ANTs Multi-Stage Image Registration¶
Library: ANTs | Docker Image: antsx/ants
Function¶
State-of-the-art image registration supporting multiple stages (rigid, affine, SyN) with configurable metrics and convergence.
Modality: Any 3D NIfTI volume pair (fixed and moving images).
Typical Use: High-quality multi-stage registration with full parameter control.
Key Parameters¶
-d (dimension), -f (fixed), -m (moving), -t (transform type), -c (convergence), -s (smoothing sigmas), -o (output)
Key Points¶
Multi-stage approach: rigid then affine then SyN. SyN is symmetric diffeomorphic. CC metric best for intra-modal, MI for inter-modal.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
dimensionality |
int |
Yes | Image dimensionality (2 or 3) | -d |
output_prefix |
string |
Yes | Output transform prefix | -o |
fixed_image |
File |
Yes | Fixed/reference image | |
moving_image |
File |
Yes | Moving image to register | |
metric |
string |
Yes | Metric specification (e.g., MI[fixed,moving,1,32,Regular,0.25]) | -m |
transform |
string |
Yes | Transform specification (e.g., Rigid[0.1]) | -t |
convergence |
string |
Yes | Convergence specification (e.g., [1000x500x250x100,1e-6,10]) | -c |
shrink_factors |
string |
Yes | Shrink factors per level (e.g., 8x4x2x1) | -f |
smoothing_sigmas |
string |
Yes | Smoothing sigmas per level (e.g., 3x2x1x0vox) | -s |
initial_moving_transform |
File |
No | Initial transform for moving image | -r |
masks |
string |
No | Mask specification (fixedMask,movingMask or single mask) | -x |
use_histogram_matching |
boolean |
No | Use histogram matching | -u |
winsorize_image_intensities |
string |
No | Winsorize intensities (e.g., [0.005,0.995]) | -w |
use_float |
boolean |
No | Use float precision instead of double | --float |
interpolation |
enum |
No | Interpolation method | -n |
verbose |
boolean |
No | Enable verbose output | -v |
write_composite_transform |
boolean |
No | Write composite transform | -z |
Accepted Input Extensions¶
- fixed_image:
.nii,.nii.gz - moving_image:
.nii,.nii.gz - initial_moving_transform:
.mat,.h5,.nii.gz,.txt
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
warped_image |
File |
$(inputs.output_prefix)Warped.nii.gz |
inverse_warped_image |
File |
$(inputs.output_prefix)InverseWarped.nii.gz |
forward_transforms |
File[] |
$(inputs.output_prefix)*GenericAffine.mat, $(inputs.output_prefix)*Warp.nii.gz |
inverse_transforms |
File[] |
$(inputs.output_prefix)*InverseWarp.nii.gz |
log |
File |
antsRegistration.log |
Output Extensions¶
- warped_image:
.nii.gz - inverse_warped_image:
.nii.gz - forward_transforms:
.mat,.nii.gz - inverse_transforms:
.nii.gz
Enum Options¶
interpolation: Linear, NearestNeighbor, BSpline, Gaussian
Docker Tags¶
Available versions: latest, master, v2.6.5, 2.6.5, v2.6.4, 2.6.4, v2.6.3, 2.6.3, v2.6.2, 2.6.2
and 5 more
Categories¶
- Structural MRI > ANTs > Registration