AFNI Skull Strip and Nonlinear Warp (@SSwarper)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Combined skull stripping and non-linear warping to template in a single optimized pipeline.
Modality: T1-weighted 3D NIfTI volume plus reference template.
Typical Use: Modern anatomical preprocessing for afni_proc.py pipelines.
Key Parameters¶
-input (T1 image), -base (template), -subid (subject ID), -odir (output dir)
Key Points¶
Preferred over separate skull-strip + registration. Output compatible with afni_proc.py.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input anatomical dataset (non-skull-stripped, ~1mm resolution) | -input |
base |
File |
Yes | Base template dataset with similar contrast | -base |
subid |
string |
Yes | Subject ID code for output datasets | -subid |
odir |
string |
No | Output directory (default is input directory) | -odir |
minp |
int |
No | Minimum patch size for 3dQwarp (default 11) | -minp |
warpscale |
double |
No | Control warp flexibility (0.1-1.0, default 1.0) | -warpscale |
skipwarp |
boolean |
No | Stop after skull-stripping, skip warping to template | -skipwarp |
deoblique |
boolean |
No | Apply obliquity correction using 3dWarp | -deoblique |
deoblique_refitly |
boolean |
No | Remove obliquity information via 3drefit | -deoblique_refitly |
unifize_off |
boolean |
No | Skip intensity uniformization step | -unifize_off |
aniso_off |
boolean |
No | Skip anisotropic smoothing preprocessing | -aniso_off |
ceil_off |
boolean |
No | Skip ceiling value capping at 98th percentile | -ceil_off |
init_skullstr_off |
boolean |
No | Skip initial skull-stripping pass | -init_skullstr_off |
cost_nl_init |
string |
No | Cost function for initial nonlinear alignment (default lpa) | -cost_nl_init |
cost_nl_final |
string |
No | Cost function for final nonlinear alignment (default pcl) | -cost_nl_final |
giant_move |
boolean |
No | Apply expanded parameter alignment for extreme angles | -giant_move |
mask_ss |
File |
No | Provide mask instead of performing skull-stripping | -mask_ss |
SSopt |
string |
No | Additional options passed to 3dSkullStrip | -SSopt |
extra_qc_off |
boolean |
No | Omit extra QC JPEG images | -extra_qc_off |
nolite |
boolean |
No | Disable lite option in 3dQwarp | -nolite |
verb |
boolean |
No | Enable verbose 3dQwarp output | -verb |
noclean |
boolean |
No | Preserve temporary files after completion | -noclean |
Accepted Input Extensions¶
- input:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - base:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - mask_ss:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
skull_stripped |
File |
anatSS.$(inputs.subid).nii, anatSS.$(inputs.subid).nii.gz |
warped |
File |
anatQQ.$(inputs.subid)+tlrc.HEAD, anatQQ.$(inputs.subid)+tlrc.BRIK, anatQQ.$(inputs.subid)+tlrc.BRIK.gz, anatQQ.$(inputs.subid).nii, anatQQ.$(inputs.subid).nii.gz |
warp |
File |
anatQQ.$(inputs.subid)_WARP+tlrc.HEAD, anatQQ.$(inputs.subid)_WARP+tlrc.BRIK, anatQQ.$(inputs.subid)_WARP+tlrc.BRIK.gz, anatQQ.$(inputs.subid)_WARP.nii, anatQQ.$(inputs.subid)_WARP.nii.gz |
affine |
File |
anatQQ.$(inputs.subid).aff12.1D |
log |
File |
$(inputs.subid)_SSwarper.log |
Output Extensions¶
- skull_stripped:
.nii,.nii.gz - warped:
+tlrc.HEAD,+tlrc.BRIK,.nii,.nii.gz - warp:
+tlrc.HEAD,+tlrc.BRIK,.nii,.nii.gz - affine:
.aff12.1D
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Structural MRI > AFNI > Brain Extraction