When you’re navigating the NICU journey, a handful of pivotal moments stand out — and MRI day is definitely one of them. For families facing a diagnosis of HIE, this scan often becomes a turning point. It’s the first time many parents hear in detail what parts of the brain may have been affected, and naturally, it raises big questions about what the future might hold.
But MRIs — especially for newborns — can feel mysterious, even intimidating. What exactly does it show? How do doctors read all those shades of gray? And what does it really mean when they say something “looks normal” or “concerning”?
Dr. Terrie Inder, one of the most respected voices in neonatal neurology, has helped make sense of MRI imaging in the tiniest patients — especially those with HIE. In this post, we’re breaking down what happens during a neonatal MRI, how to understand the science behind it, and what families should know about timing, interpretation, and how these images can help guide care and support over time.
Missed the live Q&A? No worries. Like any good partner, we took notes and are willing to share!
An MRI (Magnetic Resonance Imaging) is a special type of scan that takes detailed pictures of the inside of the body, and in the context of HIE, it helps doctors see the brain and understand how much injury has occurred, where it happened, and how the brain is healing over time.
For many parents, hearing that their baby is going for an MRI can feel overwhelming. Maybe you’ve had one yourself — the big, loud machine, the tight space, the need to stay completely still. Not many would exactly consider it a relaxing experience.
But here’s the good news: for newborns, it’s nothing like that. In fact, the goal is to have babies sleep right through it.
Before the scan, babies are usually well-fed, swaddled up snugly, and naturally fall asleep — kind of like settling in for a car ride. And unlike MRIs for older kids or adults, most neonatal MRIs are now done without any sedation or anesthesia, which is safer and more comfortable.
There’s also no radiation involved. An MRI isn’t like an X-ray or CT scan. Instead, it works using a powerful magnet and sound waves — that’s what makes all the loud knocking and humming during the scan.
Here’s where it gets a bit science-y (but stick with us — it’s pretty cool):
The MRI machine uses magnetism to vibrate tiny particles inside the body — either protons (which make up most of the water in the brain) or the water molecules themselves.
The machine vibrates them, then waits to see how quickly or slowly they relax and return to their normal state. This tiny movement tells us about the environment around those molecules — for example, if they’re in dense tissue, injured areas, or healthy white matter.
It’s like tapping a bouncy ball on different surfaces — tile, carpet, grass — and seeing how it reacts. Each surface gives a different bounce, and that helps you understand what it’s made of.
The MRI collects this information and turns it into a grid of black, white, and gray boxes, each representing a tiny slice of the brain (think thousands of these in a single image), and it’s these thousands of shades of gray that form the actual MRI picture.
From there, specialists can interpret the patterns, contrasts, and structures to see if there’s injury, how severe it might be, and what parts of the brain are affected. Different types of tissue — gray matter, white matter, injured areas — all respond differently, which helps create a more complete picture of what’s happening.
Dr. Inder says to imagine the brain as a giant warehouse, with different sections doing specific jobs to keep everything running smoothly.
The outer layer of the brain — called the cortex — is like the warehouse staff. These are the people on the floor doing the day-to-day work: sorting packages, managing incoming and outgoing materials, and making sure each task gets done. In brain terms, the cortex is responsible for things like movement, vision, hearing, and higher thinking.
If injury affects this area, the impact might show up in how a child processes information or responds to sensory input. But — and this is important — the cortex also has incredible plasticity. It’s often the best area for rewiring, rerouting, and adapting over time, especially with the help of early interventions.
Next, we have the white matter — think of this as the warehouse’s communication system. It’s the network of cables, conveyor belts, and walkie-talkies that allow different parts of the warehouse to talk to each other. White matter connects the cortex to the rest of the brain and body, helping signals travel efficiently. If there’s injury in this area, the cortex might be sending out all the right messages, but they don’t get where they need to go — or they get scrambled along the way.
The deep nuclear gray matter is the center of it all — the basal ganglia, thalamus, and internal capsule. These structures are like the warehouse’s IT system administrator. They run the whole operation behind the scenes: setting priorities, routing information, coordinating movement, and ensuring the warehouse doesn’t crash. This area is especially energy-hungry and metabolically active — meaning it’s incredibly vulnerable when oxygen or blood flow is interrupted.
In HIE, this deep central area can be significantly affected, and when it’s injured, the impact can be more severe and more complicated to recover from. That’s because these structures help manage the “big picture” — everything from tone and motor control to cognition and attention. An injury here can make it difficult for a child to show what they know or access the skills they do have. It’s not about a lack of intelligence — it’s about the brain’s ability to communicate and carry out instructions.
The location and nature of a brain injury can significantly impact the prognosis, and MRIs often reveal distinct patterns based on the type of injury:
Each of these patterns can give providers important clues about the timing and severity of the injury, helping to guide care and intervention strategies.
Understanding how an MRI evaluates the brain starts with knowing what each sequence shows us. Different types of MRI images provide different kinds of information—from basic brain structure to signs of injury and even chemical imbalances. Here’s how the process typically unfolds, step by step:
The first step in any MRI procedure is to look at the brain’s anatomy. This is done using T1 and T2 sequences, the traditional and most common MRI sequences. These sequences allow us to see the brain’s structure in high detail, using multiple views:
These scans help assess how the brain is “built,” per se, and give providers a solid foundation to learn more. They are also performed around days 12-14 to see how the brain’s anatomy has changed in response to the injury, especially after cooling if it took place.
While the T1 and T2 sequences are great for looking at the anatomy, we need additional sequences to look for signs of injury, especially in the first few days after birth (days 2-4). This is where diffusion-weighted imaging (DWI) comes in.
Diffusion imaging shows us how water molecules move in the brain. When the brain is healthy, water molecules move freely. However, when there’s an injury, the water movement can become restricted, indicating swelling or damage to the brain cells. If the injury is severe enough, the water molecules move freely after the cells die, which can be seen in the MRI as high diffusion.
Finally, an MRI spectroscopy looks at the brain’s chemistry. This technique measures the brain’s chemical composition, helping to understand any abnormalities like an unusual buildup of acids or a loss of chemicals in the brain’s “hard drive.” MRI spectroscopy is especially useful during the later days of life (from days 3-7), as it allows us to look more deeply into the chemical composition and function of the brain.
Spectroscopy can tell even more about the injury, particularly by highlighting any chemical imbalances in the brain’s structure. For example, we may see the accumulation of certain acids or a loss of key chemicals that normally help the brain function. These findings, combined with anatomical images and diffusion patterns, help paint a clearer picture of what’s happening in the brain.
When it comes to MRI imaging for babies, timing truly is everything. The brain’s response to injury evolves over time, and diffusion-weighted imaging is sensitive to those changes. That’s why interpreting an MRI, especially in the context of HIE, isn’t always black and white.
Sometimes, families hear that their baby’s MRI looks “normal,” but the diagnosis of HIE is still on the table. Understandably, this can be confusing and emotional. What does a “normal” MRI mean if there are still concerns?
That’s where the concept of pseudonormalization comes in. This refers to when a brain injury appears to “normalize” on MRI, even though the damage is still present.
The brain is a dynamic, constantly adapting environment—especially in newborns, whose brains contain more water and are still rapidly developing. Early after injury, changes may not yet be visible on imaging. Brain tissue might look healthy, even if the injury has occurred, because the entire response—like swelling or cellular breakdown—hasn’t fully set in.
Early MRIs (within the first few days): At this stage, the brain is still adjusting, and DWI may not yet show abnormalities. Even if the injury has occurred, it might not be detectable on the scan—this is the window when pseudo-normalization is most likely to mask the injury.
Days 2 to 4: This is typically the optimal window for imaging. The brain’s response to the injury is clearer, and DWI is the most sensitive to detecting damage. Abnormalities are easier to spot before the brain begins adapting and compensating.
After day 7: Here’s where it gets tricky. The brain starts to “normalize,” and while that may sound like a good thing, it means some injury markers begin to fade. The tissue might look healthier than it really is—another example of pseudo-normalization in action. If an MRI is done too late, some of the injury that would have been visible earlier may no longer appear.
This is why follow-up MRIs around days 12–14 are so important (and, in Dr. Inder’s opinion, necessary – especially if the baby is still hospitalized.)
Dr. Inder points to recent research showing that MRI findings changed in a surprisingly large percentage of cases between days 4 and 14: 20–25%. So, while the initial MRI provides a snapshot, the second one offers a more complete picture of how the brain is healing, helping families and care teams better understand what support might be needed moving forward.
And here’s something else to consider: if a baby has two MRIs that look normal but later develops motor impairments or other challenges, a follow-up MRI can help make sense of what happened. Or, if we expect poor outcomes based on early imaging, and that child goes on to surprise everyone with how well they do—MRI may help us understand the “why” behind that, too.
Many providers opt to scan again around 6 to 12 weeks of age. At that point, the brain has had some time to heal and reorganize, and imaging can give a clearer picture of how things are evolving after the initial injury.
In fact, new research is exploring just that—how a MRI around 6 weeks might help better predict outcomes and guide future care.
Between 9 and 12 months, however, it actually becomes harder to see certain types of injury on MRI. That’s because the brain is transitioning from the watery, immature infant brain to a more structured, mature one. On imaging, it’s like trying to spot a grey shirt on a grey background—there’s not much contrast. In newborns, injuries often stand out clearly. In older children, contrast improves again. But in that in-between stage? Things get murky.
MRIs done later—at 1 or 2 years—can still offer valuable insights. However, as Dr. Inder notes, waiting that long may mean missing the most critical window for early therapies and interventions. The first year of life is a powerful time for brain development. The brain is highly “plastic,” meaning it can adapt and rewire itself—and early rehab can make a real difference. The earlier we act, the more opportunity we have to influence long-term outcomes.
When we talk about MRIs as a tool for understanding brain injury in newborns, there are three important things to keep in mind:
As Dr. Inder emphasizes, MRI is currently the most reliable biomarker for understanding how a baby’s brain has been affected by HIE. While tools like Apgar scores, blood gases, early neurological exams, and EEGs all play a role, MRI provides the clearest picture of what’s happening inside the brain—and what that might mean for a child’s future. It’s the most powerful prognostic tool available, which is why it’s central to clinical care and research.
One of the significant challenges in developing new therapies for HIE is figuring out how long we need to wait to know if something is truly working. Many research studies use developmental milestones at 2 years old as a key outcome measure. But there’s a catch: children change—a lot. A child who seems mildly affected at two may face significant learning challenges by 5. Or they might catch up entirely. So, while the 2-year mark is helpful, it’s not always a stable or complete predictor of long-term development.
If we relied only on these long-term outcomes—waiting until school age or beyond—we’d face enormous delays. It could take 15 to 30 years from identifying a promising therapy to knowing whether it helps. That’s far too long, especially for families who need answers and options now.
That’s why there’s so much momentum around using MRI as an early outcome measure in clinical trials. If we can spot early signs of brain protection or reduced injury on imaging, we can say with much more confidence—and much sooner—that a therapy may be helping. It’s not a perfect solution, but it’s the best tool we have right now to speed up the path from research to real-world impact for families navigating HIE.
This large, multicenter, randomized controlled trial enrolled over 500 babies across the U.S. to test whether adding erythropoietin (EPO) to therapeutic hypothermia could improve neuroprotection. EPO is a naturally occurring hormone with potential anti-inflammatory and brain-repair properties.
In the HEAL study, MRI served as a central outcome measure. Researchers used a standardized scoring system to evaluate the extent and severity of brain injury, aiming to see if babies who received EPO had better MRI results than those who received a placebo. Blinded experts read the MRIs to ensure objectivity. Even though the results showed no significant added benefit of EPO on the overall group, MRI gave researchers essential insight into how the therapy may (or may not) influence specific brain regions and injury patterns.
One emerging area of research in HIE recovery is the use of sildenafil. The idea? Sildenafil may help improve blood flow to the brain, which is often disrupted after a hypoxic-ischemic event.
Before jumping into large-scale studies, researchers begin with smaller, early-phase trials focused on safety and pharmacokinetics—how the drug moves through a newborn’s body. These early studies aim to answer critical questions: is the medication safe for infants? Does it show any signs of benefit?
And MRI plays a central role in both these early-phase studies and larger ones, like ReAlta’s STAR study, which is studying a novel peptide’s effectiveness in treating newborns with moderate or severe HIE undergoing cooling. Even with small sample sizes, MRI can detect subtle changes in brain structure that suggest whether a therapy might be helping—or raising concerns. These scans provide an early, non-invasive look at how the brain is responding long before developmental milestones can reveal outcomes.
Dr. Inder reminds us that providers learn from every baby they care for. It’s the stories, experiences, and unique journeys of families that help shape how medical teams understand and approach care. That’s why it’s so important for families to share what’s going well, what’s challenging, and what truly matters most. Providers are listening—and organizations like ours are here to help make sure your voice is heard.
Throughout Hope in Action Awareness Month, we’ve seen how powerful advocacy can be in helping families feel supported and confident in the care their child receives. Outcomes may not always be clear—every baby is different—but providers are committed to being honest about what they know and what they’re still learning. While they may not have all the answers, they’re here to partner with you to build the strongest possible foundation for your child’s future.
They say a picture is worth a thousand words, and this is just as true when it comes to imaging —it’s one thing to hear about and quite another to see for yourself. Dr. Inder encourages families to ask their provider to walk them through the MRI images step by step. Seeing the scans firsthand can help make a complex and overwhelming situation more understandable, giving families a clearer picture of what’s happening in their child’s brain and why certain care decisions are being made.
To watch the full Q&A, visit our 2025 Awareness Month Playlist on YouTube, and click the button below for our key takeaways at a glance!
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