Tractography

What it is

A tractogram is a reconstruction of the brain’s wiring, built from diffusion MRI: the scanner measures which way water molecules are free to move in each voxel, and since water travels more easily along a nerve fibre than across it, those measurements trace out the paths that bundles of axons follow. Each thread here is a streamline, an estimate of one such path through the white matter.

The colours are not tissue types or measurements — they say which way a fibre is running at that point, the standard convention in the field:

Or, with By bundle under Bundles in the box beside the view, each of the 46 bundles the atlas names takes a colour of its own, as the field’s atlases draw them, and a tap on a fibre names its bundle whichever colouring is on.

Drag to turn the brain, and pinch or scroll over the view to zoom. Slice, near the left of the bar, puts a slider on each edge of the view, each a cut taking the brain, and the streamlines with it, away from that side: draw a slider back to its centre mark to undo its cut, Reset slice under View undoes them all, and Slice turned off shows everything whole. Brain shows or hides the MNI152 brain around the fibres, drawn as the 3D Region Atlas draws it, the MRI showing at a cut face as it does there, Brain regions beside it shows or hides the highlighted regions themselves, and Transparency raises two tall bars, the brain’s and the regions’, each making its own more see-through or more solid. Tract shows or hides the streamlines. Slice tract, on whenever Slice is turned on, cuts them with the brain, and off leaves them whole while the brain alone is cut; Offset stands their cut ends out of the brain’s cut face and Distance sets how far, in millimetres, both greyed while the brain is off; and Thicken sets how thick they are drawn. View turns the brain to one of its faces, or home to the view the page opens with, Revolve sets it turning until you take hold of it, and Export, at the end of the bar, offers the streamlines and the brain as a 3D model. The region box beside the view folds away on its tab: the regions in it are highlighted from Bundle association, below, by a press on a region a bundle’s streamlines end in, and while one is highlighted only the streamlines that run through it are drawn, and with Brain regions on the region itself stands among them in its colour, cut as the brain is, and shows on the brain’s cut face as it does on the 3D Region Atlas. The switch at the box’s top reads All through, every streamline through any highlighted region, Ending in, only those with an end in one (an end counts where the streamline stops in the region or within two millimetres of it; the tractography stops its lines just short of the grey matter, and an end in the brainstem, which the atlas does not label, is no region’s), or, with two or more highlighted, Connecting, only those with one end in one highlighted region and the other end in another, which the switch turns to as a second region is added; a press on a region’s name opens its note. Under the regions, Bundles lists the bundles the atlas names, by system: association, projection, commissural, cerebellar and the cranial nerves. L and R show or hide each side of a bundle, the switches a whole system or every bundle, and a tap on a fibre names its bundle in a small window. A press on a bundle’s name in the list, or on Alone or the name in that window, selects the bundle: it is shown alone, and Bundle association, the first button on the bar, greyed until a bundle is selected, raises a sheet with what it connects, what we think it does, what its damage does, and the regions its streamlines end in with each one’s share of the ends, a press on one highlighting it; Show the other bundles in grey, under the colour switch, keeps the rest in view in one quiet grey, so the bundle stands in its place among them; and a second press on the name, or Show all bundles, shows every bundle again. The fewer streamlines are drawn, the more finely they are drawn, smoothed into curves and rounder, and where they crowd they are shaded darker, which shows their depth. The page opens with the brain on at 65 per cent transparency, the streamlines on and nothing sliced, and remembers the rest of how you left it: the streamlines’ switches, offset and thickness, the regions highlighted with their two switches, the bundles shown and their colouring, and the view. This is a population average rather than any one person’s brain, so it shows the pathways people generally share.

Reference

Tractogram the HCP1065 population-averaged tractography atlas: Yeh FC, Population-based tract-to-region connectome of the human brain and its hierarchical topology, Nat Commun 13:4933 (2022), CC BY-SA 4.0.

Brain the MNI152 template (ICBM 2009c), McConnell Brain Imaging Centre, Montreal Neurological Institute, drawn around the streamlines as the 3D Region Atlas draws it, the MRI showing where a cut opens it.

Data provided in part by the Human Connectome Project, WU-Minn Consortium (Principal Investigators: David Van Essen and Kamil Ugurbil; 1U54MH091657) funded by the 16 NIH Institutes and Centers that support the NIH Blueprint for Neuroscience Research; and by the McDonnell Center for Systems Neuroscience at Washington University.

Rendering NiiVue (Rorden lab).