includes **normalization**, **co-registration**, **atlas registration** and **skulstripping / brain extraction**.
+This includes **normalization**, **co-registration**, **atlas registration**, **skullstripping / brain extraction**, **N4 Bias correction** and **defacing**.
+We provide means to transform images and segmentations in both directions between native and atlas space.
 
-BrainLes is written `backend-agnostic` meaning it allows to swap the registration, brain extraction tools and defacing tools.
+BrainLes is written modular and `backend-agnostic` meaning it allows to skip or swap registration, brain extraction, N4 bias correction and defacing tools.
 
 <!-- TODO include image here -->
 
@@ -125,7 +126,7 @@ moving_modalities = [
     )
 ]
 
-# instantiate and run the preprocessor using defaults for registration/ brain extraction/ defacing backends
+# instantiate and run the preprocessor using defaults for backends (registration, brain extraction, bias correction, defacing)
 preprocessor = Preprocessor(
     center_modality=center,
     moving_modalities=moving_modalities,
@@ -166,6 +167,9 @@ We currently provide support for [ANTs](https://github.com/ANTsX/ANTs) (default)
 We provide the SRI-24 atlas from this [publication](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915788/).
 However, custom atlases in NIfTI format are supported.
 
+### N4 Bias correction
+We currently provide support for N4 Bias correction based on [SimpleITK](https://simpleitk.org/)
+
 ### Brain extraction
 We currently provide support for [HD-BET](https://github.com/MIC-DKFZ/HD-BET).
 

{brainles_preprocessing-0.4.0 → brainles_preprocessing-0.5.0}/README.md

@@ -10,9 +10,10 @@
 
 `BrainLes preprocessing` is a comprehensive tool for preprocessing tasks in biomedical imaging, with a focus on (but not limited to) multi-modal brain MRI. It can be used to build modular preprocessing pipelines:
 
-This includes **normalization**, **co-registration**, **atlas registration** and **skulstripping / brain extraction**.
+This includes **normalization**, **co-registration**, **atlas registration**, **skullstripping / brain extraction**, **N4 Bias correction** and **defacing**.
+We provide means to transform images and segmentations in both directions between native and atlas space.
 
-BrainLes is written `backend-agnostic` meaning it allows to swap the registration, brain extraction tools and defacing tools.
+BrainLes is written modular and `backend-agnostic` meaning it allows to skip or swap registration, brain extraction, N4 bias correction and defacing tools.
 
 <!-- TODO include image here -->
 
@@ -86,7 +87,7 @@ moving_modalities = [
     )
 ]
 
-# instantiate and run the preprocessor using defaults for registration/ brain extraction/ defacing backends
+# instantiate and run the preprocessor using defaults for backends (registration, brain extraction, bias correction, defacing)
 preprocessor = Preprocessor(
     center_modality=center,
     moving_modalities=moving_modalities,
@@ -127,6 +128,9 @@ We currently provide support for [ANTs](https://github.com/ANTsX/ANTs) (default)
 We provide the SRI-24 atlas from this [publication](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915788/).
 However, custom atlases in NIfTI format are supported.
 
+### N4 Bias correction
+We currently provide support for N4 Bias correction based on [SimpleITK](https://simpleitk.org/)
+
 ### Brain extraction
 We currently provide support for [HD-BET](https://github.com/MIC-DKFZ/HD-BET).
 

{brainles_preprocessing-0.4.0 → brainles_preprocessing-0.5.0}/brainles_preprocessing/brain_extraction/brain_extractor.py

@@ -5,7 +5,7 @@ from pathlib import Path
 from typing import Optional, Union
 from enum import Enum
 
-from auxiliary.nifti.io import read_nifti, write_nifti
+from auxiliary.io import read_image, write_image
 from brainles_hd_bet import run_hd_bet
 
 
@@ -55,8 +55,8 @@ class BrainExtractor:
 
         try:
             # Read data
-            input_data = read_nifti(str(input_image_path))
-            mask_data = read_nifti(str(mask_path))
+            input_data = read_image(str(input_image_path))
+            mask_data = read_image(str(mask_path))
         except FileNotFoundError as e:
             raise FileNotFoundError(f"File not found: {e.filename}") from e
         except Exception as e:
@@ -70,10 +70,10 @@ class BrainExtractor:
         masked_data = input_data * mask_data
 
         try:
-            write_nifti(
+            write_image(
                 input_array=masked_data,
-                output_nifti_path=str(bet_image_path),
-                reference_nifti_path=str(input_image_path),
+                output_path=str(bet_image_path),
+                reference_path=str(input_image_path),
                 create_parent_directory=True,
             )
         except Exception as e:

{brainles_preprocessing-0.4.0 → brainles_preprocessing-0.5.0}/brainles_preprocessing/constants.py

@@ -6,8 +6,9 @@ class PreprocessorSteps(IntEnum):
     COREGISTERED = 1
     ATLAS_REGISTERED = 2
     ATLAS_CORRECTED = 3
-    BET = 4
-    DEFACED = 5
+    N4_BIAS_CORRECTED = 4
+    BET = 5
+    DEFACED = 6
 
 
 class Atlas(str, Enum):

{brainles_preprocessing-0.4.0 → brainles_preprocessing-0.5.0}/brainles_preprocessing/defacing/defacer.py

@@ -2,7 +2,7 @@ from abc import ABC, abstractmethod
 from pathlib import Path
 from typing import Union
 
-from auxiliary.nifti.io import read_nifti, write_nifti
+from auxiliary.io import read_image, write_image
 
 
 class Defacer(ABC):
@@ -52,8 +52,8 @@ class Defacer(ABC):
 
         try:
             # Read data
-            input_data = read_nifti(str(input_image_path))
-            mask_data = read_nifti(str(mask_path))
+            input_data = read_image(str(input_image_path))
+            mask_data = read_image(str(mask_path))
         except Exception as e:
             raise RuntimeError(
                 f"An error occurred while reading input files: {e}"
@@ -67,9 +67,9 @@ class Defacer(ABC):
         masked_data = input_data * mask_data
 
         # Save the defaced image
-        write_nifti(
+        write_image(
             input_array=masked_data,
-            output_nifti_path=str(defaced_image_path),
-            reference_nifti_path=str(input_image_path),
+            output_path=str(defaced_image_path),
+            reference_path=str(input_image_path),
             create_parent_directory=True,
         )

{brainles_preprocessing-0.4.0 → brainles_preprocessing-0.5.0}/brainles_preprocessing/defacing/quickshear/quickshear.py

@@ -2,10 +2,10 @@ from pathlib import Path
 from typing import Union
 
 import nibabel as nib
+from auxiliary.io import read_image, write_image
 
 from brainles_preprocessing.defacing.defacer import Defacer
 from brainles_preprocessing.defacing.quickshear.nipy_quickshear import run_quickshear
-from auxiliary.nifti.io import write_nifti
 
 
 class QuickshearDefacer(Defacer):
@@ -56,8 +56,11 @@ class QuickshearDefacer(Defacer):
 
         bet_img = nib.load(str(input_image_path))
         mask = run_quickshear(bet_img=bet_img, buffer=self.buffer)
-        write_nifti(
+
+        # transpose to match simpletik order
+        mask = mask.transpose(2, 1, 0)
+        write_image(
             input_array=mask,
-            output_nifti_path=str(mask_image_path),
-            reference_nifti_path=str(input_image_path),
+            output_path=str(mask_image_path),
+            reference_path=str(input_image_path),
         )

{brainles_preprocessing-0.4.0 → brainles_preprocessing-0.5.0}/brainles_preprocessing/modality.py

@@ -4,7 +4,7 @@ import warnings
 from pathlib import Path
 from typing import Dict, Optional, Union
 
-from auxiliary.nifti.io import read_nifti, write_nifti
+from auxiliary.io import read_image, write_image
 
 from brainles_preprocessing.brain_extraction.brain_extractor import BrainExtractor
 from brainles_preprocessing.constants import PreprocessorSteps
@@ -34,6 +34,7 @@ class Modality:
         normalized_skull_output_path (str or Path, optional): Path to save the normalized modality data with skull. Requires a normalizer.
         normalized_defaced_output_path (str or Path, optional): Path to save the normalized defaced modality data. Requires a normalizer.
         atlas_correction (bool, optional): Indicates whether atlas correction should be performed.
+        n4_bias_correction (bool, optional): Indicates whether N4 bias correction should be performed.
 
     Attributes:
         modality_name (str): Name of the modality.
@@ -47,6 +48,7 @@ class Modality:
         normalized_defaced_output_path (str or Path, optional): Path to save the normalized defaced modality data. Requires a normalizer.
         bet (bool): Indicates whether brain extraction is enabled.
         atlas_correction (bool): Indicates whether atlas correction should be performed.
+        n4_bias_correction (bool): Indicates whether N4 bias correction should be performed.
         coregistration_transform_path (str or None): Path to the coregistration transformation matrix, will be set after coregistration.
 
     Example:
@@ -72,6 +74,7 @@ class Modality:
         normalized_skull_output_path: Optional[Union[str, Path]] = None,
         normalized_defaced_output_path: Optional[Union[str, Path]] = None,
         atlas_correction: bool = True,
+        n4_bias_correction: bool = False,
     ) -> None:
         # Basics
         self.modality_name = modality_name
@@ -79,6 +82,7 @@ class Modality:
         self.current = self.input_path
         self.normalizer = normalizer
         self.atlas_correction = atlas_correction
+        self.n4_bias_correction = n4_bias_correction
         self.transformation_paths: Dict[PreprocessorSteps, Path | None] = {}
 
         # Check that atleast one output is generated
@@ -195,12 +199,12 @@ class Modality:
 
         # Normalize the image
         if self.normalizer:
-            image = read_nifti(str(self.current))
+            image = read_image(str(self.current))
             normalized_image = self.normalizer.normalize(image=image)
-            write_nifti(
+            write_image(
                 input_array=normalized_image,
-                output_nifti_path=str(self.current),
-                reference_nifti_path=str(self.current),
+                output_path=str(self.current),
+                reference_path=str(self.current),
             )
         else:
             logger.info("No normalizer specified; skipping normalization.")
@@ -505,12 +509,12 @@ class Modality:
         if normalization:
             if self.normalizer is None:
                 raise ValueError("Normalizer is required for normalization.")
-            image = read_nifti(str(self.current))
+            image = read_image(str(self.current))
             normalized_image = self.normalizer.normalize(image=image)
-            write_nifti(
+            write_image(
                 input_array=normalized_image,
-                output_nifti_path=str(output_path),
-                reference_nifti_path=str(self.current),
+                output_path=str(output_path),
+                reference_path=str(self.current),
             )
         else:
             shutil.copyfile(
@@ -534,6 +538,7 @@ class CenterModality(Modality):
         normalized_skull_output_path (str or Path, optional): Path to save the normalized modality data with skull. Requires a normalizer.
         normalized_defaced_output_path (str or Path, optional): Path to save the normalized defaced modality data. Requires a normalizer.
         atlas_correction (bool, optional): Indicates whether atlas correction should be performed.
+        n4_bias_correction (bool, optional): Indicates whether N4 bias correction should be performed.
         bet_mask_output_path (str or Path, optional): Path to save the brain extraction mask.
         defacing_mask_output_path (str or Path, optional): Path to save the defacing mask.
 
@@ -549,6 +554,7 @@ class CenterModality(Modality):
         normalized_defaced_output_path (str or Path, optional): Path to save the normalized defaced modality data. Requires a normalizer.
         bet (bool): Indicates whether brain extraction is enabled.
         atlas_correction (bool): Indicates whether atlas correction should be performed.
+        n4_bias_correction (bool): Indicates whether N4 bias correction should be performed.
         bet_mask_output_path (Path, optional): Path to save the brain extraction mask.
         defacing_mask_output_path (Path, optional): Path to save the defacing mask.
 
@@ -575,6 +581,7 @@ class CenterModality(Modality):
         normalized_skull_output_path: Optional[Union[str, Path]] = None,
         normalized_defaced_output_path: Optional[Union[str, Path]] = None,
         atlas_correction: bool = True,
+        n4_bias_correction: bool = False,
         bet_mask_output_path: Optional[Union[str, Path]] = None,
         defacing_mask_output_path: Optional[Union[str, Path]] = None,
     ) -> None:
@@ -589,6 +596,7 @@ class CenterModality(Modality):
             normalized_skull_output_path=normalized_skull_output_path,
             normalized_defaced_output_path=normalized_defaced_output_path,
             atlas_correction=atlas_correction,
+            n4_bias_correction=n4_bias_correction,
         )
         # Only for CenterModality
         self.bet_mask_output_path = (

brainles_preprocessing-0.5.0/brainles_preprocessing/n4_bias_correction/__init__.py

@@ -0,0 +1,2 @@
+from .n4_bias_corrector import N4BiasCorrector
+from .sitk.sitk_n4_bias_corrector import SitkN4BiasCorrector

brainles_preprocessing-0.5.0/brainles_preprocessing/n4_bias_correction/n4_bias_corrector.py

@@ -0,0 +1,13 @@
+from abc import ABC, abstractmethod
+from typing import Any
+
+
+class N4BiasCorrector(ABC):
+
+    @abstractmethod
+    def correct(
+        self,
+        input_img_path: Any,
+        output_img_path: Any,
+    ) -> None:
+        pass

brainles_preprocessing-0.5.0/brainles_preprocessing/n4_bias_correction/sitk/sitk_n4_bias_corrector.py

@@ -0,0 +1,82 @@
+from pathlib import Path
+from typing import Callable, Optional, Union
+
+import SimpleITK as sitk
+from auxiliary.io import write_image
+
+from brainles_preprocessing.n4_bias_correction.n4_bias_corrector import N4BiasCorrector
+
+
+class SitkN4BiasCorrector(N4BiasCorrector):
+
+    def __init__(
+        self,
+        mask_func: Optional[Callable[[sitk.Image], sitk.Image]] = None,
+        n_max_iterations: Optional[int] = None,
+        n_fitting_levels: int = 3,
+    ) -> None:
+        """
+        N4 Bias Corrector using SimpleITK.
+
+        Args:
+            mask_func (Optional[Callable[[sitk.Image], sitk.Image]], optional):
+                Function that generates a mask from an image.
+                Defaults to: `lambda img_itk: sitk.OtsuThreshold(img_itk, 0, 1, 200)`.
+            n_max_iterations (Optional[int], optional):
+                Maximum number of iterations for bias field correction.
+            n_fitting_levels (int, optional):
+                Number of fitting levels. Default is 3.
+        """
+
+        if mask_func is None:
+            mask_func = lambda img_itk: sitk.OtsuThreshold(img_itk, 0, 1, 200)
+        self.mask_func = mask_func
+        self.n_max_iterations = n_max_iterations
+        self.n_fitting_levels = n_fitting_levels
+
+    def compute_mask(self, img_itk: sitk.Image) -> sitk.Image:
+        """
+        Compute the mask for the input image using the provided mask function.
+
+        Args:
+            img_itk (SimpleITK.Image): The input image in SimpleITK format.
+
+        Returns:
+            SimpleITK.Image: The computed mask.
+        """
+
+        return self.mask_func(img_itk)
+
+    def correct(
+        self,
+        input_img_path: Union[str, Path],
+        output_img_path: Union[str, Path],
+    ) -> None:
+        """
+        Correct the bias field of the input image using SimpleITK.
+
+        Args:
+            input_img_path (Union[str, Path]): Path to the input image.
+            output_img_path (Union[str, Path]): Path where the corrected image will be saved.
+
+        Returns:
+            None
+        """
+        img_itk = sitk.ReadImage(str(input_img_path))
+
+        mask_itk = self.compute_mask(img_itk)
+
+        corrector = sitk.N4BiasFieldCorrectionImageFilter()
+        if self.n_max_iterations is not None:
+            corrector.SetMaximumNumberOfIterations(
+                [self.n_max_iterations] * self.n_fitting_levels
+            )
+
+        corrected_img = corrector.Execute(img_itk, mask_itk)
+        corrected_img = sitk.GetArrayFromImage(corrected_img)
+
+        write_image(
+            input_array=corrected_img,
+            output_path=str(output_img_path),
+            reference_path=str(input_img_path),
+        )

{brainles_preprocessing-0.4.0 → brainles_preprocessing-0.5.0}/brainles_preprocessing/preprocessor.py

@@ -1,28 +1,29 @@
-import logging
 import os
 import shutil
-import signal
 import subprocess
-import sys
 import tempfile
-import traceback
-from datetime import datetime
+import warnings
+from collections import Counter
 from functools import wraps
 from pathlib import Path
 from typing import List, Optional, Union
-import warnings
 
+from brainles_preprocessing.brain_extraction.brain_extractor import (
+    BrainExtractor,
+    HDBetExtractor,
+)
 from brainles_preprocessing.constants import Atlas, PreprocessorSteps
 from brainles_preprocessing.defacing import Defacer, QuickshearDefacer
+from brainles_preprocessing.modality import CenterModality, Modality
+from brainles_preprocessing.n4_bias_correction import (
+    N4BiasCorrector,
+    SitkN4BiasCorrector,
+)
+from brainles_preprocessing.registration import ANTsRegistrator
+from brainles_preprocessing.registration.registrator import Registrator
+from brainles_preprocessing.utils.logging_utils import LoggingManager
 from brainles_preprocessing.utils.zenodo import verify_or_download_atlases
 
-from .brain_extraction.brain_extractor import BrainExtractor, HDBetExtractor
-from .modality import Modality, CenterModality
-from .registration import ANTsRegistrator
-from .registration.registrator import Registrator
-
-from .utils.logging_utils import LoggingManager
-
 logging_man = LoggingManager(name=__name__)
 logger = logging_man.get_logger()
 
@@ -38,6 +39,7 @@ class Preprocessor:
         brain_extractor (Optional[BrainExtractor]): The brain extractor object for brain extraction.
         defacer (Optional[Defacer]): The defacer object for defacing images.
         atlas_image_path (Optional[str or Path]): Path to the atlas image for registration (default is the T1 atlas).
+        n4_bias_corrector (Optional[N4BiasCorrector]): The N4 bias corrector object for bias field correction. Defaults to SitkN4BiasCorrector with Otsu Thresholding.
         temp_folder (Optional[str or Path]): Path to a folder for storing intermediate results.
         use_gpu (Optional[bool]): Use GPU for processing if True, CPU if False, or automatically detect if None.
         limit_cuda_visible_devices (Optional[str]): Limit CUDA visible devices to a specific GPU ID.
@@ -52,6 +54,7 @@ class Preprocessor:
         brain_extractor: Optional[BrainExtractor] = None,
         defacer: Optional[Defacer] = None,
         atlas_image_path: Union[str, Path, Atlas] = Atlas.BRATS_SRI24,
+        n4_bias_corrector: Optional[N4BiasCorrector] = None,
         temp_folder: Optional[Union[str, Path]] = None,
         use_gpu: Optional[bool] = None,
         limit_cuda_visible_devices: Optional[str] = None,
@@ -68,12 +71,18 @@ class Preprocessor:
         self.center_modality = center_modality
         self.moving_modalities = moving_modalities
 
+        self._check_for_name_conflicts()
+
         if isinstance(atlas_image_path, Atlas):
             atlas_folder = verify_or_download_atlases()
             self.atlas_image_path = atlas_folder / atlas_image_path.value
         else:
             self.atlas_image_path = Path(atlas_image_path)
 
+        if n4_bias_corrector is None:
+            n4_bias_corrector = SitkN4BiasCorrector()
+        self.n4_bias_corrector = n4_bias_corrector
+
         self.registrator = registrator
         if self.registrator is None:
             logger.warning(
@@ -97,6 +106,19 @@ class Preprocessor:
             storage = tempfile.TemporaryDirectory()
             self.temp_folder = Path(storage.name)
 
+    def _check_for_name_conflicts(self):
+        """
+        Checks for name conflicts in the provided modalities.
+
+        Raises:
+            ValueError: If any modality name is non-unique.
+        """
+
+        name_counts = Counter(mod.modality_name for mod in self.all_modalities)
+        duplicates = [name for name, count in name_counts.items() if count > 1]
+        if duplicates:
+            raise ValueError(f"Duplicate modality names found: {', '.join(duplicates)}")
+
     def _configure_gpu(
         self, use_gpu: Optional[bool], limit_cuda_visible_devices: Optional[str] = None
     ) -> None:
@@ -162,6 +184,7 @@ class Preprocessor:
         save_dir_coregistration: Optional[Union[str, Path]] = None,
         save_dir_atlas_registration: Optional[Union[str, Path]] = None,
         save_dir_atlas_correction: Optional[Union[str, Path]] = None,
+        save_dir_n4_bias_correction: Optional[Union[str, Path]] = None,
         save_dir_brain_extraction: Optional[Union[str, Path]] = None,
         save_dir_defacing: Optional[Union[str, Path]] = None,
         save_dir_transformations: Optional[Union[str, Path]] = None,
@@ -175,6 +198,7 @@ class Preprocessor:
             save_dir_coregistration (str or Path, optional): Directory path to save intermediate coregistration results.
             save_dir_atlas_registration (str or Path, optional): Directory path to save intermediate atlas registration results.
             save_dir_atlas_correction (str or Path, optional): Directory path to save intermediate atlas correction results.
+            save_dir_n4_bias_correction (str or Path, optional): Directory path to save intermediate N4 bias correction results.
             save_dir_brain_extraction (str or Path, optional): Directory path to save intermediate brain extraction results.
             save_dir_defacing (str or Path, optional): Directory path to save intermediate defacing results.
             save_dir_transformations (str or Path, optional): Directory path to save transformation matrices. Defaults to None.
@@ -184,9 +208,10 @@ class Preprocessor:
 
         1. Co-registration: Aligning moving modalities to the central modality.
         2. Atlas Registration: Aligning the central modality to a predefined atlas.
-        3. Atlas Correction: Applying additional correction in atlas space if specified.
-        4. Brain Extraction: Optionally extracting brain regions using specified masks. Only executed if any modality requires a brain extraction output (or a defacing output that requires prior brain extraction).
-        5. Defacing: Optionally deface images to remove facial features. Only executed if any modality requires a defacing output.
+        3. (Optional) Atlas Correction: Applying additional correction in atlas space if specified.
+        4. (Optional) N4 Bias Correction: Applying N4 bias field correction if specified.
+        5. Brain Extraction: Optionally extracting brain regions using specified masks. Only executed if any modality requires a brain extraction output (or a defacing output that requires prior brain extraction).
+        6. Defacing: Optionally deface images to remove facial features. Only executed if any modality requires a defacing output.
 
         Results are saved in the specified directories, allowing for modular and configurable output storage.
         """
@@ -226,6 +251,12 @@ class Preprocessor:
             save_dir_atlas_correction=save_dir_atlas_correction,
         )
 
+        # Optional: N4 bias correction
+        logger.info(f"{' Checking optional N4 bias correction ':-^80}")
+        self.run_n4_bias_correction(
+            save_dir_n4_bias_correction=save_dir_n4_bias_correction,
+        )
+
         # Now we save images that are not skullstripped (current image = atlas registered or atlas registered + corrected)
         logger.info("Saving non skull-stripped images...")
         for modality in self.all_modalities:
@@ -412,6 +443,48 @@ class Preprocessor:
             save_dir=save_dir_atlas_correction,
         )
 
+    def run_n4_bias_correction(
+        self,
+        save_dir_n4_bias_correction: Optional[Union[str, Path]] = None,
+    ) -> None:
+        """
+        Apply optional N4 bias correction to modalities.
+
+        Args:
+            save_dir_n4_bias_correction (Optional[Union[str, Path]], optional): Directory path to save intermediate N4 bias correction results. Defaults to None.
+        """
+
+        n4_bias_correction_dir = self.temp_folder / "n4-bias-correction"
+        n4_bias_correction_dir.mkdir(exist_ok=True, parents=True)
+
+        for modality in self.all_modalities:
+            if modality.n4_bias_correction:
+                logger.info(
+                    f"Applying optional N4 bias correction for modality {modality.modality_name}"
+                )
+
+                output_path = (
+                    n4_bias_correction_dir
+                    / f"N4_bias_corrected__{modality.modality_name}.nii.gz"
+                )
+
+                self.n4_bias_corrector.correct(
+                    input_img_path=str(modality.current),
+                    output_img_path=str(output_path),
+                )
+
+                modality.steps[PreprocessorSteps.N4_BIAS_CORRECTED] = output_path
+                modality.current = output_path
+            else:
+                logger.info(
+                    f"Skipping optional N4 bias correction for Modality {modality.modality_name}."
+                )
+
+        self._save_output(
+            src=n4_bias_correction_dir,
+            save_dir=save_dir_n4_bias_correction,
+        )
+
     def run_brain_extraction(
         self, save_dir_brain_extraction: Optional[Union[str, Path]] = None
     ) -> None:

{brainles_preprocessing-0.4.0 → brainles_preprocessing-0.5.0}/brainles_preprocessing/registration/ANTs/ANTs.py

@@ -142,7 +142,7 @@ class ANTsRegistrator(Registrator):
         transformed_image_path: Union[str, Path],
         matrix_path: str | Path | List[str | Path],
         log_file_path: Union[str, Path],
-        interpolator: str = "linear",
+        interpolator: str = "nearestNeighbor",
         **kwargs,
     ) -> None:
         """
@@ -154,7 +154,7 @@ class ANTsRegistrator(Registrator):
             transformed_image_path (str or Path): Path to the transformed image (output).
             matrix_path (str or Path or List[str | Path]): Path to the transformation matrix or a list of matrices.
             log_file_path (str or Path): Path to the log file.
-            interpolator (str): Interpolator to use for the transformation. Default is 'linear'.
+            interpolator (str): Interpolator to use for the transformation. Default is 'nearestNeighbor'.
             **kwargs: Additional transformation parameters to update the instantiated defaults.
         Raises:
             AssertionError: If the interpolator is not valid.
@@ -231,7 +231,7 @@ class ANTsRegistrator(Registrator):
         transformed_image_path: Union[str, Path],
         matrix_path: str | Path | List[str | Path],
         log_file_path: Union[str, Path],
-        interpolator: str = "linear",
+        interpolator: str = "nearestNeighbor",
         **kwargs,
     ) -> None:
         """
@@ -243,7 +243,7 @@ class ANTsRegistrator(Registrator):
             transformed_image_path (str or Path): Path to the transformed image (output).
             matrix_path (str or Path): Path to the transformation matrix.
             log_file_path (str or Path): Path to the log file.
-            interpolator (str): Interpolator to use for the transformation. Default is 'linear'.
+            interpolator (str): Interpolator to use for the transformation. Default is 'nearestNeighbor'.
             **kwargs: Additional transformation parameters to update the instantiated defaults.
         """
         if not isinstance(matrix_path, list):

{brainles_preprocessing-0.4.0 → brainles_preprocessing-0.5.0}/brainles_preprocessing/registration/niftyreg/niftyreg.py

@@ -150,7 +150,7 @@ class NiftyRegRegistrator(Registrator):
         transformed_image_path: str,
         matrix_path: str | Path | List[str | Path],
         log_file_path: str,
-        interpolator: str = "1",
+        interpolator: str = "0",
         **kwargs: dict,
     ) -> None:
         """
@@ -226,7 +226,7 @@ class NiftyRegRegistrator(Registrator):
         transformed_image_path: str,
         matrix_path: List[str | Path],
         log_file_path: str,
-        interpolator: str = "1",
+        interpolator: str = "0",
     ) -> None:
         """
         Apply inverse transformation using NiftyReg.