AFNI 3D Despike (3dDespike)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Removes transient signal spikes from fMRI time series using an L1-norm fitting approach.
Modality: 4D fMRI NIfTI/AFNI time series.
Typical Use: Artifact removal before other preprocessing steps.
Key Parameters¶
-prefix (output), -ssave (save spike fit), -nomask (process all voxels), -NEW (updated algorithm)
Key Points¶
Run early in preprocessing pipeline (before motion correction). -NEW algorithm recommended.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input 3D+time dataset | |
prefix |
string |
Yes | Output dataset prefix | -prefix |
ignore |
int |
No | Ignore the first I points in the time series | -ignore |
corder |
int |
No | Curve fit order (default NT/30) | -corder |
cut |
string |
No | Spike threshold values (default "2.5 4.0") | -cut |
nomask |
boolean |
No | Process all voxels instead of using auto-mask | -nomask |
dilate |
int |
No | Dilation iterations for automask (default 4) | -dilate |
localedit |
boolean |
No | Use alternative spike replacement method | -localedit |
NEW |
boolean |
No | Use faster fitting method for long series | -NEW |
NEW25 |
boolean |
No | More aggressive despiking than NEW | -NEW25 |
OLD |
boolean |
No | Disable NEW processing if enabled | -OLD |
ssave |
string |
No | Save spikiness measure to 3D+time dataset | -ssave |
quiet |
boolean |
No | Suppress informational messages | -quiet |
Accepted Input Extensions¶
- input:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
despiked |
File |
$(inputs.prefix)+orig.HEAD, $(inputs.prefix)+tlrc.HEAD |
spikiness |
File |
$(inputs.ssave)+orig.HEAD, $(inputs.ssave)+tlrc.HEAD |
log |
File |
$(inputs.prefix).log |
Output Extensions¶
- despiked:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - spikiness:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Denoising