niworkflows.interfaces.norm module¶
A robust ANTs T1-to-MNI registration workflow with fallback retry.
- class niworkflows.interfaces.norm.SpatialNormalization(**inputs)[source]¶
Bases:
BaseInterface
An interface to robustly run T1-to-MNI spatial normalization.
Several settings are sequentially tried until some work.
- 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:
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
)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 string and with values which are any value) – Template specifications.
use_histogram_matching (a boolean) – Determine use of histogram matching.
- 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.
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.
- niworkflows.interfaces.norm.create_cfm(in_file, lesion_mask=None, global_mask=True, out_path=None)[source]¶
Create a mask to constrain registration.
- Parameters:
in_file (str) – Path to an existing image (usually a mask). If global_mask = True, this is used as a size/dimension reference.
out_path (str) – Path/filename for the new cost function mask.
lesion_mask (str, optional) – Path to an existing binary lesion mask.
global_mask (bool) – Create a whole-image mask (True) or limit to reference mask (False) A whole image-mask is 1 everywhere
- Returns:
Absolute path of the new cost function mask.
- Return type:
Notes
in_file and lesion_mask must be in the same image space and have the same dimensions
- niworkflows.interfaces.norm.mask(in_file, mask_file, new_name)[source]¶
Apply a binary mask to an image.
- Parameters:
in_file (str) – Path to a NIfTI file to mask
mask_file (str) – Path to a binary mask
new_name (str) – Path/filename for the masked output image.
- Returns:
Absolute path of the masked output image.
- Return type:
Notes
in_file and mask_file must be in the same image space and have the same dimensions.