ANTs SyN Registration with Defaults¶
Library: ANTs | Docker Image: antsx/ants
Function¶
Symmetric normalization registration with sensible default parameters for common registration tasks.
Modality: Any 3D NIfTI volume pair.
Typical Use: Standard registration with good defaults for structural normalization.
Key Parameters¶
-d (dimension), -f (fixed), -m (moving), -o (output prefix), -t (transform type: s=SyN, b=BSplineSyN, a=affine only)
Key Points¶
Good defaults for most use cases. Outputs forward/inverse warps and affine. Preferred over raw antsRegistration for simplicity.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
dimensionality |
int |
Yes | Image dimensionality (2 or 3) | -d |
fixed_image |
File |
Yes | Fixed/reference image | -f |
moving_image |
File |
Yes | Moving/target image to register | -m |
output_prefix |
string |
Yes | Output prefix for transform files | -o |
transform_type |
enum |
No | Transform type (t=translation, r=rigid, a=affine, s=SyN, b=b-spline SyN) | -t |
num_threads |
int |
No | Number of threads | -n |
precision |
enum |
No | Precision (f=float, d=double) | -p |
masks |
string |
No | Mask images (fixedMask,movingMask) | -x |
initial_transform |
File |
No | Initial transform | -i |
histogram_matching |
boolean |
No | Use histogram matching | -j |
reproducible |
boolean |
No | Enable reproducible mode with fixed random seed | -y |
collapse_transforms |
boolean |
No | Collapse output transforms | -z |
Accepted Input Extensions¶
- fixed_image:
.nii,.nii.gz - moving_image:
.nii,.nii.gz - initial_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 |
affine_transform |
File |
$(inputs.output_prefix)0GenericAffine.mat |
warp_field |
File |
$(inputs.output_prefix)1Warp.nii.gz |
inverse_warp_field |
File |
$(inputs.output_prefix)1InverseWarp.nii.gz |
log |
File |
antsRegistrationSyN.log |
Output Extensions¶
- warped_image:
.nii.gz - inverse_warped_image:
.nii.gz - affine_transform:
.mat - warp_field:
.nii.gz - inverse_warp_field:
.nii.gz
Enum Options¶
transform_type: t, r, a, s, sr, b, br
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