AFNI 3D Adaptive Smoothing to Target FWHM¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Adaptively smooths data to achieve a target smoothness level, accounting for existing smoothness.
Modality: 3D or 4D NIfTI/AFNI volume with mask.
Typical Use: Achieving consistent smoothness across subjects/studies.
Key Parameters¶
-input (input dataset), -prefix (output), -FWHM (target smoothness in mm), -mask (brain mask)
Key Points¶
Measures existing smoothness and adds only enough to reach target FWHM. Better than fixed-kernel smoothing.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input dataset to be smoothed | -input |
prefix |
string |
Yes | Output dataset prefix | -prefix |
FWHM |
double |
No | Target 3D FWHM in mm | -FWHM |
FWHMxy |
double |
No | Target 2D (x,y)-plane FWHM in mm (no z-axis blurring) | -FWHMxy |
blurmaster |
File |
No | Reference dataset controlling smoothness | -blurmaster |
mask |
File |
No | Mask dataset limiting blurring to masked voxels | -mask |
automask |
boolean |
No | Generate automatic mask from input dataset | -automask |
maxite |
int |
No | Maximum iteration count | -maxite |
rate |
double |
No | Scaling factor adjusting blurring speed (0.05-3.5) | -rate |
nbhd |
string |
No | Neighborhood for local smoothness computation | -nbhd |
ACF |
boolean |
No | Use autocorrelation function method for smoothness estimation | -ACF |
detrend |
boolean |
No | Remove polynomial trends from blurmaster (default) | -detrend |
nodetrend |
boolean |
No | Disable detrending | -nodetrend |
detin |
boolean |
No | Detrend input dataset before and after blurring | -detin |
unif |
boolean |
No | Standardize voxel-wise MAD before blurring | -unif |
temper |
boolean |
No | Enhance spatial uniformity of smoothness | -temper |
quiet |
boolean |
No | Suppress verbose progress messages | -quiet |
Accepted Input Extensions¶
- input:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - blurmaster:
.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 |
|---|---|---|
blurred |
File |
$(inputs.prefix)+orig.HEAD, $(inputs.prefix)+tlrc.HEAD |
log |
File |
$(inputs.prefix).log |
Output Extensions¶
- blurred:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Smoothing