ANTs Cortical Thickness Pipeline¶
Library: ANTs | Docker Image: antsx/ants
Function¶
Complete automated pipeline for cortical thickness estimation using DiReCT, including brain extraction, segmentation, and registration.
Modality: T1-weighted 3D NIfTI volume plus brain template and tissue priors.
Typical Use: Complete DiReCT-based cortical thickness measurement pipeline.
Key Parameters¶
-d (dimension), -a (anatomical image), -e (brain template), -m (brain probability mask), -p (tissue priors prefix), -o (output prefix)
Key Points¶
Runs full pipeline: N4, brain extraction, segmentation, registration, thickness. Requires template and priors. Computationally intensive.
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 (with skull) | -e |
brain_probability_mask |
File |
Yes | Brain probability mask for template | -m |
segmentation_priors |
string |
Yes | Segmentation priors pattern (e.g., priors%d.nii.gz) | -p |
segmentation_priors_dir |
Directory |
No | Directory containing segmentation priors (used with segmentation_priors pattern) | |
output_prefix |
string |
Yes | Output prefix | -o |
template_transform_prefix |
string |
No | Transform prefix to template space | -t |
registration_mask |
File |
No | Registration mask for template | -f |
extraction_registration_mask |
File |
No | Mask for brain extraction registration | -x |
quick_registration |
boolean |
No | Use quick registration (antsRegistrationSyNQuick.sh) | -q |
run_stage |
enum |
No | Stage to run (0=all, 1=extraction, 2=registration, 3=segmentation) | -y |
keep_temporary |
boolean |
No | Keep temporary files | -k |
image_suffix |
string |
No | Output image file suffix (e.g., nii.gz) | -s |
additional_thickness_priors |
string |
No | Additional classes for thickness (e.g., 4) | -c |
use_random_seeding |
boolean |
No | Use random seeding | -u |
test_mode |
boolean |
No | Test/debug mode for faster execution | -z |
Accepted Input Extensions¶
- anatomical_image:
.nii,.nii.gz - template:
.nii,.nii.gz - brain_probability_mask:
.nii,.nii.gz - registration_mask:
.nii,.nii.gz - extraction_registration_mask:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
brain_extraction_mask |
File |
$(inputs.output_prefix)BrainExtractionMask.nii.gz |
brain_segmentation |
File |
$(inputs.output_prefix)BrainSegmentation.nii.gz |
cortical_thickness |
File |
$(inputs.output_prefix)CorticalThickness.nii.gz |
brain_normalized |
File |
$(inputs.output_prefix)BrainNormalizedToTemplate.nii.gz |
subject_to_template_warp |
File |
$(inputs.output_prefix)SubjectToTemplate1Warp.nii.gz |
subject_to_template_affine |
File |
$(inputs.output_prefix)SubjectToTemplate0GenericAffine.mat |
template_to_subject_warp |
File |
$(inputs.output_prefix)TemplateToSubject0Warp.nii.gz |
template_to_subject_affine |
File |
$(inputs.output_prefix)TemplateToSubject1GenericAffine.mat |
segmentation_posteriors |
File[] |
$(inputs.output_prefix)BrainSegmentationPosteriors*.nii.gz |
log |
File |
antsCorticalThickness.log |
Output Extensions¶
- brain_extraction_mask:
.nii.gz - brain_segmentation:
.nii.gz - cortical_thickness:
.nii.gz - brain_normalized:
.nii.gz - subject_to_template_warp:
.nii.gz - subject_to_template_affine:
.mat - template_to_subject_warp:
.nii.gz - template_to_subject_affine:
.mat - segmentation_posteriors:
.nii.gz
Enum Options¶
run_stage: 0, 1, 2, 3
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 > Cortical Thickness
- Pipelines > ANTs > Structural