Note

This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the user guide for the big picture.

brainprep.interfaces.qualcheck.vbm_metrics

brainprep.interfaces.qualcheck.vbm_metrics(output_dir, ncr_threshold=4.5, iqr_threshold=4.5, dryrun=False)

CAT12 VBM quality control.

The following quality metrics are considered:

• Image Correlation Ratio (ICR) - Measures how well the subject’s image aligns with a reference template. High ICR suggests good registration quality.

• Noise to Contrast Ratio (NCR) - Assesses image clarity by comparing noise levels to tissue contrast. Lower NCR may indicate poor image quality.

• Image Quality Rating (IQR) - A composite score summarizing overall scan quality. Combines multiple metrics like noise, resolution, and bias field. Higher IQR = better quality.

Parse these metrics and applies the quality control described in [1].

Parameters:

output_dirDirectory

Working directory containing the outputs.

ncr_thresholdfloat

Quality control threshold on the NCR scores. Default 4.5.

iqr_thresholdfloat

Quality control threshold on the IQR scores. Default 4.5.

dryrunbool

If True, skip actual computation and file writing. Default False.

Returns:

group_stats_fileFile

A TSV file containing quality metrics. The table includes the columns participant_id, session, run, and ICR, NCR, IQR, as well as a binary qc column indicating the quality control result.

Notes

A qc column is added to the output table. It contains a binary flag indicating whether the NCR and ICR scores do not exceed input thresholds: qc = 1 if NCR < ncr_threshold & ICR < icr_threshold, otherwise qc = 0.

References

[1]

Benoit Dufumier, Antoine Grigis, Julie Victor, Corentin Ambroise, Vincent Frouin, and Edouard Duchesnay. OpenBHB: a large-scale multi-site brain MRI data-set for age prediction and debiasing. Neuroimage, 263(119637):119637, November 2022.