FreeSurfer MRI Watershed Skull Stripping¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Brain extraction using a hybrid watershed/surface deformation algorithm to find the brain-skull boundary.
Modality: T1-weighted 3D volume (typically MGZ format within FreeSurfer pipeline).
Typical Use: Brain extraction within recon-all pipeline.
Key Parameters¶
-T1 (specify T1 volume), -atlas (use atlas for initial estimate), -h (preflooding height, default 25)
Key Points¶
Core component of recon-all. Adjust -h parameter if too much/too little brain removed. Usually part of autorecon1.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
input |
File |
Yes | Input T1 volume | |
output |
string |
Yes | Output brain volume filename | |
atlas |
boolean |
No | Apply atlas correction to segmentation | -atlas |
brain_atlas |
File |
No | Atlas reference file | -brain_atlas |
preflooding_height |
int |
No | Preflooding height in percent | -h |
watershed_weight |
double |
No | Preweight using atlas information | -w |
basin_merge |
double |
No | Basin merging using atlas information | -b |
less |
boolean |
No | Shrink the surface (leaves less skull) | -less |
more |
boolean |
No | Expand the surface (leaves more skull) | -more |
threshold |
int |
No | Adjust watershed threshold | -t |
seed |
string |
No | Add seed point coordinates (x y z) | -s |
center |
string |
No | Brain center in voxels (x y z) | -c |
radius |
int |
No | Brain radius in voxels | -r |
t1 |
boolean |
No | Specify T1 input (grey value ~110) | -T1 |
no_seedpt |
boolean |
No | Disable seed points from atlas | -no_seedpt |
no_wta |
boolean |
No | Disable preweighting for template deformation | -no_wta |
no_ta |
boolean |
No | Disable template deformation using atlas | -no-ta |
surf |
string |
No | Save BEM surfaces to directory | -surf |
brainsurf |
string |
No | Save brain surface filename | -brainsurf |
useSRAS |
boolean |
No | Use surface RAS instead of scanner RAS | -useSRAS |
watershed_only |
boolean |
No | Use watershed algorithm only | -wat |
noT1 |
boolean |
No | Skip T1 analysis to conserve memory | -noT1 |
mask |
boolean |
No | Mask volume with brain mask | -mask |
label |
boolean |
No | Label output into anatomical structures | -LABEL |
Accepted Input Extensions¶
- input:
.mgz,.mgh,.nii,.nii.gz - brain_atlas:
.mgz,.mgh,.nii,.nii.gz,.gca
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
brain |
File |
$(inputs.output)* |
bem_surfaces |
Directory |
$(inputs.surf) |
log |
File |
mri_watershed.log |
Output Extensions¶
- brain:
.mgz,.mgh,.nii,.nii.gz
Docker Tags¶
Available versions: latest, 8.1.0, 8.0.0, 7.2.0, 7.3.0, 7.3.1, 7.3.2, 7.4.1, 7.1.1, 6.0
Categories¶
- Structural MRI > FreeSurfer > Surface Reconstruction