omni.pipelines.anat.processing#

Functions

`anat_proc`(output_path, t1, t2[, ref, ...])	Anatomical processing pipeline.
`anat_to_epi_results`(results)	Converts results of anatomical pipeline for input into EPI pipeline.

omni.pipelines.anat.processing.anat_proc(output_path: str, t1: str, t2: str, ref: str = 'T1', program: str = 'fsl', atlas: str = 'mni', atlas_label: str = 'atlas', use_eye_mask: bool = True, dilation_size: int = 30, debias_params_anat: str = '[100,3,1x1x1,3]', fractional_intensity_threshold_anat: float = 0.5, bet_method: str = 'Norm', **kwargs) → Dict[source]#

Anatomical processing pipeline.

Parameters:

output_pathstr: Output path to write out files to.
t1str: T1 image.
t2str: T2 image.
refstr: Set the image to use as a reference [T1/T2].
programstr: Program to use for alignment (‘afni’: AFNI 3dAllineate or ‘fsl’: fsl flirt).
atlasstr: Atlas to align to.
atlas_labelstr: Label suffix for atlas outputs.
use_eye_maskstr: Enhance anatomical weight mask with eye mask.
dilation_sizeint: Size of dilation kernel for weight mask.
debias_params_anatstr: Custom spline fitting string.
fractional_intensity_threshold_anatfloat: Set fractional intensity threshold for bet.
bet_methodstr: Method of brain extraction.

Returns:

Dict: Dictionary of results.

omni.pipelines.anat.processing.anat_to_epi_results(results: Dict) → Dict[source]#

Converts results of anatomical pipeline for input into EPI pipeline.

Parameters:

resultsDict: Results dictionary from anatomical pipeline.

Returns:

Dict: Converted dictionary for EPI pipeline input.