Brain Extraction Tool (BET)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Removes non-brain tissue from MRI images using a deformable surface model that iteratively fits to the brain boundary.
Modality: T1-weighted structural image (3D NIfTI). Can also process 4D fMRI with -F flag.
Typical Use: First step in structural or functional preprocessing to isolate brain tissue.
Key Parameters¶
-f (fractional intensity 0→1, default 0.5), -g (vertical gradient), -R (robust mode), -m (output binary mask)
Key Points¶
Default threshold works for most T1s. Use -R for noisy/difficult data. Lower -f (~0.3) for functional images.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input T1-weighted image | |
output |
string |
Yes | Output filename | |
overlay |
boolean |
No | Generate brain outline image | -o |
mask |
boolean |
No | Generate binary brain mask image | -m |
skull |
boolean |
No | Generate skull-stripped image | -s |
ngenerate |
boolean |
No | Do not generate the default output | -n |
frac |
double |
No | Fractional intensity threshold | -f |
vert_frac |
double |
No | Vertical gradient in fractional intensity | -g |
radius |
double |
No | Radius of the brain centre in mm | -r |
cog |
string |
No | Center of gravity vox coordinates | -c |
threshold |
boolean |
No | Use thresholding to estimate the brain centre | -t |
mesh |
boolean |
No | Generate a mesh of the brain surface | -e |
exclusive |
record(robust) | record(eye) | record(bias) | record(fov) | record(fmri) | record(betsurf) | record(betsurfT2) |
No |
Accepted Input Extensions¶
- input:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
brain_extraction |
File |
$(inputs.output).nii, $(inputs.output).nii.gz |
brain_mask |
File |
$(inputs.output)_mask.nii.gz, $(inputs.output)_mask.nii |
brain_skull |
File |
$(inputs.output)_skull.nii.gz, $(inputs.output)_skull.nii |
brain_mesh |
File |
$(inputs.output)_mesh.vtk |
brain_registration |
File[] |
$(inputs.output)_inskull_*.*, $(inputs.output)_outskin_*.*, $(inputs.output)_outskull_*.*, $(inputs.output)_skull_mask.* |
log |
File |
$(inputs.output).log |
Output Extensions¶
- brain_extraction:
.nii,.nii.gz - brain_mask:
.nii,.nii.gz - brain_skull:
.nii,.nii.gz - brain_mesh:
.vtk - brain_registration:
.nii,.nii.gz
Parameter Bounds¶
| Parameter | Min | Max |
|---|---|---|
frac |
0 | 1 |
vert_frac |
-1 | 1 |
Docker Tags¶
Available versions: latest, 6.0.4-patched2, 6.0.4-patched, 6.0.4, 6.0.4-xenial, 5.0.11, 6.0.0, 6.0.1, 5.0.9
Categories¶
- Structural MRI > FSL > Brain Extraction