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The Amazing Brain: A Sharper Image of the Pyramidal Tract

Posted on by Dr. Francis Collins

Flip the image above upside down, and the shape may remind you of something. If you think it resembles a pyramid, then you and a lot of great neuroscientists are thinking alike. What you are viewing is a colorized, 3D reconstruction of a pyramidal tract, which are bundles of nerve fibers that originate from the brain’s cerebral cortex and relay signals to the brainstem or the spinal cord. These signals control many important activities, including the voluntary movement of our arms, legs, head, and face.

For a while now, it’s been possible to combine a specialized form of magnetic resonance imaging (MRI) with computer modeling tools to produce 3D reconstructions of complicated networks of nerve fibers, such as the pyramidal tract. Still, for technical reasons, the quality of these reconstructions has remained poor in parts of the brain where nerve fibers cross at angles of 40 degrees or less.

The video above demonstrates how adding a sophisticated algorithm, called Orientation Distribution Function (ODF)-Fingerprinting, to such modeling can help overcome this problem when reconstructing a pyramidal tract. It has potential to enhance the reliability of these 3D reconstructions as neurosurgeons begin to use them to plan out their surgeries to help ensure they are carried out with the utmost safety and precision.

In the first second of the video, you see gray, fuzzy images from a diffusion MRI of the pyramidal tract. But, very quickly, a more colorful, detailed 3D reconstruction begins to appear, swiftly filling in from the top down. Colors are used to indicate the primary orientations of the nerve fibers: left to right (red), back to front (green), and top to bottom (blue). The orange, magenta, and other colors represent combinations of these primary directional orientations.

About three seconds into the video, a rough draft of the 3D reconstruction is complete. The top of the pyramidal tract looks pretty good. However, looking lower down, you can see distortions in color and relatively poor resolution of the nerve fibers in the middle of the tract—exactly where the fibers cross each other at angles of less than 40 degrees. So, researchers tapped into the power of their new ODF-Fingerprinting software to improve the image—and, starting about nine seconds into the video, you can see an impressive final result.

The researchers who produced this amazing video are Patryk Filipiak and colleagues in the NIH-supported lab of Steven Baete, Center for Advanced Imaging Innovation and Research, New York University Grossman School of Medicine, New York. The work paired diffusion MRI data from the NIH Human Connectome Project with the ODF-Fingerprinting algorithm, which was created by Baete to incorporate additional MRI imaging data on the shape of nerve fibers to infer their directionality [1].

This innovative approach to imaging recently earned Baete’s team second place in the 2021 “Show Us Your BRAINs” Photo and Video contest, sponsored by the NIH-led Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative. But researchers aren’t stopping there! They are continuing to refine ODF-Fingerprinting, with the aim of modeling the pyramidal tract in even higher resolution for use in devising new and better ways of helping people undergoing neurosurgery.


[1] Fingerprinting Orientation Distribution Functions in diffusion MRI detects smaller crossing angles. Baete SH, Cloos MA, Lin YC, Placantonakis DG, Shepherd T, Boada FE. Neuroimage. 2019 Sep;198:231-241.


Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative (NIH)

Human Connectome Project (University of Southern California, Los Angeles)

Steven Baete (Center for Advanced Imaging Innovation and Research, New York University Grossman School of Medicine, New York)

Show Us Your BRAINs! Photo and Video Contest (BRAIN Initiative/NIH)

NIH Support: National Institute of Biomedical Imaging and Bioengineering; National Institute of Neurological Disorders and Stroke; National Cancer Institute


  • Usman shoukat says:

    love this article .this help me alot in my research .thanks so much for this content.

  • Zuccheri Gianni says:

    The eye is that part of the brain that faces the world and captures its images:
    now here we have beautiful, surprising ones and promises of developments in medical care.
    And not only that: here it is the Brain that analyzes itself, in the finest structures.
    Infinite streams of Knowledge that flow into a river of Consciousness.

  • Zuccheri Gianni says:

    In considering the eye as an integral part of the Brain, can you apply what you have developed for the study of the Pyramidal pathways also for the Optical pathways?
    Unraveling numerous mysteries about Glaucoma with normal ocular pressure: a complex series and controversial hypotheses about the mechanisms that cause them.
    I am reminded of the cases that derive from anatomical constitutions in which we will be able to see how the optic nerve in certain rotations of the eyeball comes to be “stretched” with resentment on the finest network of nutritional vessels (in the most vulnerable point, when it enters the bulb itself) and nerve fibers

  • Barbara says:

    What is neuropilin/semaphorin III expression like in the pyramidal tract? And what happens when it is blocked or down-regulated in some manner? It’s likely to also have a developmental aspect as well if expression fluctuates during embryonic development. Should be worthy of a RO1 or two.

  • Zuccheri Gianni says:

    And in sleep the blockade of the commands of the cerebral motor cortex descends,
    like a safety bulkhead in the face of a wave of fallacious orders that are produced in the dream, to safeguard the integrity of the individual:
    a wise helmsman who keeps the ship anchored while the confused commander yells nonsense.

  • Phillip Huggan says:

    I have a new method of medical imaging that relies on nanotechnology, metamaterials and light slightly in the infrared. It will also be finicky regarding stillness. Light may cause cancer. Infrared will not. Metamaterials can be used to teleport light. The waveguide is placed so light from the interior of the brain is teleported outside the body through the waveguide and relit ideally focused. The patient has ingested fluorescent nanoparticles emitting in the infrared. Instead of getting hardly any signal, the nanoparticles in concert with waveguide focusing should get a volume of infrared 3d vector streaks about 10 cubic microns or a millimeter. Normally such a waveguide just teleports light from body image source to the outer skin of the waveguide channel and outwards. With nanoparticles the light will reveal detail of brain and body interiors especially. The subsconscius might be pinned down. It will require more than iron to be magicked catabolism after use. Maybe this decade.

  • US says:

    Wow, it’s really well-explained, love this.

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