FSL Convert/Combine Warps (convertwarp)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Combines multiple warp fields and affine matrices into a single composite warp for efficient one-step transformation.
Modality: Warp fields and/or affine matrices from FLIRT/FNIRT.
Typical Use: Concatenating multiple transformations (e.g., func > struct > standard) efficiently.
Key Parameters¶
-r (reference), -o (output), --premat (first affine), --warp1 (first warp), --midmat (middle affine), --warp2 (second warp), --postmat (final affine)
Key Points¶
Applying one combined warp is faster and has less interpolation error than chaining multiple transformations. Transform order: premat > warp1 > midmat > warp2 > postmat.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
reference |
File |
Yes | Reference image in target space | --ref= |
output |
string |
Yes | Output warp filename | --out= |
warp1 |
File |
No | First warp field | --warp1= |
warp2 |
File |
No | Second warp field (applied after warp1) | --warp2= |
premat |
File |
No | Pre-transform affine matrix (applied first) | --premat= |
midmat |
File |
No | Mid-warp affine transform | --midmat= |
postmat |
File |
No | Post-transform affine matrix (applied last) | --postmat= |
shiftmap |
File |
No | Shift map (fieldmap) file | --shiftmap= |
shiftdir |
enum |
No | Shift direction | --shiftdir= |
abswarp |
boolean |
No | Treat input warps as absolute | --absout |
relwarp |
boolean |
No | Treat input warps as relative | --relout |
out_abswarp |
boolean |
No | Output warp as absolute | --absout |
out_relwarp |
boolean |
No | Output warp as relative | --relout |
cons_jacobian |
boolean |
No | Constrain Jacobian | --constrainj |
jacobian_min |
double |
No | Minimum Jacobian | --jmin= |
jacobian_max |
double |
No | Maximum Jacobian | --jmax= |
verbose |
boolean |
No | Verbose output | --verbose |
Accepted Input Extensions¶
- reference:
.nii,.nii.gz - warp1:
.nii,.nii.gz - warp2:
.nii,.nii.gz - premat:
.mat - midmat:
.mat - postmat:
.mat - shiftmap:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
combined_warp |
File |
$(inputs.output).nii.gz, $(inputs.output).nii |
log |
File |
convertwarp.log |
Output Extensions¶
- combined_warp:
.nii,.nii.gz
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