AFNI 3D Merge and Smooth (3dmerge)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Combines spatial filtering and dataset merging operations, commonly used for Gaussian smoothing.
Modality: 3D or 4D NIfTI/AFNI volume.
Typical Use: Gaussian smoothing of functional data.
Key Parameters¶
-1blur_fwhm (FWHM in mm), -doall (process all sub-bricks), -prefix (output)
Key Points¶
Simple Gaussian smoothing with -1blur_fwhm. -doall applies to all volumes in 4D.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input dataset | |
prefix |
string |
Yes | Output dataset prefix | -prefix |
blur_fwhm |
double |
No | Gaussian blur with FWHM (mm) | -1blur_fwhm |
blur_sigma |
double |
No | Gaussian blur with sigma (mm) | -1blur_sigma |
blur_rms |
double |
No | Gaussian blur with RMS deviation (mm) | -1blur_rms |
thtoin |
boolean |
No | Copy threshold data over intensity data | -1thtoin |
noneg |
boolean |
No | Zero out negative intensity voxels | -1noneg |
abs |
boolean |
No | Take absolute values of intensities | -1abs |
clip |
double |
No | Clip intensities in range (-val,val) to zero | -1clip |
thresh |
double |
No | Use threshold data to censor intensities | -1thresh |
mult |
double |
No | Multiply intensities by given factor | -1mult |
zscore |
boolean |
No | Convert statistic to equivalent z-score | -1zscore |
clust |
string |
No | Form clusters with rmm vmul (e.g., "5 100") | -1clust |
clust_mean |
string |
No | Replace cluster voxels with average intensity | -1clust_mean |
clust_max |
string |
No | Replace cluster voxels with maximum intensity | -1clust_max |
filter_mean |
double |
No | Set each voxel to average intensity within radius (mm) | -1filter_mean |
filter_max |
double |
No | Maximum intensity within radius (mm) | -1filter_max |
filter_blur |
double |
No | Gaussian blur filter with FWHM (mm) | -1filter_blur |
erode |
double |
No | Set voxel to zero unless pv% of nearby voxels are nonzero | -1erode |
dilate |
boolean |
No | Restore voxels removed by erosion if neighbors exist | -1dilate |
dindex |
int |
No | Use sub-brick j as data source | -1dindex |
tindex |
int |
No | Use sub-brick k as threshold source | -1tindex |
doall |
boolean |
No | Apply options to all sub-bricks uniformly | -doall |
datum |
enum |
No | Output data storage type | -datum |
nozero |
boolean |
No | Do not write output if all zero | -nozero |
quiet |
boolean |
No | Reduce message output | -quiet |
Accepted Input Extensions¶
- input:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
merged |
File |
$(inputs.prefix)+orig.HEAD, $(inputs.prefix)+tlrc.HEAD |
log |
File |
$(inputs.prefix).log |
Output Extensions¶
- merged:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Smoothing