AFNI 3D Automatic Mask Creation (3dAutomask)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Creates a brain mask automatically from EPI data by finding connected high-intensity voxels.
Modality: 3D or 4D EPI NIfTI/AFNI volume.
Typical Use: Generating functional brain masks from EPI data.
Key Parameters¶
-prefix (output mask), -dilate (number of dilation steps), -erode (number of erosion steps), -clfrac (clip fraction)
Key Points¶
Works on EPI data directly (no structural needed). Lower -clfrac includes more voxels.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input dataset | |
prefix |
string |
Yes | Output mask dataset prefix | -prefix |
clfrac |
double |
No | Clip level fraction (0.1-0.9, default 0.5) | -clfrac |
nograd |
boolean |
No | Use fixed clip level instead of gradual method | -nograd |
peels |
int |
No | Erode then dilate mask N times to remove thin protrusions (default 1) | -peels |
dilate |
int |
No | Dilate the mask outwards N times | -dilate |
erode |
int |
No | Erode the mask inwards N times | -erode |
NN1 |
boolean |
No | Use face neighbors only (6 neighbors) | -NN1 |
NN2 |
boolean |
No | Use face and edge neighbors (18 neighbors, default) | -NN2 |
NN3 |
boolean |
No | Use face, edge, and corner neighbors (26 neighbors) | -NN3 |
nbhrs |
int |
No | Number of neighbors needed to not erode (6-26, default 17) | -nbhrs |
eclip |
boolean |
No | Remove exterior voxels below the clip threshold | -eclip |
SI |
double |
No | Zero out voxels more than N mm inferior to superior voxel | -SI |
apply_prefix |
string |
No | Apply mask to input and save masked dataset | -apply_prefix |
depth |
string |
No | Produce dataset showing peel operations to reach each voxel | -depth |
quiet |
boolean |
No | Suppress progress messages | -q |
Accepted Input Extensions¶
- input:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
mask |
File |
$(inputs.prefix)+orig.HEAD, $(inputs.prefix)+tlrc.HEAD |
masked_input |
File |
$(inputs.apply_prefix)+orig.HEAD, $(inputs.apply_prefix)+tlrc.HEAD |
depth_map |
File |
$(inputs.depth)+orig.HEAD, $(inputs.depth)+tlrc.HEAD |
log |
File |
$(inputs.prefix).log |
Output Extensions¶
- mask:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - masked_input:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - depth_map:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Parameter Bounds¶
| Parameter | Min | Max |
|---|---|---|
clfrac |
0.1 | 0.9 |
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Masking