omni.interfaces.fsl#
Functions
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Brain extraction tool. |
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Affine alignment with fsl flirt. |
- omni.interfaces.fsl.bet(out_file: str, in_file: str, fractional_intensity_threshold: float = 0.5, mask: bool = False, eye: bool = False, neck: bool = False, other_args: Optional[str] = None)[source]#
Brain extraction tool.
- Parameters:
- out_file: str
Brain extracted output image.
- in_file: str
Image to brain extract
- fractional_intensity_threshold: float
Fractional intensity threshold for bet.
- mask: bool
Controls whether a binary mask should be output
- eye: bool
Generate eye mask (mutually exclusive with neck option)
- neck: bool
Neck cleanup (mutually exclusive with eye option)
- other_args: str
Other arguments to pass in.
- omni.interfaces.fsl.flirt(out_file: str, reference: str, source: str, out_matrix: Optional[str] = None, dof: int = 12, cost: str = 'corratio', interp: str = 'sinc', other_args: Optional[str] = None)[source]#
Affine alignment with fsl flirt.
- Parameters:
- out_file: str
Aligned output image.
- reference: str
Reference image to align.
- source: str
Source image to align.
- out_matrix: str
Affine matrix file.
- dof: str
Degrees of freedom to use for alignment.
- cost: str
Cost function to use for optimization.
- interp: str
Interpolation to use for output image.
- other_args: str
Other arguments to pass in.