Mapping the Minds of Meditators:
Exploring the Neural Substrates of Mindful Awareness
Brigham & Women's Hospital, Harvard Medical School, March 2012
This study, part of Mapping the Minds of Meditators at Harvard, focused on different restful states and was co-designed by Shinzen Young and neuroscientist David Vago.

With my daughter Gurushabd and Shinzen in front of the Functional Neuroimaging Laboratory and meditation hall, formerly used by Herbert Benson when he was studying the relaxation response.
Neuroscientists associate a "restful state" with the wandering thoughts of the "monkey mind" and the default network. When a person is not actively engaged in a task, the brain's default mode becomes active, leading to a wandering mind. However, Shinzen Young uses the term "restful state" differently, so the study was designed in part to reflect how Shinzen uses this term.
In the study, participants who were selected for the fMRI started by getting an anatomical scan of their brain. My brain scan is shown below.
The meditators underwent fMRI scans with different contrasts. They spent 5 minutes using Shinzen's Do Nothing technique, which is typically considered a "restful state" equivalent to the wandering mind, and then alternating and contrasting that with focusing on somatic rest, visual rest, auditory rest, and all rest (if available) for 5 minutes each, with the sequence repeating.
As the first participant to undergo the fMRI, my experience yielded unexpected results. The neuroscientists anticipated that my "monkey mind" during the Do Nothing technique would contrast with different types of intentionally focused rest. However, while I was in the scanner, partly because I was wedged in and instructed to relax and Do Nothing, my "monkey mind" quieted down and disappeared, resulting in insufficient contrast for the data they hoped to collect.

Fresh out of the fMRI, still at rest, Alpha run.

When I came out of the scanner, Dave asked me what had happened because they didn't get a sufficient contrast state.
They didn't have a contrast for my 2-1/2 hours in the scanner, and couldn't use the data. I was like, "Wait a minute. You brought me in as an adept meditator, and I gave you how your instructions play out for an experienced meditator, and now you're telling me you can't use it because there isn't a sufficient contrast?" And they said, "Yeah, we can't use it." So then the instruction to the other meditators became, "If you go in there and this happens, we want you to fabricate mental talk as that contrast."
After my first run, Shinzen said, "Well, of course. You'll get this if you stick an experienced meditator in the fMRI." But I wonder if Shinzen thought of that before he and Dave set the study's parameters. Certainly, the neuroscientists didn't think of that; they had no clue, which is one of the points of bringing the contemplatives and the scientists together to discuss this.
They again asked me to participate in the fMRI study as the final meditator. I joked that I was the study's Alpha and Omega, the only meditator to go in twice. This time, they said, "Har-Prakash, if you don't have mental talk naturally coming up when you're not doing anything during Do Nothing, we want you to make it up." So I said, "Alright, I can do that, but isn't that going to be different? Now you have volition; you have an intention and will to create something instead of just happening on its own from the unconscious coming out and wandering around." They said, "It doesn't matter; we want you to do it anyway." They didn't think it would be a factor.

Shinzen is ready to experiment with his meditation students and big magnets.
In the fMRI, for the second time around, I had to fabricate thoughts because they weren't spontaneously arising. After five minutes, I would intentionally focus on the mental image rest state they wanted, then intentionally focus on mental talk rest, then back to fabricating thoughts, then intentionally focus on emotional body rest, then fabricating thoughts, and repeat this sequence in five-minute intervals. But the longer I'm in there, the more effort it takes to fabricate thoughts for their contrast. I want to let go because wedging my physical body in so it is immobile and telling me to relax is inclining my system to let go completely.
I'm efforting when I fabricate talk. "Okay, so think about the past! Think about the future! Evaluate now!" I'm prompting myself through the default mode categories because I know what they are. The woman assisting with the fMRI was really cute, so at some point, I thought, "Okay, fantasy. Let me try running a sexual fantasy with the image of the fMRI woman helping me." I started going in that direction and couldn't continue it. As I began fantasizing about this woman, I spontaneously switched directions and sent her loving kindness and compassion.
After the study, I told Shinzen about it, and he said, "Yeah, that's the wisdom function. The compassion got turned on; it just happens."
After I came out of 2-1/2 hours of round two, Dave said, "What happened in there?" I'm like, "Oh, fuck. What now?! I did what you asked!" He said, "We came close to pulling you out." I said, "Why?" Dave said, "Because of your physiological readings," because they hooked me up to monitor the heartbeat, the pulse, and the breath. And he said, "Those markers were right on the edge of being too high."

Getting my bearings post-fMRI.
So I said, "Oh, that's interesting. When did that happen?" And Dave said, "During the contrast 'restful state' when you were Doing Nothing." And I said, "You mean when I was fabricating and actively making stuff up?" And he said, "Yes." I said, "Well, that's because everything in my whole sensory system wanted to let go into the real Do Nothing, and I was almost sweating trying to fabricate for you to give you a contrast state. My perceptual and nervous systems wanted to let go and completely dissolve into zero. That's where it was going, so I had to do two things: keep my sensory system from dissolving into zero, and on top of that, I had to fabricate and actively work against completely letting go. 'Okay, go to the past! Go to the future.' Unlike the spontaneous monkey mind, I had to work." They didn't anticipate this kind of thing.
Something else significant happened to a friend of mine and me: there were occasions when absolute rest dissolved into absolute cessation. In other words, there was a true letting go, and the whole sensory system, including pure awareness, dissolved into nirodha, or zero, and then came back up again. During our post-fMRI interviews, my friend and I shared long and involved explanations of the significance of those absolute cessations with Dave.
If the scientists can locate this absolute cessation in their data, this might be the first time that nirodha, or a true cessation of the sensory system, has been captured somehow in an fMRI. We don't know what that will look like on an fMRI, so they're now attempting to find it in the readings.
It took quite a few explanations. My friend and I gave Dave a big dump on nirodha and cessations, and he didn't quite understand the difference between a 'little gone' and a 'complete gone,' in which the whole sensory system, including pure awareness, dissolves.
Shinzen diagrammed cessations or "gones" out on a blackboard for Dave, and he videoed the explanation because he wanted to review it to try to understand it. I empathize with him; how would he know if he'd never experienced or read about the significance of it? You can watch these videos, Arising and Passing and Arising and Passing - Part II/III, and Arising and Passing - Part III/III, on Dave Vago's YouTube channel. Later, Shinzen elaborated on this as a part of his Ten Stages on pages 40-46 in his 76-page What is Mindfulness pdf.
Jeff Warren wrote about the study here.
Dave Vago and Shinzen presented at the 2013 Buddhist Geeks Conference in Boulder, CO. Here are some images from the presentation.
Dave Vago spoke for the first half hour about the preliminary results of the Harvard study, and Shinzen spoke for the latter half. Shinzen's talk is called Divide and Conquer: Structuralism Revisited. You can see a complete video of the conference presentation here.
*See the bottom of the page for some of the study's papers.
Mapping the Meditative Mind - Neural Mechanisms and Clinical Relevance, a presentation by Dr. Dave Vago, was posted on April 20, 2020, for the USC Center for Mindfulness Science. It includes findings on the Vago-Shinzen et all Harvard study, a study with Daniel P. Brown, and mindfulness-based interventions.

Yen Chen, Sonication Process, SEMA Lab, Center for Consciousness Studies, University of Arizona, Tucson, April 2024.
Shinzen's latest venture into combining science and meditation involves working with Jay Sanguinetti and the Sonication Enhanced Mindful Awareness team at the Center for Consciousness Studies, which is associated with the University of Arizona in Tucson.
In April 2024, I visited with Shinzen and Jay and met some of the SEMA lab team. I had one sonication session and experienced what felt like letting go of the nervous system and deepening equanimity in the sensory circuits. It was subtle but unmistakable. I understand the potential now and why Shinzen and Jay are so excited about what it offers, especially when combined with personalized and customized mindful A.I. guidance.
*Vago, D. R., Pan, H., Stern, E., & Silbersweig, D. A. (2013). Neural Substrates Underlying Modalities of Awareness in Mindfulness Practice. American Neuropsychiatric Association Annual Meeting Abstracts. Neuropsychiatry Clin Neurosci, 25(2), P102.
Vago, D. R., Zeidan, F. (2016). The brain on silent: mind-wandering, mindful awareness, and states of mental tranquility. New York Academy of Sciences, 1373(1), 96-113. doi:10.1111/nyas.13171
Davis, J. H, * Vago, D. R. * (2013) Can enlightenment be traced to specific neural correlates, cognition, or behavior? No, and (a qualified) Yes. Frontiers in Human Neuroscience. 4(870). (* shared first authorship) doi:10.3389/fpsyg.2013.00870