132 feature consider synthstrip brain extraction

[MarcelRosier]

• Add SynthStrip BET
• Generalize zenodo download logic
• Fix typing error

[neuronflow]

/format

[brainless-bot]

🤖 I will now format your code with black. Check the status here.

[neuronflow]

Hmm Copilot seems to be on strike today :)

[brainless-bot]

🤖 Code Formatting Reminder

Hello there! 👋 It looks like the code in this pull request might benefit from some formatting improvements.
Fix the issues locally or use our auto format action by commenting /format on this PR!

[neuronflow]

/format

[brainless-bot]

🤖 I will now format your code with black. Check the status here.

[Copilot]

Pull Request Overview

This PR adds SynthStrip brain extraction support as an optional dependency and refactors the Zenodo download system to be more generic. It also addresses typing issues and reorganizes the project's optional dependencies.

• Adds SynthStrip brain extraction functionality with proper model handling and conforming logic
• Generalizes Zenodo download logic from atlas-specific to a reusable ZenodoRecord class
• Updates brain extraction interface to use device parameter consistently and fixes typing annotations

Reviewed Changes

Copilot reviewed 12 out of 13 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
brainles_preprocessing/brain_extraction/synthstrip.py	New SynthStrip brain extractor implementation with model loading and image processing
brainles_preprocessing/utils/zenodo.py	Refactored Zenodo utilities into generic ZenodoRecord class with improved error handling
tests/test_zenodo.py	Updated tests to work with new ZenodoRecord class structure
pyproject.toml	Added synthstrip optional dependency and reorganized dependencies
brainles_preprocessing/brain_extraction/brain_extractor.py	Updated interface to remove unused parameters and improve typing
brainles_preprocessing/modality.py	Updated to use device parameter for brain extraction
brainles_preprocessing/preprocessor/preprocessor.py	Fixed typing for use_gpu parameter and added device configuration
brainles_preprocessing/preprocessor/atlas_centric_preprocessor.py	Updated to use new fetch_atlases function
brainles_preprocessing/registration/elastix/elastix.py	Added documentation about optional dependency
brainles_preprocessing/registration/greedy/greedy.py	Added documentation about optional dependency
docs/source/brain-extraction.rst	Added documentation for new synthstrip module
README.md	Updated documentation to reflect new optional dependencies

Comments suppressed due to low confidence (2)

pyproject.toml:53

• The pathlib package version 1.0.1 does not exist. The pathlib module is part of Python's standard library since Python 3.4 and should not be listed as a dependency.

nibabel = ">=3.2.1"

brainles_preprocessing/utils/zenodo.py:71

• [nitpick] Variable name 'zenodo_response' is ambiguous. Consider renaming to 'metadata_and_url' or 'zenodo_metadata' to better reflect what it contains.

        zenodo_response = self._get_metadata_and_archive_url()

[Copilot]

The condition 'device == "cpu"' will always be False because device is a torch.device object, not a string. Use 'device.type == "cpu"' instead.

Suggested change

	if device == "cpu" and num_threads > 0:
	if device.type == "cpu" and num_threads > 0:

[Copilot]

Using assert for input validation in production code is not recommended. Consider raising a ValueError instead, as assertions can be disabled with -O flag.

Suggested change

	assert affine is not None, "Input NIfTI image must have a valid affine."
	if affine is None:
	raise ValueError("Input NIfTI image must have a valid affine.")

[neuronflow]

@MarcelRosier that sounds like a valid comment?

not sure about the rest.

[neuronflow]

cool stuff, please have a look at Copilot comments before merging.