niworkflows.interfaces.reportlets.registration module¶

ReportCapableInterfaces for registration tools.

class niworkflows.interfaces.reportlets.registration.ANTSApplyTransformsRPT(generate_report=False, **kwargs)[source]¶

Bases: RegistrationRC, FixHeaderApplyTransforms

Wrapped executable: antsApplyTransforms.

Mandatory Inputs:

input_image (a pathlike object or string representing an existing file) – Image to apply transformation to (generally a coregistered functional). Maps to a command-line argument: --input %s.
reference_image (a pathlike object or string representing an existing file) – Reference image space that you wish to warp INTO. Maps to a command-line argument: --reference-image %s.
transforms (a list of items which are a pathlike object or string representing an existing file or ‘identity’) – Transform files: will be applied in reverse order. For example, the last specified transform will be applied first. Maps to a command-line argument: %s.

Optional Inputs:

args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
default_value (a float) – Maps to a command-line argument: --default-value %g. (Nipype default value: 0.0)
dimension (2 or 3 or 4) – This option forces the image to be treated as a specified-dimensional image. If not specified, antsWarp tries to infer the dimensionality from the input image. Maps to a command-line argument: --dimensionality %d.
environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})
float (a boolean) – Use float instead of double for computations. Maps to a command-line argument: --float %d. (Nipype default value: False)
input_image_type (0 or 1 or 2 or 3) – Option specifying the input image type of scalar (default), vector, tensor, or time series. Maps to a command-line argument: --input-image-type %d.
interpolation (‘Linear’ or ‘NearestNeighbor’ or ‘CosineWindowedSinc’ or ‘WelchWindowedSinc’ or ‘HammingWindowedSinc’ or ‘LanczosWindowedSinc’ or ‘MultiLabel’ or ‘Gaussian’ or ‘BSpline’ or ‘GenericLabel’) – Maps to a command-line argument: %s. (Nipype default value: Linear)
interpolation_parameters (a tuple of the form: (an integer) or a tuple of the form: (a float, a float) or a tuple of the form: (a string))
invert_transform_flags (a list of items which are a boolean)
num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)
out_postfix (a string) – Postfix that is appended to all output files (default = _trans). (Nipype default value: _trans)
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
output_image (a string) – Output file name. Maps to a command-line argument: --output %s.
print_out_composite_warp_file (a boolean) – Output a composite warp file instead of a transformed image. Requires inputs: output_image.

Outputs:

out_report (a pathlike object or string representing a file) – Filename for the visual report.
output_image (a pathlike object or string representing an existing file) – Warped image.

class niworkflows.interfaces.reportlets.registration.ANTSRegistrationRPT(generate_report=False, **kwargs)[source]¶

Bases: RegistrationRC, FixHeaderRegistration

Wrapped executable: antsRegistration.

Mandatory Inputs:

fixed_image (a list of items which are a pathlike object or string representing an existing file) – Image to which the moving_image should be transformed(usually a structural image).
metric (a list of items which are ‘CC’ or ‘MeanSquares’ or ‘Demons’ or ‘GC’ or ‘MI’ or ‘Mattes’ or a list of items which are ‘CC’ or ‘MeanSquares’ or ‘Demons’ or ‘GC’ or ‘MI’ or ‘Mattes’) – The metric(s) to use for each stage. Note that multiple metrics per stage are not supported in ANTS 1.9.1 and earlier.
metric_weight (a list of items which are a float or a list of items which are a float) – The metric weight(s) for each stage. The weights must sum to 1 per stage. Requires inputs: metric. (Nipype default value: [1.0])
moving_image (a list of items which are a pathlike object or string representing an existing file) – Image that will be registered to the space of fixed_image. This is theimage on which the transformations will be applied to.
shrink_factors (a list of items which are a list of items which are an integer)
smoothing_sigmas (a list of items which are a list of items which are a float)
transforms (a list of items which are ‘Rigid’ or ‘Affine’ or ‘CompositeAffine’ or ‘Similarity’ or ‘Translation’ or ‘BSpline’ or ‘GaussianDisplacementField’ or ‘TimeVaryingVelocityField’ or ‘TimeVaryingBSplineVelocityField’ or ‘SyN’ or ‘BSplineSyN’ or ‘Exponential’ or ‘BSplineExponential’) – Maps to a command-line argument: %s.

Optional Inputs:

args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
collapse_output_transforms (a boolean) – Collapse output transforms. Specifically, enabling this option combines all adjacent linear transforms and composes all adjacent displacement field transforms before writing the results to disk. Maps to a command-line argument: --collapse-output-transforms %d. (Nipype default value: True)
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
convergence_threshold (a list of at least 1 items which are a float) – Requires inputs: number_of_iterations. (Nipype default value: [1e-06])
convergence_window_size (a list of at least 1 items which are an integer) – Requires inputs: convergence_threshold. (Nipype default value: [10])
dimension (3 or 2) – Image dimension (2 or 3). Maps to a command-line argument: --dimensionality %d. (Nipype default value: 3)
environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})
fixed_image_mask (a pathlike object or string representing an existing file) – Mask used to limit metric sampling region of the fixed imagein all stages. Maps to a command-line argument: %s. Mutually exclusive with inputs: fixed_image_masks.
fixed_image_masks (a list of items which are a pathlike object or string representing an existing file or ‘NULL’) – Masks used to limit metric sampling region of the fixed image, defined per registration stage(Use “NULL” to omit a mask at a given stage). Mutually exclusive with inputs: fixed_image_mask.
float (a boolean) – Use float instead of double for computations. Maps to a command-line argument: --float %d.
initial_moving_transform (a list of items which are a pathlike object or string representing an existing file) – A transform or a list of transforms that should be applied before the registration begins. Note that, when a list is given, the transformations are applied in reverse order. Maps to a command-line argument: %s. Mutually exclusive with inputs: initial_moving_transform_com.
initial_moving_transform_com (0 or 1 or 2) – Align the moving_image and fixed_image before registration using the geometric center of the images (=0), the image intensities (=1), or the origin of the images (=2). Maps to a command-line argument: %s. Mutually exclusive with inputs: initial_moving_transform.
initialize_transforms_per_stage (a boolean) – Initialize linear transforms from the previous stage. By enabling this option, the current linear stage transform is directly initialized from the previous stages linear transform; this allows multiple linear stages to be run where each stage directly updates the estimated linear transform from the previous stage. (e.g. Translation -> Rigid -> Affine). . Maps to a command-line argument: --initialize-transforms-per-stage %d. (Nipype default value: False)
interpolation (‘Linear’ or ‘NearestNeighbor’ or ‘CosineWindowedSinc’ or ‘WelchWindowedSinc’ or ‘HammingWindowedSinc’ or ‘LanczosWindowedSinc’ or ‘BSpline’ or ‘MultiLabel’ or ‘Gaussian’ or ‘GenericLabel’) – Maps to a command-line argument: %s. (Nipype default value: Linear)
interpolation_parameters (a tuple of the form: (an integer) or a tuple of the form: (a float, a float) or a tuple of the form: (a string))
invert_initial_moving_transform (a list of items which are a boolean) – One boolean or a list of booleans that indicatewhether the inverse(s) of the transform(s) definedin initial_moving_transform should be used. Mutually exclusive with inputs: initial_moving_transform_com. Requires inputs: initial_moving_transform.
metric_item_trait (‘CC’ or ‘MeanSquares’ or ‘Demons’ or ‘GC’ or ‘MI’ or ‘Mattes’)
metric_stage_trait (‘CC’ or ‘MeanSquares’ or ‘Demons’ or ‘GC’ or ‘MI’ or ‘Mattes’ or a list of items which are ‘CC’ or ‘MeanSquares’ or ‘Demons’ or ‘GC’ or ‘MI’ or ‘Mattes’)
metric_weight_item_trait (a float) – (Nipype default value: 1.0)
metric_weight_stage_trait (a float or a list of items which are a float)
moving_image_mask (a pathlike object or string representing an existing file) – Mask used to limit metric sampling region of the moving imagein all stages. Mutually exclusive with inputs: moving_image_masks. Requires inputs: fixed_image_mask.
moving_image_masks (a list of items which are a pathlike object or string representing an existing file or ‘NULL’) – Masks used to limit metric sampling region of the moving image, defined per registration stage(Use “NULL” to omit a mask at a given stage). Mutually exclusive with inputs: moving_image_mask.
num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)
number_of_iterations (a list of items which are a list of items which are an integer)
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
output_inverse_warped_image (a boolean or a pathlike object or string representing a file) – Requires inputs: output_warped_image.
output_transform_prefix (a string) – Maps to a command-line argument: %s. (Nipype default value: transform)
output_warped_image (a boolean or a pathlike object or string representing a file)
radius_bins_item_trait (an integer) – (Nipype default value: 5)
radius_bins_stage_trait (an integer or a list of items which are an integer)
radius_or_number_of_bins (a list of items which are an integer or a list of items which are an integer) – The number of bins in each stage for the MI and Mattes metric, the radius for other metrics. Requires inputs: metric_weight. (Nipype default value: [5])
random_seed (an integer) – Fixed seed for random number generation. Maps to a command-line argument: --random-seed %d.
restore_state (a pathlike object or string representing an existing file) – Filename for restoring the internal restorable state of the registration. Maps to a command-line argument: --restore-state %s.
restrict_deformation (a list of items which are a list of items which are 0.0 <= a floating point number <= 1.0) – This option allows the user to restrict the optimization of the displacement field, translation, rigid or affine transform on a per-component basis. For example, if one wants to limit the deformation or rotation of 3-D volume to the first two dimensions, this is possible by specifying a weight vector of ‘1x1x0’ for a deformation field or ‘1x1x0x1x1x0’ for a rigid transformation. Low-dimensional restriction only works if there are no preceding transformations.
sampling_percentage (a list of items which are 0.0 <= a floating point number <= 1.0 or None or a list of items which are 0.0 <= a floating point number <= 1.0 or None) – The metric sampling percentage(s) to use for each stage. Requires inputs: sampling_strategy.
sampling_percentage_item_trait (0.0 <= a floating point number <= 1.0 or None)
sampling_percentage_stage_trait (0.0 <= a floating point number <= 1.0 or None or a list of items which are 0.0 <= a floating point number <= 1.0 or None)
sampling_strategy (a list of items which are ‘None’ or ‘Regular’ or ‘Random’ or None or a list of items which are ‘None’ or ‘Regular’ or ‘Random’ or None) – The metric sampling strategy (strategies) for each stage. Requires inputs: metric_weight.
sampling_strategy_item_trait (‘None’ or ‘Regular’ or ‘Random’ or None)
sampling_strategy_stage_trait (‘None’ or ‘Regular’ or ‘Random’ or None or a list of items which are ‘None’ or ‘Regular’ or ‘Random’ or None)
save_state (a pathlike object or string representing a file) – Filename for saving the internal restorable state of the registration. Maps to a command-line argument: --save-state %s.
sigma_units (a list of items which are ‘mm’ or ‘vox’) – Units for smoothing sigmas. Requires inputs: smoothing_sigmas.
transform_parameters (a list of items which are a tuple of the form: (a float) or a tuple of the form: (a float, a float, a float) or a tuple of the form: (a float, an integer, an integer, an integer) or a tuple of the form: (a float, an integer, a float, a float, a float, a float) or a tuple of the form: (a float, a float, a float, an integer) or a tuple of the form: (a float, an integer, an integer, an integer, an integer))
use_estimate_learning_rate_once (a list of items which are a boolean)
use_histogram_matching (a boolean or a list of items which are a boolean) – Histogram match the images before registration. (Nipype default value: True)
verbose (a boolean) – Maps to a command-line argument: -v. (Nipype default value: False)
winsorize_lower_quantile (0.0 <= a floating point number <= 1.0) – The Lower quantile to clip image ranges. Maps to a command-line argument: %s. (Nipype default value: 0.0)
winsorize_upper_quantile (0.0 <= a floating point number <= 1.0) – The Upper quantile to clip image ranges. Maps to a command-line argument: %s. (Nipype default value: 1.0)
write_composite_transform (a boolean) – Maps to a command-line argument: --write-composite-transform %d. (Nipype default value: False)

Outputs:

composite_transform (a pathlike object or string representing an existing file) – Composite transform file.
elapsed_time (a float) – The total elapsed time as reported by ANTs.
forward_invert_flags (a list of items which are a boolean) – List of flags corresponding to the forward transforms.
forward_transforms (a list of items which are a pathlike object or string representing an existing file) – List of output transforms for forward registration.
inverse_composite_transform (a pathlike object or string representing a file) – Inverse composite transform file.
inverse_warped_image (a pathlike object or string representing a file) – Outputs the inverse of the warped image.
metric_value (a float) – The final value of metric.
out_report (a pathlike object or string representing a file) – Filename for the visual report.
reverse_forward_invert_flags (a list of items which are a boolean) – List of flags corresponding to the forward transforms reversed for antsApplyTransform.
reverse_forward_transforms (a list of items which are a pathlike object or string representing an existing file) – List of output transforms for forward registration reversed for antsApplyTransform.
reverse_invert_flags (a list of items which are a boolean) – List of flags corresponding to the reverse transforms.
reverse_transforms (a list of items which are a pathlike object or string representing an existing file) – List of output transforms for reverse registration.
save_state (a pathlike object or string representing a file) – The saved registration state to be restored.
warped_image (a pathlike object or string representing a file) – Outputs warped image.

class niworkflows.interfaces.reportlets.registration.ApplyTOPUPRPT(generate_report=False, **kwargs)[source]¶

Bases: RegistrationRC, ApplyTOPUP

Wrapped executable: applytopup.

Mandatory Inputs:

encoding_file (a pathlike object or string representing an existing file) – Name of text file with PE directions/times. Maps to a command-line argument: --datain=%s.
in_files (a list of items which are a pathlike object or string representing an existing file) – Name of file with images. Maps to a command-line argument: --imain=%s.

Optional Inputs:

args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
datatype (‘char’ or ‘short’ or ‘int’ or ‘float’ or ‘double’) – Force output data type. Maps to a command-line argument: -d=%s.
environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})
in_index (a list of items which are an integer) – Comma separated list of indices corresponding to –datain. Maps to a command-line argument: --inindex=%s.
in_topup_fieldcoef (a pathlike object or string representing an existing file) – Topup file containing the field coefficients. Maps to a command-line argument: --topup=%s. Requires inputs: in_topup_movpar.
in_topup_movpar (a pathlike object or string representing an existing file) – Topup movpar.txt file. Requires inputs: in_topup_fieldcoef.
interp (‘trilinear’ or ‘spline’) – Interpolation method. Maps to a command-line argument: --interp=%s.
method (‘jac’ or ‘lsr’) – Use jacobian modulation (jac) or least-squares resampling (lsr). Maps to a command-line argument: --method=%s.
out_corrected (a pathlike object or string representing a file) – Output (warped) image. Maps to a command-line argument: --out=%s.
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.
wm_seg (a pathlike object or string representing a file) – Reference white matter segmentation mask. Maps to a command-line argument: -wmseg %s.

Outputs:

out_corrected (a pathlike object or string representing an existing file) – Name of 4D image file with unwarped images.
out_report (a pathlike object or string representing a file) – Filename for the visual report.

class niworkflows.interfaces.reportlets.registration.ApplyXFMRPT(generate_report=False, **kwargs)[source]¶

Bases: FLIRTRPT, ApplyXFM

Wrapped executable: flirt.

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Input file. Maps to a command-line argument: -in %s (position: 0).
reference (a pathlike object or string representing an existing file) – Reference file. Maps to a command-line argument: -ref %s (position: 1).

Optional Inputs:

angle_rep (‘quaternion’ or ‘euler’) – Representation of rotation angles. Maps to a command-line argument: -anglerep %s.
apply_isoxfm (a float) – As applyxfm but forces isotropic resampling. Maps to a command-line argument: -applyisoxfm %f. Mutually exclusive with inputs: apply_xfm.
apply_xfm (a boolean) – Apply transformation supplied by in_matrix_file or uses_qform to use the affine matrix stored in the reference header. Maps to a command-line argument: -applyxfm. (Nipype default value: True)
args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
bbrslope (a float) – Value of bbr slope. Maps to a command-line argument: -bbrslope %f.
bbrtype (‘signed’ or ‘global_abs’ or ‘local_abs’) – Type of bbr cost function: signed [default], global_abs, local_abs. Maps to a command-line argument: -bbrtype %s.
bgvalue (a float) – Use specified background value for points outside FOV. Maps to a command-line argument: -setbackground %f.
bins (an integer) – Number of histogram bins. Maps to a command-line argument: -bins %d.
coarse_search (an integer) – Coarse search delta angle. Maps to a command-line argument: -coarsesearch %d.
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
cost (‘mutualinfo’ or ‘corratio’ or ‘normcorr’ or ‘normmi’ or ‘leastsq’ or ‘labeldiff’ or ‘bbr’) – Cost function. Maps to a command-line argument: -cost %s.
cost_func (‘mutualinfo’ or ‘corratio’ or ‘normcorr’ or ‘normmi’ or ‘leastsq’ or ‘labeldiff’ or ‘bbr’) – Cost function. Maps to a command-line argument: -searchcost %s.
datatype (‘char’ or ‘short’ or ‘int’ or ‘float’ or ‘double’) – Force output data type. Maps to a command-line argument: -datatype %s.
display_init (a boolean) – Display initial matrix. Maps to a command-line argument: -displayinit.
dof (an integer) – Number of transform degrees of freedom. Maps to a command-line argument: -dof %d.
echospacing (a float) – Value of EPI echo spacing - units of seconds. Maps to a command-line argument: -echospacing %f.
environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})
fieldmap (a pathlike object or string representing a file) – Fieldmap image in rads/s - must be already registered to the reference image. Maps to a command-line argument: -fieldmap %s.
fieldmapmask (a pathlike object or string representing a file) – Mask for fieldmap image. Maps to a command-line argument: -fieldmapmask %s.
fine_search (an integer) – Fine search delta angle. Maps to a command-line argument: -finesearch %d.
force_scaling (a boolean) – Force rescaling even for low-res images. Maps to a command-line argument: -forcescaling.
in_matrix_file (a pathlike object or string representing a file) – Input 4x4 affine matrix. Maps to a command-line argument: -init %s.
in_weight (a pathlike object or string representing an existing file) – File for input weighting volume. Maps to a command-line argument: -inweight %s.
interp (‘trilinear’ or ‘nearestneighbour’ or ‘sinc’ or ‘spline’) – Final interpolation method used in reslicing. Maps to a command-line argument: -interp %s.
min_sampling (a float) – Set minimum voxel dimension for sampling. Maps to a command-line argument: -minsampling %f.
no_clamp (a boolean) – Do not use intensity clamping. Maps to a command-line argument: -noclamp.
no_resample (a boolean) – Do not change input sampling. Maps to a command-line argument: -noresample.
no_resample_blur (a boolean) – Do not use blurring on downsampling. Maps to a command-line argument: -noresampblur.
no_search (a boolean) – Set all angular searches to ranges 0 to 0. Maps to a command-line argument: -nosearch.
out_file (a pathlike object or string representing a file) – Registered output file. Maps to a command-line argument: -out %s (position: 2).
out_log (a pathlike object or string representing a file) – Output log. Requires inputs: save_log.
out_matrix_file (a pathlike object or string representing a file) – Output affine matrix in 4x4 asciii format. Maps to a command-line argument: -omat %s (position: 3).
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.
padding_size (an integer) – For applyxfm: interpolates outside image by size. Maps to a command-line argument: -paddingsize %d.
pedir (an integer) – Phase encode direction of EPI - 1/2/3=x/y/z & -1/-2/-3=-x/-y/-z. Maps to a command-line argument: -pedir %d.
ref_weight (a pathlike object or string representing an existing file) – File for reference weighting volume. Maps to a command-line argument: -refweight %s.
rigid2D (a boolean) – Use 2D rigid body mode - ignores dof. Maps to a command-line argument: -2D.
save_log (a boolean) – Save to log file.
schedule (a pathlike object or string representing an existing file) – Replaces default schedule. Maps to a command-line argument: -schedule %s.
searchr_x (a list of from 2 to 2 items which are an integer) – Search angles along x-axis, in degrees. Maps to a command-line argument: -searchrx %s.
searchr_y (a list of from 2 to 2 items which are an integer) – Search angles along y-axis, in degrees. Maps to a command-line argument: -searchry %s.
searchr_z (a list of from 2 to 2 items which are an integer) – Search angles along z-axis, in degrees. Maps to a command-line argument: -searchrz %s.
sinc_width (an integer) – Full-width in voxels. Maps to a command-line argument: -sincwidth %d.
sinc_window (‘rectangular’ or ‘hanning’ or ‘blackman’) – Sinc window. Maps to a command-line argument: -sincwindow %s.
uses_qform (a boolean) – Initialize using sform or qform. Maps to a command-line argument: -usesqform.
verbose (an integer) – Verbose mode, 0 is least. Maps to a command-line argument: -verbose %d.
wm_seg (a pathlike object or string representing a file) – White matter segmentation volume needed by BBR cost function. Maps to a command-line argument: -wmseg %s.
wmcoords (a pathlike object or string representing a file) – White matter boundary coordinates for BBR cost function. Maps to a command-line argument: -wmcoords %s.
wmnorms (a pathlike object or string representing a file) – White matter boundary normals for BBR cost function. Maps to a command-line argument: -wmnorms %s.

Outputs:

out_file (a pathlike object or string representing an existing file) – Path/name of registered file (if generated).
out_log (a pathlike object or string representing a file) – Path/name of output log (if generated).
out_matrix_file (a pathlike object or string representing an existing file) – Path/name of calculated affine transform (if generated).
out_report (a pathlike object or string representing a file) – Filename for the visual report.

class niworkflows.interfaces.reportlets.registration.BBRegisterRPT(generate_report=False, **kwargs)[source]¶

Bases: RegistrationRC, BBRegister

Wrapped executable: bbregister.

Mandatory Inputs:

contrast_type (‘t1’ or ‘t2’ or ‘bold’ or ‘dti’) – Contrast type of image. Maps to a command-line argument: --%s.
source_file (a pathlike object or string representing a file) – Source file to be registered. Maps to a command-line argument: --mov %s.
subject_id (a string) – Freesurfer subject id. Maps to a command-line argument: --s %s.

Optional Inputs:

args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
dof (6 or 9 or 12) – Number of transform degrees of freedom. Maps to a command-line argument: --%d.
environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})
epi_mask (a boolean) – Mask out B0 regions in stages 1 and 2. Maps to a command-line argument: --epi-mask.
fsldof (an integer) – Degrees of freedom for initial registration (FSL). Maps to a command-line argument: --fsl-dof %d.
init (‘coreg’ or ‘rr’ or ‘spm’ or ‘fsl’ or ‘header’ or ‘best’) – Initialize registration with mri_coreg, spm, fsl, or header. Maps to a command-line argument: --init-%s. Mutually exclusive with inputs: init_reg_file.
init_cost_file (a boolean or a pathlike object or string representing a file) – Output initial registration cost file. Maps to a command-line argument: --initcost %s.
init_reg_file (a pathlike object or string representing an existing file) – Existing registration file. Maps to a command-line argument: --init-reg %s. Mutually exclusive with inputs: init.
intermediate_file (a pathlike object or string representing an existing file) – Intermediate image, e.g. in case of partial FOV. Maps to a command-line argument: --int %s.
out_fsl_file (a boolean or a pathlike object or string representing a file) – Write the transformation matrix in FSL FLIRT format. Maps to a command-line argument: --fslmat %s.
out_lta_file (a boolean or a pathlike object or string representing a file) – Write the transformation matrix in LTA format. Maps to a command-line argument: --lta %s. (Nipype default value: True)
out_reg_file (a pathlike object or string representing a file) – Output registration file. Maps to a command-line argument: --reg %s.
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
reg_frame (an integer) – 0-based frame index for 4D source file. Maps to a command-line argument: --frame %d. Mutually exclusive with inputs: reg_middle_frame.
reg_middle_frame (a boolean) – Register middle frame of 4D source file. Maps to a command-line argument: --mid-frame. Mutually exclusive with inputs: reg_frame.
registered_file (a boolean or a pathlike object or string representing a file) – Output warped sourcefile either True or filename. Maps to a command-line argument: --o %s.
spm_nifti (a boolean) – Force use of nifti rather than analyze with SPM. Maps to a command-line argument: --spm-nii.
subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.

Outputs:

init_cost_file (a pathlike object or string representing an existing file) – Output initial registration cost file.
min_cost_file (a pathlike object or string representing an existing file) – Output registration minimum cost file.
out_fsl_file (a pathlike object or string representing an existing file) – Output FLIRT-style registration file.
out_lta_file (a pathlike object or string representing an existing file) – Output LTA-style registration file.
out_reg_file (a pathlike object or string representing an existing file) – Output registration file.
out_report (a pathlike object or string representing a file) – Filename for the visual report.
registered_file (a pathlike object or string representing an existing file) – Registered and resampled source file.

class niworkflows.interfaces.reportlets.registration.FLIRTRPT(generate_report=False, **kwargs)[source]¶

Bases: RegistrationRC, FLIRT

Wrapped executable: flirt.

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Input file. Maps to a command-line argument: -in %s (position: 0).
reference (a pathlike object or string representing an existing file) – Reference file. Maps to a command-line argument: -ref %s (position: 1).

Optional Inputs:

angle_rep (‘quaternion’ or ‘euler’) – Representation of rotation angles. Maps to a command-line argument: -anglerep %s.
apply_isoxfm (a float) – As applyxfm but forces isotropic resampling. Maps to a command-line argument: -applyisoxfm %f. Mutually exclusive with inputs: apply_xfm.
apply_xfm (a boolean) – Apply transformation supplied by in_matrix_file or uses_qform to use the affine matrix stored in the reference header. Maps to a command-line argument: -applyxfm.
args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
bbrslope (a float) – Value of bbr slope. Maps to a command-line argument: -bbrslope %f.
bbrtype (‘signed’ or ‘global_abs’ or ‘local_abs’) – Type of bbr cost function: signed [default], global_abs, local_abs. Maps to a command-line argument: -bbrtype %s.
bgvalue (a float) – Use specified background value for points outside FOV. Maps to a command-line argument: -setbackground %f.
bins (an integer) – Number of histogram bins. Maps to a command-line argument: -bins %d.
coarse_search (an integer) – Coarse search delta angle. Maps to a command-line argument: -coarsesearch %d.
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
cost (‘mutualinfo’ or ‘corratio’ or ‘normcorr’ or ‘normmi’ or ‘leastsq’ or ‘labeldiff’ or ‘bbr’) – Cost function. Maps to a command-line argument: -cost %s.
cost_func (‘mutualinfo’ or ‘corratio’ or ‘normcorr’ or ‘normmi’ or ‘leastsq’ or ‘labeldiff’ or ‘bbr’) – Cost function. Maps to a command-line argument: -searchcost %s.
datatype (‘char’ or ‘short’ or ‘int’ or ‘float’ or ‘double’) – Force output data type. Maps to a command-line argument: -datatype %s.
display_init (a boolean) – Display initial matrix. Maps to a command-line argument: -displayinit.
dof (an integer) – Number of transform degrees of freedom. Maps to a command-line argument: -dof %d.
echospacing (a float) – Value of EPI echo spacing - units of seconds. Maps to a command-line argument: -echospacing %f.
environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})
fieldmap (a pathlike object or string representing a file) – Fieldmap image in rads/s - must be already registered to the reference image. Maps to a command-line argument: -fieldmap %s.
fieldmapmask (a pathlike object or string representing a file) – Mask for fieldmap image. Maps to a command-line argument: -fieldmapmask %s.
fine_search (an integer) – Fine search delta angle. Maps to a command-line argument: -finesearch %d.
force_scaling (a boolean) – Force rescaling even for low-res images. Maps to a command-line argument: -forcescaling.
in_matrix_file (a pathlike object or string representing a file) – Input 4x4 affine matrix. Maps to a command-line argument: -init %s.
in_weight (a pathlike object or string representing an existing file) – File for input weighting volume. Maps to a command-line argument: -inweight %s.
interp (‘trilinear’ or ‘nearestneighbour’ or ‘sinc’ or ‘spline’) – Final interpolation method used in reslicing. Maps to a command-line argument: -interp %s.
min_sampling (a float) – Set minimum voxel dimension for sampling. Maps to a command-line argument: -minsampling %f.
no_clamp (a boolean) – Do not use intensity clamping. Maps to a command-line argument: -noclamp.
no_resample (a boolean) – Do not change input sampling. Maps to a command-line argument: -noresample.
no_resample_blur (a boolean) – Do not use blurring on downsampling. Maps to a command-line argument: -noresampblur.
no_search (a boolean) – Set all angular searches to ranges 0 to 0. Maps to a command-line argument: -nosearch.
out_file (a pathlike object or string representing a file) – Registered output file. Maps to a command-line argument: -out %s (position: 2).
out_log (a pathlike object or string representing a file) – Output log. Requires inputs: save_log.
out_matrix_file (a pathlike object or string representing a file) – Output affine matrix in 4x4 asciii format. Maps to a command-line argument: -omat %s (position: 3).
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.
padding_size (an integer) – For applyxfm: interpolates outside image by size. Maps to a command-line argument: -paddingsize %d.
pedir (an integer) – Phase encode direction of EPI - 1/2/3=x/y/z & -1/-2/-3=-x/-y/-z. Maps to a command-line argument: -pedir %d.
ref_weight (a pathlike object or string representing an existing file) – File for reference weighting volume. Maps to a command-line argument: -refweight %s.
rigid2D (a boolean) – Use 2D rigid body mode - ignores dof. Maps to a command-line argument: -2D.
save_log (a boolean) – Save to log file.
schedule (a pathlike object or string representing an existing file) – Replaces default schedule. Maps to a command-line argument: -schedule %s.
searchr_x (a list of from 2 to 2 items which are an integer) – Search angles along x-axis, in degrees. Maps to a command-line argument: -searchrx %s.
searchr_y (a list of from 2 to 2 items which are an integer) – Search angles along y-axis, in degrees. Maps to a command-line argument: -searchry %s.
searchr_z (a list of from 2 to 2 items which are an integer) – Search angles along z-axis, in degrees. Maps to a command-line argument: -searchrz %s.
sinc_width (an integer) – Full-width in voxels. Maps to a command-line argument: -sincwidth %d.
sinc_window (‘rectangular’ or ‘hanning’ or ‘blackman’) – Sinc window. Maps to a command-line argument: -sincwindow %s.
uses_qform (a boolean) – Initialize using sform or qform. Maps to a command-line argument: -usesqform.
verbose (an integer) – Verbose mode, 0 is least. Maps to a command-line argument: -verbose %d.
wm_seg (a pathlike object or string representing a file) – White matter segmentation volume needed by BBR cost function. Maps to a command-line argument: -wmseg %s.
wmcoords (a pathlike object or string representing a file) – White matter boundary coordinates for BBR cost function. Maps to a command-line argument: -wmcoords %s.
wmnorms (a pathlike object or string representing a file) – White matter boundary normals for BBR cost function. Maps to a command-line argument: -wmnorms %s.

Outputs:

out_file (a pathlike object or string representing an existing file) – Path/name of registered file (if generated).
out_log (a pathlike object or string representing a file) – Path/name of output log (if generated).
out_matrix_file (a pathlike object or string representing an existing file) – Path/name of calculated affine transform (if generated).
out_report (a pathlike object or string representing a file) – Filename for the visual report.

class niworkflows.interfaces.reportlets.registration.FUGUERPT(generate_report=False, **kwargs)[source]¶

Bases: RegistrationRC, FUGUE

Wrapped executable: fugue.

Optional Inputs:

args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
asym_se_time (a float) – Set the fieldmap asymmetric spin echo time (sec). Maps to a command-line argument: --asym=%.10f.
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
despike_2dfilter (a boolean) – Apply a 2D de-spiking filter. Maps to a command-line argument: --despike.
despike_threshold (a float) – Specify the threshold for de-spiking (default=3.0). Maps to a command-line argument: --despikethreshold=%s.
dwell_time (a float) – Set the EPI dwell time per phase-encode line - same as echo spacing - (sec). Maps to a command-line argument: --dwell=%.10f.
dwell_to_asym_ratio (a float) – Set the dwell to asym time ratio. Maps to a command-line argument: --dwelltoasym=%.10f.
environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})
fmap_in_file (a pathlike object or string representing an existing file) – Filename for loading fieldmap (rad/s). Maps to a command-line argument: --loadfmap=%s.
fmap_out_file (a pathlike object or string representing a file) – Filename for saving fieldmap (rad/s). Maps to a command-line argument: --savefmap=%s.
forward_warping (a boolean) – Apply forward warping instead of unwarping. (Nipype default value: False)
fourier_order (an integer) – Apply Fourier (sinusoidal) fitting of order N. Maps to a command-line argument: --fourier=%d.
icorr (a boolean) – Apply intensity correction to unwarping (pixel shift method only). Maps to a command-line argument: --icorr. Requires inputs: shift_in_file.
icorr_only (a boolean) – Apply intensity correction only. Maps to a command-line argument: --icorronly. Requires inputs: unwarped_file.
in_file (a pathlike object or string representing an existing file) – Filename of input volume. Maps to a command-line argument: --in=%s.
mask_file (a pathlike object or string representing an existing file) – Filename for loading valid mask. Maps to a command-line argument: --mask=%s.
median_2dfilter (a boolean) – Apply 2D median filtering. Maps to a command-line argument: --median.
no_extend (a boolean) – Do not apply rigid-body extrapolation to the fieldmap. Maps to a command-line argument: --noextend.
no_gap_fill (a boolean) – Do not apply gap-filling measure to the fieldmap. Maps to a command-line argument: --nofill.
nokspace (a boolean) – Do not use k-space forward warping. Maps to a command-line argument: --nokspace.
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.
pava (a boolean) – Apply monotonic enforcement via PAVA. Maps to a command-line argument: --pava.
phase_conjugate (a boolean) – Apply phase conjugate method of unwarping. Maps to a command-line argument: --phaseconj.
phasemap_in_file (a pathlike object or string representing an existing file) – Filename for input phase image. Maps to a command-line argument: --phasemap=%s.
poly_order (an integer) – Apply polynomial fitting of order N. Maps to a command-line argument: --poly=%d.
save_fmap (a boolean) – Write field map volume. Mutually exclusive with inputs: save_unmasked_fmap.
save_shift (a boolean) – Write pixel shift volume. Mutually exclusive with inputs: save_unmasked_shift.
save_unmasked_fmap (a boolean) – Saves the unmasked fieldmap when using –savefmap. Maps to a command-line argument: --unmaskfmap. Mutually exclusive with inputs: save_fmap.
save_unmasked_shift (a boolean) – Saves the unmasked shiftmap when using –saveshift. Maps to a command-line argument: --unmaskshift. Mutually exclusive with inputs: save_shift.
shift_in_file (a pathlike object or string representing an existing file) – Filename for reading pixel shift volume. Maps to a command-line argument: --loadshift=%s.
shift_out_file (a pathlike object or string representing a file) – Filename for saving pixel shift volume. Maps to a command-line argument: --saveshift=%s.
smooth2d (a float) – Apply 2D Gaussian smoothing of sigma N (in mm). Maps to a command-line argument: --smooth2=%.2f.
smooth3d (a float) – Apply 3D Gaussian smoothing of sigma N (in mm). Maps to a command-line argument: --smooth3=%.2f.
unwarp_direction (‘x’ or ‘y’ or ‘z’ or ‘x-’ or ‘y-’ or ‘z-’) – Specifies direction of warping (default y). Maps to a command-line argument: --unwarpdir=%s.
unwarped_file (a pathlike object or string representing a file) – Apply unwarping and save as filename. Maps to a command-line argument: --unwarp=%s. Mutually exclusive with inputs: warped_file. Requires inputs: in_file.
warped_file (a pathlike object or string representing a file) – Apply forward warping and save as filename. Maps to a command-line argument: --warp=%s. Mutually exclusive with inputs: unwarped_file. Requires inputs: in_file.
wm_seg (a pathlike object or string representing a file) – Reference white matter segmentation mask. Maps to a command-line argument: -wmseg %s.

Outputs:

fmap_out_file (a pathlike object or string representing a file) – Fieldmap file.
out_report (a pathlike object or string representing a file) – Filename for the visual report.
shift_out_file (a pathlike object or string representing a file) – Voxel shift map file.
unwarped_file (a pathlike object or string representing a file) – Unwarped file.
warped_file (a pathlike object or string representing a file) – Forward warped file.

class niworkflows.interfaces.reportlets.registration.MRICoregRPT(generate_report=False, **kwargs)[source]¶

Bases: RegistrationRC, MRICoreg

Wrapped executable: mri_coreg.

Mandatory Inputs:

reference_file (a pathlike object or string representing a file) – Reference (target) file. Maps to a command-line argument: --ref %s. Mutually exclusive with inputs: subject_id.
source_file (a pathlike object or string representing a file) – Source file to be registered. Maps to a command-line argument: --mov %s.
subject_id (a string) – Freesurfer subject ID (implies reference_mask == aparc+aseg.mgz unless otherwise specified). Maps to a command-line argument: --s %s (position: 1). Mutually exclusive with inputs: reference_file. Requires inputs: subjects_dir.

Optional Inputs:

args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
brute_force_limit (a float) – Constrain brute force search to +/- lim. Maps to a command-line argument: --bf-lim %g. Mutually exclusive with inputs: no_brute_force.
brute_force_samples (an integer) – Number of samples in brute force search. Maps to a command-line argument: --bf-nsamp %d. Mutually exclusive with inputs: no_brute_force.
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
conform_reference (a boolean) – Conform reference without rescaling. Maps to a command-line argument: --conf-ref.
dof (6 or 9 or 12) – Number of transform degrees of freedom. Maps to a command-line argument: --dof %d.
environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})
ftol (a float) – Floating-point tolerance (default=1e-7). Maps to a command-line argument: --ftol %e.
initial_rotation (a tuple of the form: (a float, a float, a float)) – Initial rotation in degrees. Maps to a command-line argument: --rot %g %g %g.
initial_scale (a tuple of the form: (a float, a float, a float)) – Initial scale. Maps to a command-line argument: --scale %g %g %g.
initial_shear (a tuple of the form: (a float, a float, a float)) – Initial shear (Hxy, Hxz, Hyz). Maps to a command-line argument: --shear %g %g %g.
initial_translation (a tuple of the form: (a float, a float, a float)) – Initial translation in mm (implies no_cras0). Maps to a command-line argument: --trans %g %g %g.
linmintol (a float) – Maps to a command-line argument: --linmintol %e.
max_iters (an integer >= 1) – Maximum iterations (default: 4). Maps to a command-line argument: --nitersmax %d.
no_brute_force (a boolean) – Do not brute force search. Maps to a command-line argument: --no-bf.
no_coord_dithering (a boolean) – Turn off coordinate dithering. Maps to a command-line argument: --no-coord-dither.
no_cras0 (a boolean) – Do not set translation parameters to align centers of source and reference files. Maps to a command-line argument: --no-cras0.
no_intensity_dithering (a boolean) – Turn off intensity dithering. Maps to a command-line argument: --no-intensity-dither.
no_smooth (a boolean) – Do not apply smoothing to either reference or source file. Maps to a command-line argument: --no-smooth.
num_threads (an integer) – Number of OpenMP threads. Maps to a command-line argument: --threads %d.
out_lta_file (a bool or None or a pathlike object or string representing a file) – Output registration file (LTA format). Maps to a command-line argument: --lta %s. (Nipype default value: True)
out_params_file (a bool or None or a pathlike object or string representing a file) – Output parameters file. Maps to a command-line argument: --params %s.
out_reg_file (a bool or None or a pathlike object or string representing a file) – Output registration file (REG format). Maps to a command-line argument: --regdat %s.
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
ref_fwhm (a float) – Apply smoothing to reference file. Maps to a command-line argument: --ref-fwhm.
reference_mask (a bool or None or a string) – Mask reference volume with given mask, or None if False. Maps to a command-line argument: --ref-mask %s (position: 2).
saturation_threshold (0.0 <= a floating point number <= 100.0) – Saturation threshold (default=9.999). Maps to a command-line argument: --sat %g.
sep (a list of from 1 to 2 items which are any value) – Set spatial scales, in voxels (default [2, 4]). Maps to a command-line argument: --sep %s....
source_mask (a string) – Mask source file with given mask. Maps to a command-line argument: --mov-mask.
source_oob (a boolean) – Count source voxels that are out-of-bounds as 0. Maps to a command-line argument: --mov-oob.
subjects_dir (a pathlike object or string representing an existing directory) – FreeSurfer SUBJECTS_DIR. Maps to a command-line argument: --sd %s.

Outputs:

out_lta_file (a pathlike object or string representing an existing file) – Output LTA-style registration file.
out_params_file (a pathlike object or string representing an existing file) – Output parameters file.
out_reg_file (a pathlike object or string representing an existing file) – Output registration file.
out_report (a pathlike object or string representing a file) – Filename for the visual report.

class niworkflows.interfaces.reportlets.registration.ResampleBeforeAfterRPT(generate_report=True, **kwargs)[source]¶

Bases: SimpleBeforeAfterRPT

Mandatory Inputs:

after (a pathlike object or string representing an existing file) – File after.
base (‘before’ or ‘after’) – (Nipype default value: before)
before (a pathlike object or string representing an existing file) – File before.

Optional Inputs:

after_label (a string) – (Nipype default value: after)
before_label (a string) – (Nipype default value: before)
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
dismiss_affine (a boolean) – Rotate image(s) to cardinal axes. (Nipype default value: False)
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
wm_seg (a pathlike object or string representing a file) – Reference white matter segmentation mask.

Outputs:

out_report (a pathlike object or string representing a file) – Filename for the visual report.

class niworkflows.interfaces.reportlets.registration.SimpleBeforeAfterRPT(generate_report=True, **kwargs)[source]¶

Bases: RegistrationRC, ReportingInterface

Mandatory Inputs:

after (a pathlike object or string representing an existing file) – File after.
before (a pathlike object or string representing an existing file) – File before.

Optional Inputs:

after_label (a string) – (Nipype default value: after)
before_label (a string) – (Nipype default value: before)
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
dismiss_affine (a boolean) – Rotate image(s) to cardinal axes. (Nipype default value: False)
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
wm_seg (a pathlike object or string representing a file) – Reference white matter segmentation mask.

Outputs:

out_report (a pathlike object or string representing a file) – Filename for the visual report.

class niworkflows.interfaces.reportlets.registration.SpatialNormalizationRPT(generate_report=False, **kwargs)[source]¶

Bases: RegistrationRC, SpatialNormalization

Mandatory Inputs:

moving (‘T1w’ or ‘boldref’) – Registration type. (Nipype default value: T1w)
moving_image (a pathlike object or string representing an existing file) – Image to apply transformation to.
orientation (‘RAS’ or ‘LAS’) – Modify template orientation (should match input image). (Nipype default value: RAS)
reference (‘T1w’ or ‘T2w’ or ‘boldref’ or ‘PDw’) – Set the reference modality for registration. (Nipype default value: T1w)

Optional Inputs:

compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
explicit_masking (a boolean) – Set voxels outside the masks to zero thus creating an artificial border that can drive the registration. Requires reliable and accurate masks. See https://sourceforge.net/p/advants/discussion/840261/thread/27216e69/#c7ba. (Nipype default value: True)
flavor (‘precise’ or ‘testing’ or ‘fast’) – Registration settings parameter set. (Nipype default value: precise)
float (a boolean) – Use single precision calculations. (Nipype default value: False)
initial_moving_transform (a pathlike object or string representing an existing file) – Transform for initialization.
lesion_mask (a pathlike object or string representing an existing file) – Lesion mask image.
moving_mask (a pathlike object or string representing an existing file) – Moving image mask.
num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 4)
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
reference_image (a pathlike object or string representing an existing file) – Override the reference image.
reference_mask (a pathlike object or string representing an existing file) – Reference image mask.
settings (a list of items which are a pathlike object or string representing an existing file) – Pass on the list of settings files.
template (a string) – Define the template to be used. (Nipype default value: MNI152NLin2009cAsym)
template_resolution (1 or 2 or None) – (DEPRECATED) template resolution.
template_spec (a dictionary with keys which are a value of class ‘str’ and with values which are any value) – Template specifications.

Outputs:

composite_transform (a pathlike object or string representing an existing file) – Composite transform file.
elapsed_time (a float) – The total elapsed time as reported by ANTs.
forward_invert_flags (a list of items which are a boolean) – List of flags corresponding to the forward transforms.
forward_transforms (a list of items which are a pathlike object or string representing an existing file) – List of output transforms for forward registration.
inverse_composite_transform (a pathlike object or string representing a file) – Inverse composite transform file.
inverse_warped_image (a pathlike object or string representing a file) – Outputs the inverse of the warped image.
metric_value (a float) – The final value of metric.
out_report (a pathlike object or string representing a file) – Filename for the visual report.
reference_image (a pathlike object or string representing an existing file) – Reference image used for registration target.
reverse_forward_invert_flags (a list of items which are a boolean) – List of flags corresponding to the forward transforms reversed for antsApplyTransform.
reverse_forward_transforms (a list of items which are a pathlike object or string representing an existing file) – List of output transforms for forward registration reversed for antsApplyTransform.
reverse_invert_flags (a list of items which are a boolean) – List of flags corresponding to the reverse transforms.
reverse_transforms (a list of items which are a pathlike object or string representing an existing file) – List of output transforms for reverse registration.
save_state (a pathlike object or string representing a file) – The saved registration state to be restored.
warped_image (a pathlike object or string representing a file) – Outputs warped image.