omni.pipelines.epi.processing#
Functions
|
EPI pipeline. |
- omni.pipelines.epi.processing.epi_proc(output_path: str, epi: str, epi_moco: str, ref_epi: str, ref_epi_bet: str, ref_epi_bet_mask: str, anat_bet_mask: str, anat_weight_mask: str, atlas_align_affine: str, t1: str = None, t2: str = None, t1_bet: str = None, t2_bet: str = None, initial_synth_model: str = 'rbf(0;4)+rbf(1;4)+rbf(0;4)*rbf(1;4)', final_synth_model: str = 'rbf(0;12)+rbf(1;12)+rbf(0;12)*rbf(1;12)', program: str = 'fsl', bandwidth: int = 16, initial_affine: str = None, skip_affine: bool = False, skip_synthtarget_affine: bool = False, resolution_pyramid: List[float] = [4, 2, 1], synthtarget_max_iterations: List[int] = [2000, 500, 100], synthtarget_err_tol: List[float] = [0.0001, 0.0001, 0.0005], synthtarget_step_size: List[float] = [0.001, 0.001, 0.001], resample_resolution: float = 1, sigma_t2: float = 0.5, use_initializing_warp: bool = False, skip_synth_warp: bool = False, contrast_enhance_method: str = 'lce', initial_warp_field: str = None, distortion_correction_step_size: List[float] = [3, 1, 0.1], distortion_correction_smoothing: str = '2x1x0x0', distortion_correction_shrink_factors: str = '4x3x2x1', field_variance: int = 0, warp_direction: str = 'none', noise_mask_dilation_size: int = 2, noise_mask_iterations: int = 20, noise_mask_sigma: float = 2, data_resolution: float = None, atlas: str = 'mni', atlas_label: str = 'atlas', use_allineate: bool = False, rigid_body_params: str = None, **kwargs)[source]#
EPI pipeline.
- Parameters:
- output_pathstr
Output path to write out files to.
- epistr
EPI image to apply final transforms to.
- epi_mocostr
EPI image that has been motion corrected/framewise aligned.
- ref_epistr
Reference EPI image.
- ref_epi_betstr
Skullstripped reference EPI image.
- ref_epi_bet_maskstr
Reference EPI brain mask.
- anat_bet_maskstr
Anatomical brain mask.
- anat_weight_maskstr
Anatomical weight mask.
- atlas_align_affinestr
Affine alignment file for anat to atlas (afni)
- t1: str
T1.
- t2str
T2.
- t1_betstr
T1 skullstripped.
- t2_betstr
T2 skullstripped.
- inital_synth_modelstr
Initial model used to generate synthetic image.
- final_synth_modelstr
Final model used to generate synthetic image.
- programstr
Program to use for affine alignment.
- bandwidthint
Bandwidth for Epanechnikov kernel.
- initial_affinestr
Initial affine alignment file.
- skip_affinebool
Skip affine alignment step.
- skip_synthtarget_affinebool
Skip synthtarget affine alignment step.
- resolution_pyramidList[float]
Resampling pyramid to use for affine alignment (mm).
- synthtarget_max_iterationsList[int]
Max iterations for each SynthTarget call.
- synthtarget_err_tol: List[float]
Error tolerance level for each SynthTarget call.
- synthtarget_step_size: List[float]
Step size for gradient descent.
- resample_resolutionfloat
Resample resolution space to do warps on (mm).
- sigma_t2float
Parameter to smooth T2 for initial warp.
- use_initializing_warpbool
Uses initializing warp step from the T2 initial warp.
- skip_synth_warpbool
Skip synth warp refinement step.
- contrast_enhance_methodstr
Method to use for contrast enhancement.
- initial_warp_field: str
Uses this file as an initial warp field instead of computing it, this should be from ref_epi -> T2.
- distortion_correction_step_sizeList[float]
Set the gradient descent step size for each iteration of warp.
- distortion_correction_smoothing: str
Smoothing kernel size for each level of optimization.
- distortion_correction_shrink_factors: str
Resampling factor for each level of optimization.
- field_varianceint
Regularization parameter of SyN algorithm to use for the distortion correction.
- warp_direction: str
Warp direction
- noise_mask_dilation_sizeint
Dilation size for noise mask.
- noise_mask_iterationsint
Number of iterations to run noise mask LDA.
- noise_mask_sigmafloat
Size of gaussian smoothing kernel for noise mask.
- atlasstr
Set atlas to align to.
- atlas_labelstr
Label suffix for atlas outputs.
- data_resolutionfloat
Resolution to resample the data for output (mm).
- use_allineate: bool
Specifies that 3DAllineate was used for framewise alignment.
- rigid_body_params: str
Rigid body transform to use if 3DAllineate enabled.
- Returns:
- Dict
Dictionary of results.