Changed workflow for setting the masking value in the skull stripping

[nicmuenster]

This change implements the the same process as in the defacing step to either use a global custom value for all inputs or the minimum value within the input image as the background value when masking an inage

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[nicmuenster]

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[Copilot]

Pull request overview

Aligns skull-stripping mask application with the defacing workflow by supporting either a global masking/background value or a per-image minimum when filling voxels outside the brain mask.

Changes:

• Added masking_value support to BrainExtractor and updated apply_mask() to fill outside-mask voxels using either the provided global value or the per-image minimum.
• Updated HDBetExtractor and SynthStripExtractor constructors to accept/forward masking_value.
• Minor whitespace cleanup in the registration package init.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.

File	Description
brainles_preprocessing/registration/__init__.py	Removes stray blank lines/whitespace.
brainles_preprocessing/brain_extraction/brain_extractor.py	Introduces masking_value state and updates mask application to use background fill logic consistent with defacing.
brainles_preprocessing/brain_extraction/synthstrip.py	Adds masking_value parameter to the extractor constructor (currently not applied during extract() output writing).

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[Copilot]

masking_value is added to the constructor and forwarded to BrainExtractor, but SynthStripExtractor.extract() never uses self.masking_value when writing the masked output (it still hard-codes bg = np.min([0, img_data.min()])). This makes the new parameter ineffective and the docstring misleading. Update extract() to fill background using the same masking_value/per-image-min logic as BrainExtractor.apply_mask (or drop the parameter if not supported).

[Copilot]

apply_mask() now supports a global masking_value and falls back to per-image minimum when unset, but the existing unit test only asserts that an output file is created. Please extend tests to assert that voxels outside the mask are set to the expected value for both cases (default min-per-image and a custom masking_value).

[neuronflow]

Do we need changes here?

preprocessing/brainles_preprocessing/brain_extraction/synthstrip.py

Line 220 in 22661a6

# write the masked output

[nicmuenster]

From my understanding, updating the synthstrip init is still necessary, given that while the center modality might be handled without the apply_mask function in the preprocessor workflow (as seen here)

atlas_mask = self.center_modality.extract_brain_region( brain_extractor=self.brain_extractor, bet_dir_path=bet_dir, use_gpu=self.use_gpu, )

the moving modalities are then afterwards still handled by the apply_mask function:

for moving_modality in self.moving_modalities: moving_modality.apply_bet_mask( brain_extractor=self.brain_extractor, mask_path=atlas_mask, bet_dir=bet_dir, )
One thing to consider however, is that in the synthstrip workflow the minimum between 0 and the input min is taken, so min values above 0 would be handled slightly different now, but this missmatch actually also exists for the current state as well.