Finding the Target: Beam F3, Neuronavigation and fMRI-Guided TMS

TMS for depression aims at the left dorsolateral prefrontal cortex (DLPFC), and there are four main ways to find it: the 5-cm rule, the Beam F3 scalp method, MRI-based neuronavigation, and functional-connectivity (fMRI) targeting. The simple 5-cm rule often misses the intended region, but the best head-to-head trials show that a better scalp method (Beam F3) performs about as well as a simpler one, and that connectivity-guided targeting has produced mixed results: one large trial found no benefit, while newer trials of accelerated protocols found faster or larger improvement.

In short, precision probably matters more than it once seemed, but the size of the advantage, and which patients gain from it, are still being worked out.

Why targeting is a problem at all

The DLPFC is not a visible landmark. It cannot be felt through the scalp, and its position relative to the skull varies from person to person. A TMS coil stimulates a small patch of cortex directly beneath it, and one influential hypothesis is that the antidepressant effect depends on reaching the part of the DLPFC that is functionally linked to deeper mood circuits. The neuroscience of TMS explains that network idea in more detail.

Every targeting method is an attempt to answer one question: where on this person's head should the coil sit? The methods differ in how much information they use to answer it.

Method 1: the 5-cm rule

The oldest approach starts at the motor cortex "hand spot", the place where a pulse makes the fingers twitch, and moves the coil 5 cm forward. It is fast, needs no equipment beyond a ruler, and uses a location the team has to find anyway for motor threshold dosing.

Its weakness was documented early. In a 2001 neuronavigation check of 22 people, the 5-cm position landed on the intended DLPFC region (Brodmann area 9) in only 7; in the other 15 the coil center sat more dorsally (higher on the head), for example over premotor cortex. A fixed distance ignores differences in head size and brain anatomy.

Method 2: Beam F3

The Beam F3 method, published in 2009, locates the "F3" electrode position from the international EEG 10-20 system, which lies over the left DLPFC, using three simple head measurements instead of the full 10-20 measurement. It scales with head size, which the 5-cm rule does not. Its original validation was small: 10 healthy adults, with the authors noting that further study might be warranted.

Beam F3 is now built into ordinary clinical equipment. NeuroStar, for example, ships separate single-use head-strap packs for the standard 5-cm method and for the Beam F3 method.

The obvious question is whether the more anatomical method actually helps patients. A 2023 randomized trial (Trapp et al.) put that to the test with 105 patients assigned to Beam F3 or a 5.5-cm rule. There was no significant difference on any outcome, and remission rates were nearly identical: 22% vs 21% on the PHQ-9 and 20% vs 19% on the MADRS (5.5 cm vs F3). The authors concluded the two methods are in clinical equipoise for people with a head circumference of 60 cm or less.

Method 3: MRI-guided neuronavigation

Neuronavigation uses the patient's own structural MRI scan. A tracking camera follows the head and the coil in real time and shows the coil's position on the brain image, so the team can aim at a chosen anatomical point and return to it every session. Some cleared systems, such as Magstim's Horizon "with Navigation" (cleared 2019), include this capability.

The first randomized test (Fitzgerald et al., 2009) compared the 5-cm rule (n=27) with MRI-navigated targeting of the junction of Brodmann areas 46 and 9 (n=24) in treatment-resistant depression. MADRS outcomes were better with navigation at 4 weeks, though the authors stressed that larger samples were needed.

Navigation is designed to make placement more accurate and repeatable, but anatomy alone does not say which part of the DLPFC is the best target. That question led to the fourth method.

Method 4: functional-connectivity (fMRI) targeting

In 2012, Fox and colleagues analyzed resting-state fMRI from 98 healthy people and found that DLPFC sites with better reported antidepressant efficacy were more strongly anticorrelated with the subgenual cingulate cortex (sgACC), a deep region involved in mood. The optimum coordinates lay in Brodmann area 46. This was a retrospective connectivity analysis, not a treatment trial, but it gave a testable hypothesis: aim each patient's coil at the DLPFC spot most anticorrelated with their own sgACC.

SAINT (Stanford Neuromodulation Therapy) is built on this idea. Its FDA-cleared system uses software to choose an individual target from structural and functional MRI, and the coil is placed by neuronavigation. FDA's summary defines "SAINT Technology" as the combination of that individualized target with an accelerated five-day protocol, which means the targeting and the dosing were tested together rather than separately. The SAINT guide covers its trial results.

Does precision targeting improve outcomes? The head-to-head trials

Two patterns stand out. First, the largest of these trials, BRIGhTMIND, was negative: connectivity-guided iTBS (n=128) did no better than navigated standard rTMS (n=127), with an adjusted difference of about one-third of a point on the depression scale. But it compared two different stimulation protocols as well as two targets, and its comparison arm was already MRI-navigated, so it was a demanding test.

Second, the positive results come from accelerated protocols. In Li 2026, the advantage over the 5-cm rule was clear at week 2 (8.79 percentage points greater reduction on the HAM-D-17) but had faded by week 12. In Taylor 2026, the authors estimated a "number needed to scan" of 5, meaning about five people would need an MRI for one to gain the extra benefit; the paper also carries two published correction notices. A 2026 meta-analysis of accelerated iTBS similarly found larger effects in protocols that used functional-connectivity neuronavigation, though fewer than half of the included trials were at low risk of bias.

A reasonable reading is that precise targeting may speed or strengthen response in accelerated protocols, where a lot of stimulation is concentrated into a short time, while for standard daily courses the extra benefit over a good scalp method has not been demonstrated. Accelerated iTBS also worked without any neuronavigation in a 2025 sham-controlled trial of 100 patients (response 52% vs 22%), so navigation is not a prerequisite for benefit.

Targeting and dose are linked

Choosing a spot is only half of the problem. The coil also has to deliver enough energy to that spot, and intensity is usually set from the motor threshold, measured over a different part of the brain. SAINT handles this by adjusting its intensity for the depth of the prefrontal target relative to the motor cortex. The motor threshold guide explains why scalp-to-cortex distance matters.

Practical trade-offs

Cost and coverage follow the complexity. Medicare's hospital outpatient rates, for example, include a separate code for SAINT's personalized target development, priced at $950.50 in 2026, on top of treatment-day payments. Standard TMS billing (CPT 90867) already includes "cortical mapping" as part of the initial session. Coverage for navigation-dependent protocols varies by plan; the payer guides such as Cigna's TMS criteria cover what is known.

Questions worth asking a TMS team

• Which targeting method will be used, and why that one for me?
• If a scalp method is used, is it the 5-cm rule or Beam F3, and how is the position recorded so it is the same each session?
• If an MRI or fMRI is involved, who reads it, and what happens if the scan shows something unexpected?
• Is the targeting method part of an FDA-cleared protocol, or an added step?
• Who checks coil position during treatment, and is the physician involved in mapping? (See who delivers TMS.)

What the first mapping session feels like from the patient's side is described in your first TMS session and mapping. For how targeting fits with device choice, see TMS devices compared; for whether imaging can predict who will respond, see predictors and biomarkers.

More on the full range of TMS approaches is in the TMS guide, and the TMS therapy page covers TMS as part of psychiatric care.

Frequently asked questions

Do I need an MRI before TMS?

Not for standard TMS, which can be targeted with a scalp method such as the 5-cm rule or Beam F3. An MRI is required for neuronavigated or connectivity-targeted protocols such as SAINT.

Is the 5-cm rule outdated?

In one imaging check it missed the intended region in 15 of 22 people, and Beam F3 was designed to scale with head measurements. A 2023 randomized trial found similar outcomes with Beam F3 and a 5.5-cm rule, so a scalp method used carefully remains acceptable.

What is the sgACC and why does it matter for targeting?

The subgenual anterior cingulate cortex is a deep brain region involved in mood. In a 2012 retrospective analysis, DLPFC sites whose activity ran opposite to it were the ones with better reported outcomes, which is the basis for connectivity-guided targeting. Trials testing the idea have had mixed results.

Does neuronavigation make TMS more comfortable?

Not directly. It is a way of placing the coil accurately and consistently; it does not change the sensation of the pulses.

Can my target change during a course?

The goal is to treat the same spot every session. Teams record the position (by measurements, head-strap settings or navigation software) so that it can be reproduced.

Sources

1. Transcranial magnetic stimulation in therapy studies: examination of the reliability of 'standard' coil positioning by neuronavigation. Biological Psychiatry, 2001. pubmed.ncbi.nlm.nih.gov
2. An efficient and accurate new method for locating the F3 position for prefrontal TMS applications. Brain Stimulation, 2009. pubmed.ncbi.nlm.nih.gov
3. 510(k) Summary K231926 – NeuroStar Advanced Therapy System. U.S. FDA, 2024. accessdata.fda.gov
4. A randomized trial comparing beam F3 and 5.5 cm targeting in rTMS treatment of depression demonstrates similar effectiveness. Brain Stimulation, 2023. pubmed.ncbi.nlm.nih.gov
5. A randomized trial of rTMS targeted with MRI based neuro-navigation in treatment-resistant depression. Neuropsychopharmacology, 2009. pubmed.ncbi.nlm.nih.gov
6. Efficacy of transcranial magnetic stimulation targets for depression is related to intrinsic functional connectivity with the subgenual cingulate. Biological Psychiatry, 2012. pubmed.ncbi.nlm.nih.gov
7. Connectivity-guided intermittent theta burst versus repetitive transcranial magnetic stimulation for treatment-resistant depression: a randomized controlled trial. Nature Medicine, 2024. pubmed.ncbi.nlm.nih.gov
8. Individualized Connectivity-Guided Versus Conventional Targeting of Accelerated Theta-Burst Stimulation in Depression: A Randomized, Double-Blind, Parallel-Design Trial. American Journal of Psychiatry, 2026. pubmed.ncbi.nlm.nih.gov
9. Connectivity- vs Scalp-Based Targeting of Accelerated Transcranial Magnetic Stimulation for Depression: A Randomized Clinical Trial. JAMA Psychiatry, 2026. jamanetwork.com
10. 510(k) Summary K220177 – Magnus Neuromodulation System with SAINT Technology. U.S. FDA, 2022. accessdata.fda.gov
11. Stanford Accelerated Intelligent Neuromodulation Therapy for Treatment-Resistant Depression. American Journal of Psychiatry, 2020. pubmed.ncbi.nlm.nih.gov
12. 510(k) Summary K243869 – Magstim Horizon 3.0 (with earlier Horizon clearances). U.S. FDA, 2025. accessdata.fda.gov
13. Accelerated intermittent theta-burst stimulation for major depressive episodes: systematic review and dose-response meta-analysis. Brain Stimulation, 2026. pubmed.ncbi.nlm.nih.gov
14. Accelerated Theta-Burst Stimulation for Treatment-Resistant Depression: A Randomized Clinical Trial. JAMA Psychiatry, 2025. pmc.ncbi.nlm.nih.gov
15. Addendum B – OPPS Payment by HCPCS Code for CY 2026 (October 2026). CMS, 2026. cms.gov
16. Billing and Coding: Transcranial Magnetic Stimulation (A57528). CMS, 2026. cms.gov

Educational information, not medical advice. Whether TMS or any treatment fits you is a decision to make with a psychiatrist who knows your history.