ANTs N4 Bias Field Correction¶
Library: ANTs | Docker Image: antsx/ants
Function¶
Advanced bias field (intensity inhomogeneity) correction using the N4 algorithm with iterative B-spline fitting.
Modality: 3D NIfTI volume (any MRI contrast), optional brain mask.
Typical Use: Removing intensity inhomogeneity before segmentation or registration.
Key Parameters¶
-d (dimension), -i (input), -o (output [,bias_field]), -x (mask), -s (shrink factor), -c (convergence)
Key Points¶
Gold standard for bias correction. Use mask to restrict correction to brain. -s 4 speeds up computation.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input_image |
File |
Yes | Input image for bias correction | -i |
output_prefix |
string |
Yes | Output image prefix | -o |
dimensionality |
int |
No | Image dimensionality (2, 3, or 4) | -d |
mask_image |
File |
No | Binary mask to restrict correction region | -x |
weight_image |
File |
No | Weight image for voxel weighting during fitting | -w |
shrink_factor |
int |
No | Shrink factor for faster processing (1-4 typical) | -s |
convergence |
string |
No | Convergence parameters [iterations,threshold] e.g. [50x50x50x50,0.0] | -c |
bspline_fitting |
string |
No | B-spline fitting parameters [splineDistance,splineOrder] e.g. [180,3] | -b |
histogram_sharpening |
string |
No | Histogram sharpening [FWHM,wienerNoise,numBins] e.g. [0.15,0.01,200] | -t |
rescale_intensities |
boolean |
No | Rescale intensities between 0 and 1 | -r |
verbose |
boolean |
No | Enable verbose output | -v |
Accepted Input Extensions¶
- input_image:
.nii,.nii.gz - mask_image:
.nii,.nii.gz - weight_image:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
corrected_image |
File |
$(inputs.output_prefix)_corrected.nii.gz |
bias_field |
File |
$(inputs.output_prefix)_biasfield.nii.gz |
log |
File |
N4BiasFieldCorrection.log |
Output Extensions¶
- corrected_image:
.nii.gz - bias_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¶
- Utilities > ANTs > Preprocessing Utilities