AFNI 3D Cluster Size Simulation (3dClustSim)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Simulates null distribution of cluster sizes for determining cluster-extent thresholds that control family-wise error rate.
Modality: Brain mask (3D NIfTI/AFNI) plus smoothness estimates from 3dFWHMx.
Typical Use: Determining cluster size thresholds for multiple comparison correction.
Key Parameters¶
-mask (brain mask), -acf (ACF parameters from 3dFWHMx), -athr (per-voxel alpha), -pthr (per-voxel p thresholds)
Key Points¶
Use ACF-based smoothness (not FWHM) from 3dFWHMx on residuals. Updated in 2016 for non-Gaussian assumptions.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
prefix |
string |
Yes | Output filename prefix | -prefix |
nxyz |
string |
No | Size of 3D grid (n1 n2 n3, default 64 64 32) | -nxyz |
dxyz |
string |
No | Voxel dimensions in mm (d1 d2 d3, default 3.5 3.5 3.5) | -dxyz |
mask |
File |
No | Mask dataset defining analysis region | -mask |
BALL |
boolean |
No | Restrict simulation to spherical volume | -BALL |
inset |
File[] |
No | Use these volumes as simulations | -inset |
fwhm |
double |
No | Gaussian filter width in mm (not recommended) | -fwhm |
acf |
string |
No | ACF parameters (a b c) from 3dFWHMx | -acf |
nopad |
boolean |
No | Disable edge padding | -nopad |
pthr |
string |
No | Per-voxel p-value thresholds | -pthr |
athr |
string |
No | Whole-volume alpha significance levels | -athr |
iter |
int |
No | Number of Monte Carlo simulations (default 10000) | -iter |
seed |
int |
No | Random number seed | -seed |
niml |
boolean |
No | Output in NIML/XML format | -niml |
both |
boolean |
No | Output both NIML and .1D formats | -both |
nodec |
boolean |
No | Remove decimal places from thresholds | -nodec |
quiet |
boolean |
No | Suppress progress messages | -quiet |
Accepted Input Extensions¶
- mask:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - inset:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
clustsim_1D |
File[] |
$(inputs.prefix).NN*.1D |
clustsim_niml |
File[] |
$(inputs.prefix).NN*.niml |
log |
File |
$(inputs.prefix).log |
Output Extensions¶
- clustsim_1D:
.1D - clustsim_niml:
.niml
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Multiple Comparisons