AFNI 3D Skull Strip¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Removes non-brain tissue using a modified spherical surface expansion algorithm adapted from BET.
Modality: T1-weighted or T2-weighted 3D NIfTI/AFNI volume.
Typical Use: Brain extraction for structural or functional images in AFNI pipelines.
Key Parameters¶
-input (input dataset), -prefix (output prefix), -push_to_edge (expand mask), -orig_vol (output original volume)
Key Points¶
Often more aggressive than BET. Use -push_to_edge if too much brain is removed. Works on T1 or T2 images.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input volume | -input |
prefix |
string |
Yes | Output volume prefix | -prefix |
mask_vol |
boolean |
No | Output mask volume instead of skull-stripped volume | -mask_vol |
orig_vol |
boolean |
No | Preserve original intensity values | -orig_vol |
skulls |
boolean |
No | Output skull surface models | -skulls |
niter |
int |
No | Iteration count (default 250) | -niter |
shrink_fac |
double |
No | Brain/non-brain intensity threshold (0-1, default 0.6) | -shrink_fac |
var_shrink_fac |
boolean |
No | Vary shrink factor across iterations (default) | -var_shrink_fac |
no_var_shrink_fac |
boolean |
No | Keep constant shrink factor | -no_var_shrink_fac |
shrink_fac_bot_lim |
double |
No | Minimum shrink factor (default 0.65-0.4) | -shrink_fac_bot_lim |
init_radius |
double |
No | Initial sphere radius in mm | -init_radius |
exp_frac |
double |
No | Expansion speed (default 0.1) | -exp_frac |
push_to_edge |
boolean |
No | Aggressive push to brain edges | -push_to_edge |
no_push_to_edge |
boolean |
No | Disable aggressive edge push (default) | -no_push_to_edge |
touchup |
boolean |
No | Include uncovered areas (default) | -touchup |
no_touchup |
boolean |
No | Skip touchup operations | -no_touchup |
fill_hole |
double |
No | Fill holes up to R pixels | -fill_hole |
smooth_final |
int |
No | Final smoothing iterations (default 20) | -smooth_final |
avoid_vent |
boolean |
No | Avoid ventricles (default) | -avoid_vent |
no_avoid_vent |
boolean |
No | Disable ventricle avoidance | -no_avoid_vent |
avoid_eyes |
boolean |
No | Avoid eyes (default) | -avoid_eyes |
no_avoid_eyes |
boolean |
No | Disable eye avoidance | -no_avoid_eyes |
use_edge |
boolean |
No | Edge detection to reduce leakage (default) | -use_edge |
no_use_edge |
boolean |
No | Disable edge detection | -no_use_edge |
blur_fwhm |
double |
No | Blur kernel width (recommended 2-4) | -blur_fwhm |
monkey |
boolean |
No | Process monkey brain data | -monkey |
marmoset |
boolean |
No | Process marmoset brain data | -marmoset |
rat |
boolean |
No | Process rat brain data | -rat |
Accepted Input Extensions¶
- input:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
skull_stripped |
File |
$(inputs.prefix)+orig.HEAD, $(inputs.prefix)+tlrc.HEAD |
mask |
File |
$(inputs.prefix)_mask+orig.HEAD, $(inputs.prefix)_mask+tlrc.HEAD |
log |
File |
$(inputs.prefix).log |
Output Extensions¶
- skull_stripped:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - mask:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Parameter Bounds¶
| Parameter | Min | Max |
|---|---|---|
shrink_fac |
0 | 1 |
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Structural MRI > AFNI > Brain Extraction