ANTs DiReCT Cortical Thickness (KellyKapowski)¶
Library: ANTs | Docker Image: antsx/ants
Function¶
Estimates cortical thickness using the DiReCT algorithm from segmentation data.
Modality: Tissue segmentation image plus GM and WM probability maps (3D NIfTI).
Typical Use: Computing cortical thickness from pre-existing tissue segmentation.
Key Parameters¶
-d (dimension), -s (segmentation image), -g (GM probability), -w (WM probability), -o (output thickness map), -c (convergence)
Key Points¶
Core thickness estimation engine used by antsCorticalThickness.sh. Requires good segmentation as input.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
dimensionality |
int |
Yes | Image dimensionality (2 or 3) | -d |
segmentation_image |
File |
Yes | Segmentation image with labeled tissues | -s |
gray_matter_prob |
File |
Yes | Gray matter probability image | -g |
white_matter_prob |
File |
Yes | White matter probability image | -w |
output_image |
string |
Yes | Output cortical thickness image | -o |
convergence |
string |
No | Convergence parameters [iterations,convergenceThreshold,thicknessPrior] | -c |
thickness_prior |
double |
No | Prior estimate for cortical thickness | -t |
gradient_step |
double |
No | Gradient descent step size | -r |
smoothing_sigma |
double |
No | Gradient field smoothing parameter | -m |
number_integration_points |
int |
No | Number of integration points | -n |
verbose |
boolean |
No | Enable verbose output | -v |
Accepted Input Extensions¶
- segmentation_image:
.nii,.nii.gz - gray_matter_prob:
.nii,.nii.gz - white_matter_prob:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
thickness_image |
File |
$(inputs.output_image) |
log |
File |
KellyKapowski.log |
Output Extensions¶
- thickness_image:
.nii,.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 > Cortical Thickness