omni.pipelines.epi.align#
Functions
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Affine align func to anat |
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Combine transforms to produce preprocessed files. |
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Distortion correction. |
- omni.pipelines.epi.align.align_affine_epi_to_anat(output_path: str, ref_epi_bet: str, initial_synth_model: str = 'rbf(0;4)+rbf(1;4)+rbf(0;4)*rbf(1;4)', t1_bet: str = None, t2_bet: str = None, 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], max_iterations: List[int] = [2000, 500, 100], err_tol: List[float] = [0.0001, 0.0001, 0.0005], step_size: List[float] = [0.001, 0.001, 0.001])[source]#
Affine align func to anat
- Parameters:
- output_path: str
Output path to write out files to.
- ref_epi_bet: str
Reference EPI skullstripped.
- initial_synth_model: str
Synth model.
- t1_bet: str
T1 skullstripped.
- t2_bet: str
T2 skullstripped.
- bandwidth: int
Bandwidth for blurring kernel.
- program: str
Program to use for affine alignment.
- initial_affine: str
Initial affine to use instead of using internal flirt alignment.
- skip_affine: bool
Skip affine alignment step.
- skip_synthtarget_affine: bool
Skip synthtarget affine alignment step.
- resolution_pyramid: List[float]
Resampling pyramid to use for affine alignment (mm).
- max_iterations: List[int]
Max iterations for each SynthTarget call.
- err_tol: List[float]
Error tolerance level for each SynthTarget call.
- step_size: List[float]
Step size for gradient descent.
- Returns:
- str
Final func to anat affine (afni).
- str
Final anat to func affine (afni).
- omni.pipelines.epi.align.combine_transforms(output_path: str, raw_epi: str, final_epi_to_synth_warp: str, final_epi_to_anat_affine: str, atlas_align_affine: str, atlas: str = 'mni', atlas_label: str = 'atlas', data_resolution: float = None, use_allineate: bool = False, rigid_body_params: str = None)[source]#
Combine transforms to produce preprocessed files.
- Parameters:
- output_path: str
Output path to write out files to.
- raw_epi: str
EPI to align to atlas.
- final_epi_to_synth_warp: str
Undistorting warp for EPI.
- final epi_to_anat_affine: str
Affine transform from EPI to anat.
- atlas_align_affine: str
Affine transform from anat to atlas.
- atlas: str
Atlas being aligned to (must match to affine provided).
- atlas_labelstr
Label suffix for atlas outputs.
- use_allineate: bool
Specifies that 3dAllineate was used for framewise alignment.
- rigid_Body_params: str
Rigid body transform to use if allineate enabled.
- Returns:
- str
Atlas aligned EPI.
- omni.pipelines.epi.align.distortion_correction(output_path: str, epi_moco: str, ref_epi: str, t1: str, t2: str, anat_bet_mask: str, anat_weight_mask: str, final_anat_to_epi_affine: str, final_epi_to_anat_affine: str, final_synth_model: str = 'rbf(0;12)+rbf(1;12)+rbf(0;12)*rbf(1;12)', bandwidth: int = 16, 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, SyN_step_size: List[float] = [3, 1, 0.1], SyN_smoothing: str = '2x1x0x0', SyN_shrink_factors: str = '4x3x2x1', SyN_field_variance: int = 0, noise_mask_dilation_size: int = 2, noise_mask_iterations: int = 20, noise_mask_sigma: float = 2, warp_direction: str = 'none', autobox_mask: str = None)[source]#
Distortion correction.
- Parameters:
- output_path: str
Output path to write out files to.
- epi_mocostr
EPI image that has been motion corrected/framewise aligned.
- ref_epi: str
Reference EPI image.
- t1: str
T1.
- t2: str
T2.
- anat_bet_mask: str
Anatomical brain mask.
- anat_weight_mask: str
Anatomical weight mask.
- final_anat_to_epi_affine: str
Final anat to epi affine (afni).
- final_epi_to_anat_affine: str
Final epi to anat affine (afni).
- final_synth_model: str
Synth model.
- bandwidth: int
Bandwidth for blurring kernel.
- resample_resolution: float
Resample resolution space to do warps on (mm).
- sigma_t2: float
Parameter to smooth T2 for initial warp.
- use_initializing_warp: bool
Uses initializing warp from the T2 initial warp.
- skip_synth_warp: bool
Skip the synth warp step, will only use initial T2 warp solution.
- contrast_enhance_method: str
Contrast enhancement method to use, by default “lce”.
- initial_warp_field: str
Uses this file as an initial warp field instead of computing it, this should be from ref_epi -> T2.
- SyN_step_sizeList[float]
Set the gradient descent step size for each iteration of warp.
- SyN_smoothing: str
Smoothing kernel size for each level of optimization.
- SyN_shrink_factors: str
Resampling factor for each level of optimization.
- SyN_field_variance: int
Field variance for SyN.
- noise_mask_dilation_sizeint
Dilation size for noise mask.
- noise_mask_iterations: int
Number of iterations to run noise mask LDA.
- noise_mask_sigma: float
Size of gaussian smoothing kernel for noise mask.
- warp_direction: str
Warp direction
- autobox_mask: int
mask defining the autobox
- Returns:
- str
Final synthetic to EPI warp (Distort synthetic to match EPI)
- str
Final EPI to synthetic warp (Undistort EPI to match synthetic)