ANTs Template-Based Brain Extraction¶
Library: ANTs | Docker Image: antsx/ants
Function¶
High-quality brain extraction using registration to a brain template and tissue priors for robust skull stripping.
Modality: T1-weighted 3D NIfTI volume plus brain template and brain probability mask.
Typical Use: High-quality skull stripping, especially for challenging datasets.
Key Parameters¶
-d (dimension, 3), -a (anatomical image), -e (brain template), -m (brain probability mask), -o (output prefix)
Key Points¶
More robust than BET for difficult cases. Requires template and prior. Slower but generally more accurate.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
dimensionality |
int |
Yes | Image dimensionality (2 or 3) | -d |
anatomical_image |
File |
Yes | Input anatomical T1 image | -a |
template |
File |
Yes | Brain extraction template (head with skull) | -e |
brain_probability_mask |
File |
Yes | Brain probability mask for template | -m |
output_prefix |
string |
Yes | Output prefix | -o |
registration_mask |
File |
No | Registration mask for template | -f |
keep_temporary_files |
boolean |
No | Keep temporary files | -k |
image_suffix |
string |
No | Output image file suffix (e.g., nii.gz) | -s |
rotation_search |
string |
No | Rotation search parameters (step,arcFraction) | -R |
translation_search |
string |
No | Translation search parameters (step,range) | -T |
use_floatingpoint |
boolean |
No | Use single floating point precision | -q |
use_random_seeding |
boolean |
No | Use random seeding | -u |
Accepted Input Extensions¶
- anatomical_image:
.nii,.nii.gz - template:
.nii,.nii.gz - brain_probability_mask:
.nii,.nii.gz - registration_mask:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
brain_extracted |
File |
$(inputs.output_prefix)BrainExtractionBrain.nii.gz |
brain_mask |
File |
$(inputs.output_prefix)BrainExtractionMask.nii.gz |
brain_n4 |
File |
$(inputs.output_prefix)BrainExtractionBrain_N4.nii.gz |
registration_template |
File |
$(inputs.output_prefix)BrainExtractionPrior*Warped.nii.gz |
log |
File |
antsBrainExtraction.log |
Output Extensions¶
- brain_extracted:
.nii.gz - brain_mask:
.nii.gz - brain_n4:
.nii.gz - registration_template:
.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 > Brain Extraction