omni.pipelines.func.processing#
Functions
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Functional processing pipeline |
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Converts results of functional pipeline for input into EPI pipeline. |
- omni.pipelines.func.processing.func_proc(output_path: str, func: str, TR: float, moco: str = 'allineate', use_allineate: bool = True, slice_times: List = None, fractional_intensity_threshold_func: float = 0.5, debias_params_func: str = '[200,3,1x1x1,3]', loops: List[int] = [1, 1, 1], subsample: List[int] = [5, 3, 1], borders: List[int] = [1, 1, 1], initial_warp_field: str = None, **kwargs) Dict[source]#
Functional processing pipeline
- Parameters:
- output_path: str
Output path to write out files to.
- func: str
Functional image.
- TR: float
Repetition time of scan.
- moco: str
Motion correction method to use.
- use_allineatebool
Sets whether to use 3dAllineate for framewise alignment instead.
- slice_times: List
List of slice times.
- fractional_intensity_threshold: float
Fractional intensity threshold for bet.
- debias_params_func: str
Custom spline fitting string.
- loops: List[int]
Number of loops for SpaceTimeRealign.
- subsample: List[int]
Subsampling for SpaceTimeRealign.
- borders: List[int]
borders for SpaceTimeRealign
- initial_warp_field: str
An initial warp field for distortion correction, to be used to provide more accurate brain extraction.
- Returns:
- Dict
Dictionary of results.
- omni.pipelines.func.processing.func_to_epi_results(results: Dict, use_allineate: bool) Dict[source]#
Converts results of functional pipeline for input into EPI pipeline.
- Parameters:
- results: Dict
Results dictionary from functional pipeline.
- use_allineate: bool
Specify inputs when 3dAllineate used for framewise alignment.
- Returns:
- Dict
Converted dictionary for EPI pipeline input.