FSL Apply Topup Distortion Correction¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Applies the susceptibility-induced off-resonance field estimated by topup to correct distortions in EPI images.
Modality: 3D or 4D EPI NIfTI plus topup output (movpar.txt and fieldcoef files).
Typical Use: Applying distortion correction to fMRI or DWI data using pre-computed topup results.
Key Parameters¶
--imain (input images), --topup (topup output prefix), --datain (acquisition parameters), --inindex (index into datain), --out (output), --method (jac or lsr)
Key Points¶
Use after running topup. --method=jac applies Jacobian modulation (recommended for fMRI). Can apply to multiple images at once.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input image(s) to correct | --imain= |
topup_fieldcoef |
File |
Yes | Topup field coefficients file (_fieldcoef.nii.gz from topup) | |
topup_movpar |
File |
Yes | Topup movement parameters file (_movpar.txt from topup) | |
encoding_file |
File |
Yes | Acquisition parameters file (same as used for topup) | --datain= |
inindex |
string |
Yes | Comma-separated indices into encoding_file for each input image | --inindex= |
output |
string |
Yes | Output basename for corrected images | --out= |
method |
enum |
No | Resampling method (jac=Jacobian, lsr=least-squares) | --method= |
interp |
enum |
No | Interpolation method (only for method=jac) | --interp= |
datatype |
enum |
No | Force output data type | --datatype= |
verbose |
boolean |
No | Verbose output | -v |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - topup_fieldcoef:
.nii,.nii.gz - topup_movpar:
.txt - encoding_file:
.txt
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
corrected_images |
File |
$(inputs.output).nii.gz, $(inputs.output).nii |
log |
File |
applytopup.log |
err_log |
File |
applytopup.err.log |
Output Extensions¶
- corrected_images:
.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¶
- Functional MRI > FSL > Distortion Correction