FMRIB's Utility for Geometrically Unwarping EPIs (FUGUE)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Corrects geometric distortions in EPI images caused by magnetic field inhomogeneity using acquired fieldmap data.
Modality: 3D/4D EPI NIfTI plus preprocessed fieldmap (in rad/s).
Typical Use: Distortion correction when fieldmap data is available.
Key Parameters¶
--loadfmap (fieldmap), --dwell (echo spacing in seconds), --unwarpdir (phase-encode direction: x/y/z/-x/-y/-z)
Key Points¶
Requires preprocessed fieldmap (e.g., from fsl_prepare_fieldmap). Dwell time and unwarp direction must match acquisition parameters.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | EPI image to unwarp | -i |
phasemap |
File |
No | Unwrapped phase image (or two-echo phase difference) | -p |
loadfmap |
File |
No | Pre-calculated fieldmap in rad/s | --loadfmap= |
loadshift |
File |
No | Pre-calculated voxel shift map | --loadshift= |
unwarp |
string |
No | Output unwarped image filename | -u |
warp |
string |
No | Output forward warped image filename | -w |
savefmap |
string |
No | Save fieldmap in rad/s | --savefmap= |
saveshift |
string |
No | Save voxel shift map | --saveshift= |
dwell |
double |
No | EPI dwell time / echo spacing (seconds) | --dwell= |
asym |
double |
No | Asymmetry time (echo time difference) in ms | --asym= |
unwarpdir |
enum |
No | Phase-encode / unwarp direction | --unwarpdir= |
mask |
File |
No | Brain mask image | --mask= |
smooth2 |
double |
No | 2D Gaussian smoothing sigma | -s |
smooth3 |
double |
No | 3D Gaussian smoothing sigma | --smooth3= |
median |
boolean |
No | Apply 2D median filter | -m |
poly |
int |
No | 3D polynomial fitting degree | --poly= |
fourier |
int |
No | 3D sinusoidal fitting degree | --fourier= |
despike |
boolean |
No | Apply despiking filter | --despike |
phaseconj |
boolean |
No | Use phase conjugate method | --phaseconj |
nokspace |
boolean |
No | Use image-space forward warping | --nokspace |
icorr |
boolean |
No | Apply intensity correction | --icorr |
icorronly |
boolean |
No | Only apply intensity correction (no unwarp) | --icorronly |
noextend |
boolean |
No | Do not extend shifted voxels outside FOV | --noextend |
verbose |
boolean |
No | Verbose output | -v |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - phasemap:
.nii,.nii.gz - loadfmap:
.nii,.nii.gz - loadshift:
.nii,.nii.gz - mask:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
unwarped_image |
File |
$(inputs.unwarp).nii.gz, $(inputs.unwarp).nii |
warped_image |
File |
$(inputs.warp).nii.gz, $(inputs.warp).nii |
fieldmap_output |
File |
$(inputs.savefmap).nii.gz, $(inputs.savefmap).nii |
shiftmap_output |
File |
$(inputs.saveshift).nii.gz, $(inputs.saveshift).nii |
log |
File |
fugue.log |
Output Extensions¶
- unwarped_image:
.nii,.nii.gz - warped_image:
.nii,.nii.gz - fieldmap_output:
.nii,.nii.gz - shiftmap_output:
.nii,.nii.gz
Enum Options¶
unwarpdir: x, y, z, x-, y-, z-
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