Frozen Site-Probe Accuracy Is Not a Standalone Harmonization Score: An Audit of Evaluation Practice for Multi-Site MRI

Image-level MRI harmonization is often evaluated with a frozen site probe, a site classifier trained on raw scans and applied unchanged to harmonized ones: a drop in its accuracy is read as removal of site effects. We audit this practice on ABIDE I (1,112 T1-weighted scans, 17 sites) with ten output sets from seven harmonization methods and controls for chance, head shape, intensity, preprocessing and target alignment. We find that this verdict depends on how the probe is trained, even among probes that classify raw scans well: across random seeds, its balanced accuracy on the same CycleGAN outputs ranges from 0.13 to 0.59 (chance: 0.06). Low frozen-probe accuracy can also arise without harmonization: a Gaussian blur, which increases the intensity distance to the target site, lowers this accuracy to chance. Moreover, where the frozen probe fails, probes trained on the harmonized scans still recover the site, even from intensity histograms alone: on HACA3 outputs, the frozen probe scores 0.25, a probe trained on those outputs 0.75, and one using only their intensity histograms 0.71. Low frozen-probe accuracy therefore does not show that site information has been removed. We recommend reporting several probes trained to convergence, probes trained on harmonized scans, and target alignment.