FSL Eddy Current and Motion Correction (eddy)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Corrects eddy current-induced distortions and subject movement in diffusion MRI data using a Gaussian process model.
Modality: 4D diffusion-weighted NIfTI with b-values (.bval), b-vectors (.bvec), acquisition parameters, and index files.
Typical Use: Primary preprocessing step for diffusion MRI after topup distortion correction.
Key Parameters¶
--imain (input DWI), --bvals, --bvecs, --acqp (acquisition params), --index (volume indices), --topup (topup output), --out (output)
Key Points¶
Should follow topup if available. Outputs rotated bvecs to account for motion. Use --repol for outlier replacement. GPU version (eddy_cuda) much faster.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input DWI image | --imain= |
bvals |
File |
Yes | b-values file | --bvals= |
bvecs |
File |
Yes | b-vectors file | --bvecs= |
acqp |
File |
Yes | Acquisition parameters file | --acqp= |
index |
File |
Yes | Index file mapping volumes to acquisition parameters | --index= |
mask |
File |
Yes | Brain mask | --mask= |
output |
string |
Yes | Output basename | --out= |
topup |
string |
No | Topup results basename | --topup= |
repol |
boolean |
No | Detect and replace outlier slices | --repol |
slm |
string |
No | Second level model (none/linear/quadratic) | --slm= |
niter |
int |
No | Number of iterations | --niter= |
fwhm |
string |
No | FWHM for conditioning regularisation (comma-separated) | --fwhm= |
flm |
string |
No | First level EC model (movement/linear/quadratic/cubic) | --flm= |
interp |
string |
No | Interpolation model (spline/trilinear) | --interp= |
dont_sep_offs_move |
boolean |
No | Do not separate field offset from subject movement | --dont_sep_offs_move |
nvoxhp |
int |
No | Number of voxels for hyperparameter estimation (default 1000) | --nvoxhp= |
data_is_shelled |
boolean |
No | Assume data is shelled (skip check) | --data_is_shelled |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - bvals:
.bval - bvecs:
.bvec - acqp:
.txt - index:
.txt - mask:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
corrected_image |
File |
$(inputs.output).nii.gz, $(inputs.output).nii |
rotated_bvecs |
File |
$(inputs.output).eddy_rotated_bvecs |
parameters |
File |
$(inputs.output).eddy_parameters |
log |
File |
eddy.log |
Output Extensions¶
- corrected_image:
.nii,.nii.gz - rotated_bvecs:
.eddy_rotated_bvecs - parameters:
.eddy_parameters
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¶
- Diffusion MRI > FSL > Preprocessing