ANTs Motion Correction¶
Library: ANTs | Docker Image: antsx/ants
Function¶
Motion correction for time series data using ANTs registration framework with rigid or affine transformations.
Modality: 4D fMRI or dynamic PET NIfTI time series.
Typical Use: High-quality motion correction using ANTs registration framework.
Key Parameters¶
-d (dimension), -a (compute average), -o (output), -u (use fixed reference), -m (metric)
Key Points¶
Can compute average image and motion-correct simultaneously. Uses ANTs optimization. Slower than MCFLIRT.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
dimensionality |
int |
Yes | Image dimensionality (2 or 3) | -d |
fixed_image |
File |
Yes | Fixed/reference 3D image | |
moving_image |
File |
Yes | Moving 4D time series image | |
output_prefix |
string |
Yes | Output transform prefix | -o |
metric |
string |
Yes | Metric specification (e.g., MI[fixed,moving,1,32,Regular,0.1]) | -m |
transform |
string |
Yes | Transform type (e.g., Rigid[0.1] or Affine[0.1]) | -t |
iterations |
string |
Yes | Iterations at each level (e.g., 100x50x30) | -i |
shrink_factors |
string |
Yes | Shrink factors at each level (e.g., 4x2x1) | -f |
smoothing_sigmas |
string |
Yes | Smoothing sigmas at each level (e.g., 2x1x0) | -s |
num_images |
int |
No | Number of images to use from time series | -n |
use_fixed_reference |
boolean |
No | Use fixed reference for all time points | -u |
use_scale_estimator |
boolean |
No | Use scale estimator | -e |
write_displacement |
boolean |
No | Write 4D displacement field | -w |
average_image |
boolean |
No | Average the input time series | -a |
verbose |
boolean |
No | Enable verbose output | -v |
Accepted Input Extensions¶
- fixed_image:
.nii,.nii.gz - moving_image:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
corrected_image |
File |
$(inputs.output_prefix)_corrected.nii.gz |
average_image |
File |
$(inputs.output_prefix)_avg.nii.gz |
motion_parameters |
File[] |
$(inputs.output_prefix)MOCOparams.csv |
displacement_field |
File |
$(inputs.output_prefix)Warp.nii.gz |
log |
File |
antsMotionCorr.log |
Output Extensions¶
- corrected_image:
.nii.gz - average_image:
.nii.gz - motion_parameters:
.csv - displacement_field:
.nii.gz
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¶
- Functional MRI > ANTs > Motion Correction