Motion Correction using FLIRT (MCFLIRT)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Intra-modal motion correction for fMRI time series using rigid-body (6-DOF) transformations optimized for fMRI data.
Modality: 4D fMRI NIfTI time series.
Typical Use: Correcting head motion in functional data; motion parameters used as nuisance regressors.
Key Parameters¶
-refvol (reference volume index), -cost (cost function), -plots (output motion parameter plots), -mats (save transformation matrices)
Key Points¶
Default reference is middle volume. Use -plots for motion parameter files (6 columns: 3 rotations + 3 translations). Motion params useful as nuisance regressors.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input 4D timeseries to motion-correct | -in |
output |
string |
Yes | Output filename | -out |
ref_vol |
int |
No | Reference volume number (default is middle volume) | -refvol |
ref_file |
File |
No | External reference image for motion correction | -reffile |
mean_vol |
boolean |
No | Register to mean volume | -meanvol |
cost |
enum |
No | Cost function for optimization | -cost |
dof |
int |
No | Degrees of freedom (default 6) | -dof |
init |
File |
No | Initial transformation matrix | -init |
interpolation |
enum |
No | Final interpolation method | |
save_mats |
boolean |
No | Save transformation matrices | -mats |
save_plots |
boolean |
No | Save motion parameter plots | -plots |
save_rms |
boolean |
No | Save RMS displacement parameters | -rmsabs |
stats |
boolean |
No | Produce variance and std dev images | -stats |
stages |
int |
No | Number of search stages (default 3) | -stages |
bins |
int |
No | Number of histogram bins | -bins |
smooth |
double |
No | Smoothing for cost function (FWHM in mm) | -smooth |
scaling |
double |
No | Scaling factor | -scaling |
rotation |
int |
No | Rotation tolerance scaling factor | -rotation |
edge |
boolean |
No | Use contour for coarse search | -edge |
gdt |
boolean |
No | Use gradient for coarse search | -gdt |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - ref_file:
.nii,.nii.gz - init:
.mat
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
motion_corrected |
File |
$(inputs.output).nii.gz, $(inputs.output).nii |
motion_parameters |
File |
$(inputs.output).par |
mean_image |
File |
$(inputs.output)_mean_reg.nii.gz, $(inputs.output)_mean_reg.nii |
variance_image |
File |
$(inputs.output)_variance.nii.gz, $(inputs.output)_variance.nii |
std_image |
File |
$(inputs.output)_sigma.nii.gz, $(inputs.output)_sigma.nii |
transformation_matrices |
File[] |
$(inputs.output).mat/MAT_* |
rms_files |
File[] |
$(inputs.output)_abs.rms, $(inputs.output)_rel.rms, $(inputs.output)_abs_mean.rms, $(inputs.output)_rel_mean.rms |
log |
File |
mcflirt.log |
Output Extensions¶
- motion_corrected:
.nii,.nii.gz - motion_parameters:
.par - mean_image:
.nii,.nii.gz - variance_image:
.nii,.nii.gz - std_image:
.nii,.nii.gz - transformation_matrices:
.mat - rms_files:
.rms
Enum Options¶
cost: mutualinfo, corratio, normcorr, normmi, leastsquares
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 > Motion Correction