FSL Apply Warp Field (applywarp)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Applies linear and/or non-linear warp fields to transform images between coordinate spaces.
Modality: 3D or 4D NIfTI volume plus warp field and/or affine matrix.
Typical Use: Applying normalization warps to functional data or atlas labels.
Key Parameters¶
-i (input), -r (reference), -o (output), -w (warp field), --premat (pre-warp affine), --postmat (post-warp affine), --interp (interpolation)
Key Points¶
Can chain affine + nonlinear transforms in one step. Use --interp=nn for label images, --interp=spline for continuous images. Reference defines output grid.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input image to be warped | --in= |
reference |
File |
Yes | Reference image | --ref= |
output |
string |
Yes | Output filename | --out= |
warp |
File |
No | Warp field file | --warp= |
premat |
File |
No | Pre-transform affine matrix (applied first) | --premat= |
postmat |
File |
No | Post-transform affine matrix (applied last) | --postmat= |
relwarp |
boolean |
No | Treat warp as relative (x' = x + w(x)) | --rel |
abswarp |
boolean |
No | Treat warp as absolute (x' = w(x)) | --abs |
interp |
enum |
No | Interpolation method | --interp= |
supersample |
boolean |
No | Enable supersampling | --super |
superlevel |
string |
No | Supersampling level (integer or 'a' for auto) | --superlevel= |
mask |
File |
No | Mask in reference space | --mask= |
datatype |
enum |
No | Output data type | --datatype= |
padding_size |
int |
No | Padding size | --paddingsize= |
verbose |
boolean |
No | Verbose output | -v |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - reference:
.nii,.nii.gz - warp:
.nii,.nii.gz - premat:
.mat - postmat:
.mat - mask:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
warped_image |
File |
$(inputs.output).nii.gz, $(inputs.output).nii |
log |
File |
applywarp.log |
Output Extensions¶
- warped_image:
.nii,.nii.gz
Enum Options¶
interp: nn, trilinear, sinc, spline
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¶
- Utilities > FSL > Warp Utilities