AFNI 3D Smoothness Estimation (3dFWHMx)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Estimates spatial smoothness of data using the autocorrelation function (ACF) model.
Modality: Residual 4D NIfTI/AFNI from GLM analysis plus brain mask.
Typical Use: Getting smoothness estimates for 3dClustSim.
Key Parameters¶
-input (residuals), -mask (brain mask), -acf (output ACF parameters), -detrend (detrend order)
Key Points¶
Run on residuals (not original data). ACF model accounts for non-Gaussian spatial structure. Output feeds into 3dClustSim.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input dataset | -input |
mask |
File |
No | Use only nonzero voxels in mask | -mask |
automask |
boolean |
No | Generate mask automatically from input | -automask |
demed |
boolean |
No | Subtract median of each voxel time series | -demed |
unif |
boolean |
No | Normalize voxel time series to same MAD | -unif |
detrend |
int |
No | Remove polynomial trends up to order q | -detrend |
detprefix |
string |
No | Save detrended dataset with prefix | -detprefix |
geom |
boolean |
No | Compute geometric mean of FWHM (default) | -geom |
arith |
boolean |
No | Compute arithmetic mean of FWHM | -arith |
combine |
boolean |
No | Combine measurements along each axis | -combine |
acf |
string |
No | Compute ACF fit (output a b c parameters) | -acf |
ACF |
string |
No | Same as -acf but with comment lines | -ACF |
out |
string |
Yes | Output filename for FWHM results | -out |
compat |
boolean |
No | Compatibility mode with older 3dFWHM | -compat |
difMAD |
boolean |
No | Use first/second neighbor differences with MAD | -2difMAD |
Accepted Input Extensions¶
- input:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - mask:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
fwhm_output |
File |
$(inputs.out) |
acf_output |
File |
$(inputs.acf) |
detrended |
File |
$(inputs.detprefix)+orig.*, $(inputs.detprefix).nii* |
log |
File |
3dFWHMx.log |
Output Extensions¶
- fwhm_output:
.1D - acf_output:
.1D - detrended:
+orig.HEAD,+orig.BRIK,.nii,.nii.gz
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Multiple Comparisons