EDDY Quality Control

FSL provides two QC tools for eddy output: eddy_quad for individual subjects and eddy_squad for group-level summaries.

Per-Subject: eddy_quad

eddy_quad generates an HTML/PDF report with motion plots, outlier maps, and summary statistics for a single subject.

eddy_quad "$eddy_dir/${subj}_eddy" \
    -idx "$config_dir/index.txt" \
    -par "$config_dir/acqp.txt" \
    -m "$mask_dir/${subj}_topup_Tmean_brain_mask.nii.gz" \
    -b "$nifti_dir/${subj}_dti.bval" \
    -v

The first argument is the eddy output prefix (without .nii.gz) — the same prefix you passed to eddy's --out flag.

Key Metrics

Metric	Concern Threshold
Average absolute motion	> 2 mm
Average relative motion	> 1 mm
Outlier slices	> 10%

The qc.pdf report also shows motion traces (translation and rotation over volumes) and an outlier map showing which slices in which volumes were flagged. Scattered outliers are normal; clusters of outliers across consecutive volumes indicate a period of severe motion.

Group-Level: eddy_squad

After running eddy_quad for all subjects, eddy_squad produces scatter plots that make it easy to spot outlier subjects across the group:

# Create a list of all eddy_quad output directories
ls -d "$base_dir"/eddy/sub-*/*_eddy.qc > squad_list.txt

# Run eddy_squad
eddy_squad squad_list.txt -o "$base_dir/qc/eddy_squad_report"

The output group_qc.pdf plots each subject as a point for motion and outlier metrics. Subjects that fall far from the cluster are worth inspecting more closely.

Using These Metrics

Subjects exceeding the thresholds above (absolute motion > 2 mm, relative motion > 1 mm, or outlier slices > 10%) should generally be excluded. Define your thresholds before you start processing and report them in your methods section.

References

• Bastiani M, Cottaar M, Fitzgibbon SP, et al. (2019). Automated quality control for within and between studies diffusion MRI data using a non-parametric framework for movement and distortion correction. NeuroImage, 184, 801-812.
• FSL eddy_quad documentation: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddyqc/UsersGuide