The present study aimed to investigate whether magnetoencephalography (MEG) information could result in the detection of subtle anatomical abnormalities at re-review of conventional magnetic resonance imaging (MRI) by a new MEG guided post-image processing technology. Eight paediatric patients with tuberous sclerosis complex (TSC) confirmed by clinical and neuroimaging findings were retrospectively studied. MEG data were recorded using a whole-cortex CTF OMEGA system. Irritable zones were localized using synthetic aperture magnetometry (SAM). A new MEG guided post-image processing technology was employed to identify the "small tubers" found only by SAM. MRI detected 42 tubers for the 8 patients. SAM found 51 irritable zones, and 31 out of the 51 zones were around tubers (31/42, 74%). Among 20 of the 51 zones, which did not have corresponding MRI tubers, we detected 14 subtle lesions in total; 9 of 14 were found in low frequency band (1-35 Hz); 5 of 14 were found in high frequency band (35-60 Hz and 60-120 Hz). SAM appeared to offer more detection of irritable zones and beneficial frequency descriptions. The majority of these irritable zones detected only by SAM were indicated to be small tubers by MEG guided post-image processing technology. This technology might be a powerful tool in the detection of subtle structural abnormalities. © 2007 Elsevier B.V. All rights reserved.