fMRI-Guided TMS: When It's Needed and How It's Used

fMRI is not required for conventional TMS. Standard TMS targets the left dorsolateral prefrontal cortex using scalp measurements — typically measuring from the spot that makes the thumb twitch (the motor threshold location) and moving about 5.5 cm forward. That works without any brain scan, and it is the method most TMS clinics use. An fMRI is only needed when the protocol calls for personalized, connectivity-based targeting — which is the case for SAINT®.

So the honest answer to ‘When is an fMRI needed before TMS?’ is: only when you are pursuing a connectivity-guided protocol like SAINT®. If a clinic offers ‘accelerated TMS’ or a ‘5-day protocol’ without a brain MRI, that is not the fMRI-guided SAINT® protocol. [[BEAM F3 vs fMRI targeting|/learn/beam-f3-vs-fmri-tms]].

In SAINT®, you undergo a structural MRI (a detailed 3D map of your brain's anatomy) and a resting-state functional MRI (fMRI), which measures how different brain regions communicate while you lie still. No injections or dyes are involved. A proprietary algorithm analyzes the fMRI to find the precise spot in the left dorsolateral prefrontal cortex whose activity is most strongly anticorrelated with the subgenual anterior cingulate cortex — a deeper region involved in mood regulation. That spot becomes your personalized target.

Conventional TMS does not use this scan; it targets the DLPFC with scalp measurements alone. The fMRI is what lets SAINT® personalize the target to your brain rather than a population average.

Not necessarily. An fMRI is one component of SAINT®, but SAINT® is a complete system: the FDA-cleared Magnus Neuromodulation System, its proprietary targeting software, the fMRI-guided target, the intermittent theta burst schedule (10 sessions/day for 5 days), and Magnus-trained staff. A clinic could in principle use an fMRI for targeting without delivering the full SAINT® protocol or using the Magnus system.

If a clinic says it uses fMRI but cannot confirm it runs the Magnus Neuromodulation System with SAINT Technology, it is not delivering SAINT®. The 5-check test — Magnus provider locator listing, brain MRI for targeting, Magnus system/software, FDA-cleared 5-day protocol, and adults-only — is the way to tell. [[What is a verified SAINT® provider?|/learn/what-is-a-verified-saint-provider]].

SAINT® coverage is limited and plan-specific. The MRI required for SAINT® may or may not be covered by your plan, and prior authorization is often involved. We do not promise coverage — we verify your benefits for free so you know what your plan covers before you commit. [[Check your insurance benefits — free|/check-insurance-options]] or call 954-827-9793.

Functional magnetic resonance imaging (fMRI) measures brain activity by detecting changes in blood flow. Unlike a structural MRI, which shows anatomy, fMRI shows which brain regions are active and how they communicate. In SAINT®, a resting-state fMRI is used — you simply lie still in the scanner; no task is required.

The 'right' spot for TMS stimulation varies from brain to brain. Conventional TMS targets the left dorsolateral prefrontal cortex using scalp landmarks — a population average that may not be optimal for any individual. fMRI-guided targeting computes your individual target from your brain's functional connectivity, which may improve precision. This is a key differentiator of SAINT®.

Functional connectivity refers to how different brain regions communicate — which areas activate together at rest. SAINT® uses resting-state fMRI to measure functional connectivity between your prefrontal cortex and deeper mood circuits, particularly the subgenual anterior cingulate cortex, a region involved in mood regulation.

Based on your fMRI, a proprietary algorithm selects the stimulation target in the left dorsolateral prefrontal cortex that best connects functionally to the subgenual anterior cingulate cortex. This target is unique to you — it is not a standard landmark. The algorithm was developed at Stanford and is part of the Magnus Neuromodulation System.

Before SAINT® treatment, you undergo a structural and functional MRI. The algorithm analyzes your brain's functional connectivity and selects your individualized target. The coil is then positioned at that target during each of the 50 sessions over five days. This is why an MRI is required and why people who cannot have an MRI are not candidates. Learn more: [[Does SAINT® require an MRI?|/learn/does-saint-tms-require-an-mri]].

Learn more about SAINT\u00ae TMS.

Conventional TMS targets the left dorsolateral prefrontal cortex using scalp measurements from the motor-threshold location — often the '5.5 cm rule' or a similar landmark method. fMRI-guided targeting replaces the ruler with a brain scan and an algorithm that computes your individual target from your functional connectivity. This is the core technical difference between SAINT® and conventional TMS.

Learn more about SAINT\u00ae vs traditional TMS.

The process:

1. 1.You undergo a structural and functional MRI before treatment.
2. 2.The algorithm analyzes your brain's functional connectivity.
3. 3.It selects the target in your prefrontal cortex that best connects to mood circuits.
4. 4.The coil is positioned at your individualized target during each session.