AFNI 3D Nonlinear Warp (3dQwarp)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Non-linear registration using cubic polynomial basis functions for precise anatomical alignment.
Modality: T1-weighted 3D NIfTI/AFNI volumes (source and base, both skull-stripped).
Typical Use: High-accuracy normalization to template.
Key Parameters¶
-source (moving), -base (reference), -prefix (output), -blur (smoothing), -minpatch (minimum patch size)
Key Points¶
Both images should be skull-stripped. Use -blur 0 3 for typical T1 registration. Usually preceded by 3dAllineate.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
source |
File |
Yes | Source dataset to be warped | -source |
base |
File |
Yes | Base/template dataset | -base |
prefix |
string |
Yes | Output dataset prefix | -prefix |
allineate |
boolean |
No | Perform preliminary affine alignment via 3dAllineate | -allineate |
allin |
boolean |
No | Short form of -allineate | -allin |
allinfast |
boolean |
No | Fast affine alignment | -allinfast |
blur |
string |
No | Gaussian smoothing in voxels FWHM (one or two values) | -blur |
pblur |
boolean |
No | Progressive blurring scaled with patch size | -pblur |
minpatch |
int |
No | Minimum patch size (odd integer, default 25) | -minpatch |
maxlev |
int |
No | Maximum refinement level | -maxlev |
inilev |
int |
No | Initial refinement level | -inilev |
iniwarp |
File |
No | Initial warp dataset | -iniwarp |
duplo |
boolean |
No | Start with coarse resolution warping | -duplo |
nowarp |
boolean |
No | Do not save the warp transformation | -nowarp |
iwarp |
boolean |
No | Compute and save inverse warp | -iwarp |
nodset |
boolean |
No | Do not save warped source dataset | -nodset |
emask |
File |
No | Exclusion mask dataset | -emask |
noweight |
boolean |
No | Do not use weighting | -noweight |
penfac |
double |
No | Penalty factor for warp smoothness | -penfac |
verb |
boolean |
No | Verbose output | -verb |
quiet |
boolean |
No | Suppress progress messages | -quiet |
Accepted Input Extensions¶
- source:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - base:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - iniwarp:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK,.1D,.txt - emask:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
warped |
File |
$(inputs.prefix)+*.HEAD |
warp |
File |
$(inputs.prefix)_WARP+*.HEAD |
inverse_warp |
File |
$(inputs.prefix)_WARPINV+*.HEAD |
log |
File |
$(inputs.prefix).log |
Output Extensions¶
- warped:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - warp:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - inverse_warp:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Structural MRI > AFNI > Registration