AI Unlocks Brainstem White Matter Pathway Mapping

New software can automatically segment eight distinct bundles in diffusion MRI scans, revealing structural changes in neurological conditions

Feb. 9, 2026 at 7:23pm

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Researchers at MIT, Harvard, and Massachusetts General Hospital have developed an AI-powered software called BrainStem Bundle Tool (BSBT) that can automatically segment eight distinct bundles of white matter fibers in the brainstem from diffusion MRI scans. This breakthrough allows for a much finer-grained assessment of how these crucial neural pathways are affected by trauma, neurodegeneration, and other conditions. The tool has already revealed distinct patterns of structural changes in patients with Parkinson's, multiple sclerosis, Alzheimer's, and traumatic brain injury, and has shown potential to track recovery in coma patients.

Why it matters

The brainstem is a critical region of the brain that controls many essential functions like consciousness, sleep, breathing, and motion, but it has been difficult to image in detail using existing tools. This new AI-powered software provides researchers and clinicians with an unprecedented ability to assess the structural integrity of the brainstem's white matter pathways, which could lead to new biomarkers and insights into a wide range of neurological conditions.

The details

The BrainStem Bundle Tool (BSBT) works by tracing fiber bundles that extend from neighboring brain regions into the brainstem, creating a "probabilistic fiber map." A convolutional neural network then combines this map with multiple imaging channels to distinguish eight individual bundles within the brainstem. The tool was trained on 30 diffusion MRI scans from the Human Connectome Project and validated against post-mortem brain dissections. Tests showed BSBT could reliably identify the same bundles in repeat scans of the same patients.

  • The study was published on February 10, 2026 in the Proceedings of the National Academy of Sciences.

The players

Mark Olchanyi

A doctoral candidate in MIT's Medical Engineering and Medical Physics Program and the lead author of the study.

Emery N. Brown

The Edward Hood Taplin Professor of Computational Neuroscience and Medical Engineering at MIT, Olchanyi's thesis supervisor, and a co-senior author of the study.

BrainStem Bundle Tool (BSBT)

The AI-powered software developed by the research team that can automatically segment eight distinct bundles of white matter fibers in the brainstem from diffusion MRI scans.

Human Connectome Project (HCP)

A research project that provided the 30 diffusion MRI scans used to train the BSBT neural network.

Juan Eugenio Iglesias

A co-senior author of the study.

Brian Edlow

A co-senior author of the study.

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What they’re saying

“The brainstem is a region of the brain that is essentially not explored because it is tough to image. People don't really understand its makeup from an imaging perspective. We need to understand what the organization of the white matter is in humans and how this organization breaks down in certain disorders.”

— Mark Olchanyi, Doctoral candidate, MIT Medical Engineering and Medical Physics Program (Mirage News)

“The brainstem is one of the body's most important control centers. Mark's algorithms are a significant contribution to imaging research and to our ability to understand the regulation of fundamental physiology. By enhancing our capacity to image the brainstem, he offers us new access to vital physiological functions such as control of the respiratory and cardiovascular systems, temperature regulation, how we stay awake during the day and how we sleep at night.”

— Emery N. Brown, Edward Hood Taplin Professor of Computational Neuroscience and Medical Engineering, MIT (Mirage News)

What’s next

The researchers plan to continue testing the BrainStem Bundle Tool (BSBT) on larger patient datasets to further validate its ability to detect structural changes in the brainstem associated with various neurological conditions. They also aim to explore how the tool could be used to track recovery and disease progression over time.

The takeaway

This new AI-powered software represents a significant breakthrough in our ability to image and analyze the intricate white matter pathways of the brainstem, which play a crucial role in regulating many of the body's most essential functions. By providing a fine-grained assessment of brainstem structure, BSBT has the potential to unlock new biomarkers and insights that could aid in the diagnosis, monitoring, and treatment of a wide range of neurological disorders.