ANTs Combined Atropos with N4 Bias Correction¶
Library: ANTs | Docker Image: antsx/ants
Function¶
Iteratively combines N4 bias field correction with Atropos segmentation for improved results on biased images.
Modality: Brain-extracted 3D NIfTI volume plus brain mask.
Typical Use: Iterative N4 + segmentation for better results on images with bias field.
Key Parameters¶
-d (dimension), -a (anatomical image), -x (mask), -c (number of classes), -o (output prefix), -n (number of iterations)
Key Points¶
Iterative approach: N4 correction improves segmentation, which improves next N4 iteration. Superior to running separately.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
dimensionality |
int |
Yes | Image dimensionality (2 or 3) | -d |
input_image |
File |
Yes | Input anatomical image (typically T1) | -a |
mask_image |
File |
Yes | Binary mask defining region of interest | -x |
output_prefix |
string |
Yes | Output prefix | -o |
num_classes |
int |
Yes | Number of tissue classes | -c |
n4_atropos_iterations |
int |
No | Number of N4-Atropos iterations | -m |
atropos_iterations |
int |
No | Number of Atropos iterations per N4 iteration | -n |
prior_images |
string |
No | Prior probability images pattern (e.g., prior%d.nii.gz) | -p |
prior_weight |
double |
No | Atropos prior probability weight | -w |
n4_shrink_factor |
int |
No | N4 shrink factor | -f |
n4_convergence |
string |
No | N4 convergence parameters | -e |
n4_bspline |
string |
No | N4 B-spline parameters | -q |
atropos_icm |
string |
No | Atropos ICM parameters | -i |
use_euclidean_distance |
boolean |
No | Use Euclidean distance in distance prior | -j |
posterior_for_n4 |
int[] |
No | Posterior labels for N4 weight mask | -y |
image_suffix |
string |
No | Output image file suffix (e.g., nii.gz) | -s |
keep_temporary |
boolean |
No | Keep temporary files | -k |
use_random_seeding |
boolean |
No | Use random seeding | -u |
Accepted Input Extensions¶
- input_image:
.nii,.nii.gz - mask_image:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
segmentation |
File |
$(inputs.output_prefix)Segmentation.nii.gz |
posteriors |
File[] |
$(inputs.output_prefix)SegmentationPosteriors*.nii.gz |
bias_corrected |
File |
$(inputs.output_prefix)Segmentation0N4.nii.gz |
log |
File |
antsAtroposN4.log |
Output Extensions¶
- segmentation:
.nii.gz - posteriors:
.nii.gz - bias_corrected:
.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¶
- Structural MRI > ANTs > Segmentation
- Pipelines > ANTs > Structural