BEAM F3 vs fMRI-Guided TMS: How Clinics Aim the Magnet
BEAM F3 estimates where a brain region usually sits from three head measurements. fMRI-guided SAINT® finds your own target from a brain scan. The difference matters because the connectivity target is different for each person, and only the scan-based, FDA-cleared approach is SAINT®.
Key takeaways
- BEAM F3 finds a standard scalp spot (the F3 position) from head measurements — a population stand-in, not a personal target.
- fMRI-guided SAINT® uses your own brain’s functional connectivity to pick where to stimulate.
- Head measurements can’t see brain function, so they can’t reliably match a scan-based target.
- SAINT® requires the MRI target, FDA-cleared software, and the Magnus Medical system — only from verified providers.
- The 79% remission result comes from MRI-guided SAINT®; it doesn’t transfer to a different targeting method.
What is the BEAM F3 method?
The BEAM F3 method is a quick way to find a standard scalp spot — the F3 EEG position — from three head measurements, used as a stand-in for the left dorsolateral prefrontal cortex. It was developed to make standard TMS easier to set up without neuronavigation equipment.
The “F3” in BEAM F3 refers to the F3 electrode position — a standard landmark on the scalp that approximates the left dorsolateral prefrontal cortex, the area most TMS protocols target for depression. Measuring the head and landing on that average coordinate is fast and needs no scanner, which is why many standard-TMS clinics use it.
But “average coordinate” is the key phrase: BEAM F3 tells a clinic where that region usually sits, not where it sits in you, and nothing about how it communicates with the deeper mood circuits TMS is meant to influence.
What is fMRI-guided (connectivity-guided) TMS?
A resting-state brain MRI shows which part of your prefrontal cortex works in sync or in opposition to a deeper mood-related area (the subgenual cingulate). SAINT® software uses that connectivity data to pick the exact spot to stimulate for you — a target that is individual, not an average.
Before SAINT® treatment, you have a resting-state functional MRI. Software analyzes the functional connectivity — how brain regions talk to each other — and selects the exact spot on your prefrontal cortex that has the strongest link to the subgenual cingulate, a deeper area involved in mood. That spot is unique to you and becomes the target for all 50 sessions.
Two ways to aim the magnet
Head measurements
\u2192 one average spot on an average head.
Brain MRI (fMRI)
\u2192 your spot, from your own connectivity.
Both approaches end with a coil on your head. The difference is how that coordinate is chosen. Does SAINT® require an MRI? explains why the scan is required, not optional.
Can head measurements find the same target as an fMRI?
No. Head measurements estimate where the region usually sits on an average head; they can’t see brain function. The connectivity target is different for each person, so a scalp estimate and a scan-based target don’t reliably match. That is why SAINT® requires the scan.
A scalp position is a reasonable starting point, but the part of the prefrontal cortex that best connects to your subgenual cingulate varies from person to person. Measuring the outside of your head can’t reveal that internal connectivity, so a head-measurement target and a scan-based target can land in different places.
Is BEAM F3 the same as SAINT?
No. SAINT® requires a personalized MRI target, FDA-cleared targeting software, and the Magnus Medical system — delivered only by providers on Magnus Medical’s locator. A clinic that says head measurements use “the same measurements and algorithm” as an fMRI is not describing SAINT®.
SAINT\u00ae (Stanford Accelerated Intelligent Neuromodulation Therapy) is one specific, FDA-cleared protocol: the Magnus Neuromodulation System, its own targeting software, and delivery only by providers listed on Magnus Medical’s provider locator. Other clinics may use an MRI to aim TMS without offering SAINT\u00ae \u2014 that is a different treatment. See our SAINT® vs lower-cost “accelerated TMS” comparison.
Which is better for treatment-resistant depression?
The SAINT® controlled trial (79% remission) used MRI-guided targeting; those results don’t transfer to programs that target differently. Ask your doctor which method a clinic uses and what results it has. Individual results vary.
We make no head-to-head superiority claim. What we can say factually: in the 2022 double-blind, sham-controlled randomized trial, 79% of the active-treatment group reached remission (Cole et al., Am J Psychiatry 2022;179(2):132–141), and that trial used MRI-guided targeting. Results from those trials can’t be assumed for a program that targets differently. Ask your doctor which method a clinic uses and what results it has published.
Understanding SAINT® TMS: How It Works & What to Expect
SAINT® is an FDA-cleared treatment for adults with major depressive disorder who have not improved on antidepressants in the current episode. These videos explain how it works and how it differs from conventional TMS.
SAINT® is an FDA-cleared, fMRI-guided form of TMS developed at Stanford. Most patients complete treatment in one week — not the six weeks standard TMS requires.
Follow a real patient through the five-day SAINT® treatment week
Is SAINT® TMS Right for You?
Tried antidepressants without enough relief? SAINT® TMS is an FDA-cleared, fMRI-guided treatment for adults with major depressive disorder who have not improved enough with antidepressant medication.
SAINT® uses a personalized brain target and delivers treatment over five consecutive days. It differs from standard TMS in its targeting approach, treatment schedule, and research background. In a small randomized trial, 11 of 14 people receiving active treatment reached remission at the four-week assessment, compared with 2 of 15 receiving sham treatment. Results vary, and a five-day treatment course does not guarantee remission in five days.
How SAINT® Works and How It Differs From Conventional TMS
SAINT® is an FDA-cleared treatment for adults with major depressive disorder who have not improved on antidepressants in the current episode. This video explains how it works, and how it differs from conventional TMS.
Conventional TMS usually means about 30 visits over 6 to 9 weeks. SAINT is five visits over five days.
What makes it different: SAINT is the only FDA-cleared depression treatment that uses an fMRI scan to personalize the stimulation target to your individual brain. A 45-minute scan maps your brain and identifies the specific circuit linked to depression. Treatment is then delivered as ten 10-minute sessions per day, with 50-minute breaks between them, across five consecutive days.
In clinical trials, 79% of participants reached remission, with an average of 2.6 days to remission. SAINT is generally well tolerated; the most common side effects reported were mild headache and temporary scalp discomfort at the treatment site.
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Sources: Cole et al., American Journal of Psychiatry 2020;177:716-726 and 2022;179(2):132-141. magnusmedical.com/depression-therapy. PubMed 34711062. FDA 510(k) K220177.
Insurance coverage for SAINT is currently limited and varies by plan. Individual results may vary. This video is educational and is not medical advice. Talk to a qualified clinician about whether SAINT is appropriate for you. If you are in crisis, call or text 988.
Frequently Asked Questions
What is the BEAM F3 method?
The BEAM F3 method is a quick way to find a standard scalp spot — the F3 EEG position — from three head measurements, used as a stand-in for the left dorsolateral prefrontal cortex. It was developed to make standard TMS easier to set up without neuronavigation equipment.
What is fMRI-guided (connectivity-guided) TMS?
A resting-state brain MRI shows which part of your prefrontal cortex works in sync or in opposition to a deeper mood-related area (the subgenual cingulate). SAINT® software uses that connectivity data to pick the exact spot to stimulate for you — a target that is individual, not an average.
Can head measurements find the same target as an fMRI?
No. Head measurements estimate where the region usually sits on an average head; they can’t see brain function. The connectivity target is different for each person, so a scalp estimate and a scan-based target don’t reliably match. That is why SAINT® requires the scan.
Is BEAM F3 the same as SAINT?
No. SAINT® requires a personalized MRI target, FDA-cleared targeting software, and the Magnus Medical system — delivered only by providers on Magnus Medical’s locator. A clinic that says head measurements use “the same measurements and algorithm” as an fMRI is not describing SAINT®.
Which is better for treatment-resistant depression?
The SAINT® controlled trial (79% remission) used MRI-guided targeting; those results don’t transfer to programs that target differently. Ask your doctor which method a clinic uses and what results it has. Individual results vary.
Cited Research
Important Safety Information
SAINT® is not for everyone. It is contraindicated for people with non-removable magnetic-sensitive metal in or near the head, certain implanted devices, or increased intracranial pressure. Possible side effects include headache, fatigue, scalp discomfort and anxiety; TMS carries a small risk of seizure. If you are in crisis, call or text 988.
SAINT® is delivered only by verified providers on the Magnus Medical system. Programs described as SAINT “alternatives”, “equivalents” or “fMRI-guided accelerated TMS” are not SAINT®, are not affiliated with us, and SAINT® results do not apply to them. Read our SAINT® disclaimer.
See if SAINT® is a fit, free
Speak with our clinical team. A free consultation is the best way to get answers specific to your situation.
SAINT® is a registered trademark of Stanford University, exclusively licensed to Magnus Medical, Inc. Neuro Wellness TMS Centers of America does not name or endorse any competitor. Individual results vary. No outcome is guaranteed. Coverage varies by plan.
Related Patient Education
SAINT® Accelerated TMS
The 5-day, fMRI-guided protocol offered at our clinic
What Is TMS Therapy?
How transcranial magnetic stimulation works for depression
Cost & Insurance
Benefits verification, CPT codes, and self-pay options
Am I a Candidate?
Screening factors for TMS and SAINT® eligibility
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Contact & Directions
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Does SAINT® Require an MRI?
Why the brain scan is part of the SAINT® protocol
fMRI-Guided TMS for Depression
How personalized targeting works in SAINT®
What Is a Verified SAINT® Provider?
How to confirm a clinic on Magnus Medical’s locator
SAINT® vs Lower-Cost Accelerated TMS
What a copied 5-day schedule is and isn’t