omni.pipelines.anat.segmentation#
Functions
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Brain extraction |
- omni.pipelines.anat.segmentation.brain_extraction(output_path: str, t1_debias: str = None, t2_debias: str = None, fractional_intensity_threshold: float = 0.5, method: str = 'Norm', use_eye_mask: bool = True)[source]#
Brain extraction
- Parameters:
- output_pathstr
Output path to write out files to.
- t1_debiasstr
T1 image.
- t2_debiasstr
T2 image.
- fractional_intensity_thresholdfloat
Fractional intensity threshold for bet.
- methodstr
Method for brain extraction (T1/Norm).
- use_eye_maskbool
Use eye mask for anatomical mask.
- Returns:
- str
Eye mask.
- str
Anatomical mask.
- str
Brain extracted T1 debiased.
- str
Brain extracted T2 debiased.