From c5859c447d6ec77366ddfcbf8af3b9adce20abca Mon Sep 17 00:00:00 2001 From: nicmuenster Date: Wed, 28 Jan 2026 13:55:46 +0100 Subject: [PATCH 1/3] Vhanged workflow for setting the masking value in the skull stripping process to either a global custom value for all inputs or the minimum value within the input image --- .../brain_extraction/brain_extractor.py | 41 +++++++++++++++++-- .../brain_extraction/synthstrip.py | 9 ++-- 2 files changed, 44 insertions(+), 6 deletions(-) diff --git a/brainles_preprocessing/brain_extraction/brain_extractor.py b/brainles_preprocessing/brain_extraction/brain_extractor.py index 03a716b..1c63709 100644 --- a/brainles_preprocessing/brain_extraction/brain_extractor.py +++ b/brainles_preprocessing/brain_extraction/brain_extractor.py @@ -4,6 +4,7 @@ from pathlib import Path from typing import Optional, Union from enum import Enum +import numpy as np from auxiliary.io import read_image, write_image from brainles_hd_bet import run_hd_bet @@ -14,7 +15,23 @@ class Mode(Enum): ACCURATE = "accurate" -class BrainExtractor: +class BrainExtractor(ABC): + def __init__( + self, + masking_value: Optional[Union[int, float]] = None, + ): + """ + Base class for skull stripping medical images using brain masks. + + Subclasses should implement the `extract` method to generate a skull stripped image + based on the provided input image and mask. + """ + # Just as in the defacer, masking value is a global value defined across all images and modalities + # If no value is passed, the minimum of a given input image is chosen + # TODO: Consider extending this to modality-specific masking values in the future, this should + # probably be implemented as a property of the the specific modality + self.masking_value = masking_value + @abstractmethod def extract( self, @@ -63,8 +80,17 @@ def apply_mask( if input_data.shape != mask_data.shape: raise ValueError("Input image and mask must have the same dimensions.") - # Mask and save it - masked_data = input_data * mask_data + # check whether a global masking value was passed, otherwise choose minimum + if self.masking_value is None: + current_masking_value = np.min(input_data) + else: + current_masking_value = ( + np.array(self.masking_value).astype(input_data.dtype).item() + ) + # Apply mask (element-wise either input or masking value) + masked_data = np.where( + mask_data.astype(bool), input_data, current_masking_value + ) try: write_image( @@ -78,6 +104,15 @@ def apply_mask( class HDBetExtractor(BrainExtractor): + def __init__(self, masking_value: Optional[Union[int, float]] = None): + """ + Brain extraction HDBet implementation. + + Args: + masking_value (Optional[Union[int, float]], optional): global value to be inserted in the masked areas. Default is None which leads to the minimum of each respective image. + """ + super().__init__(masking_value=masking_value) + def extract( self, input_image_path: Union[str, Path], diff --git a/brainles_preprocessing/brain_extraction/synthstrip.py b/brainles_preprocessing/brain_extraction/synthstrip.py index 0ea3135..eed97d6 100644 --- a/brainles_preprocessing/brain_extraction/synthstrip.py +++ b/brainles_preprocessing/brain_extraction/synthstrip.py @@ -21,7 +21,9 @@ class SynthStripExtractor(BrainExtractor): - def __init__(self, border: int = 1): + def __init__( + self, border: int = 1, masking_value: Optional[Union[int, float]] = None + ): """ Brain extraction using SynthStrip with preprocessing conforming to model requirements. @@ -31,9 +33,10 @@ def __init__(self, border: int = 1): Args: border (int): Mask border threshold in mm. Defaults to 1. - """ + masking_value (Optional[Union[int, float]], optional): global value to be inserted in the masked areas. Default is None which leads to the minimum of each respective image. - super().__init__() + """ + super().__init__(masking_value=masking_value) self.border = border def _setup_model(self, device: torch.device) -> StripModel: From 2395565cef4b4fd3a40ca618cdfa86dcc70bd15b Mon Sep 17 00:00:00 2001 From: "brainless-bot[bot]" <153751247+brainless-bot[bot]@users.noreply.github.com> Date: Wed, 28 Jan 2026 13:17:08 +0000 Subject: [PATCH 2/3] Autoformat with black --- brainles_preprocessing/registration/__init__.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/brainles_preprocessing/registration/__init__.py b/brainles_preprocessing/registration/__init__.py index e38d97d..9eea05d 100644 --- a/brainles_preprocessing/registration/__init__.py +++ b/brainles_preprocessing/registration/__init__.py @@ -1,6 +1,5 @@ import warnings - try: from .ANTs.ANTs import ANTsRegistrator except ImportError: @@ -11,7 +10,6 @@ from .niftyreg.niftyreg import NiftyRegRegistrator - try: from .elastix.elastix import ElastixRegistrator except ImportError: From 776cf77d0d102f936932495790a1cc2affeb538b Mon Sep 17 00:00:00 2001 From: neuronflow <7048826+neuronflow@users.noreply.github.com> Date: Wed, 28 Jan 2026 14:31:26 +0100 Subject: [PATCH 3/3] Update brainles_preprocessing/brain_extraction/brain_extractor.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- brainles_preprocessing/brain_extraction/brain_extractor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/brainles_preprocessing/brain_extraction/brain_extractor.py b/brainles_preprocessing/brain_extraction/brain_extractor.py index 1c63709..fb662d6 100644 --- a/brainles_preprocessing/brain_extraction/brain_extractor.py +++ b/brainles_preprocessing/brain_extraction/brain_extractor.py @@ -29,7 +29,7 @@ def __init__( # Just as in the defacer, masking value is a global value defined across all images and modalities # If no value is passed, the minimum of a given input image is chosen # TODO: Consider extending this to modality-specific masking values in the future, this should - # probably be implemented as a property of the the specific modality + # probably be implemented as a property of the specific modality self.masking_value = masking_value @abstractmethod