Cortex can obscure the bundle beneath it. Changing transparency is a display experiment: it tests visibility while preserving the reconstruction being viewed.
Rotate the atlas until you can name what lies in front, behind and beneath the displayed structures.
Compare
Open Explore anatomy and change Cortical surface from Defined toward Transparent. Compare the same CST sample, then restore the lesson scene.
Read the neighbours
The cortical layer and the pathway are separate display objects.
Showing a previously obscured segment changes what you can see, not the underlying diffusion acquisition.
Explain before revealing
What has been established when a segment appears after changing opacity?
Explanation
That the previous display obscured it. This isolates a visibility issue. It does not demonstrate new fibres, improved reconstruction accuracy or functional preservation.
In a surgical discussion
Before explaining an apparent interruption biologically, establish whether the segment is hidden by display settings or absent from the reconstruction.
Pathway colour represents local orientation; cortical and network colours have separate legends. Opacity controls visibility, line count reflects sampling, and a trace sweeps along shape. None measures conduction, velocity or fibre density.
Ask the learner to answer before opening the explanation. Compare the answer with the named structures and the cited method. Teaching point: That the previous display obscured it. This isolates a visibility issue. It does not demonstrate new fibres, improved reconstruction accuracy or functional preservation.
This relationship draws on 3 cited sources.
Relationship 2 of 4 · model metric
Line count is a sampling choice
Orient
A dense bundle can look authoritative even when the apparent density is largely a display choice. Compare the named samples without treating their number of lines as an axon census.
Select each structure to light it on the atlas, then rotate until you can name what lies in front, behind and beneath it.
Targets
CST · corticospinal tract
OR · optic radiation
Compare
Compare CST and OR as separately identified samples. Read the sampled-path caption and distinguish the displayed population from biological fibre number.
Read the neighbours
The installed atlas caps the number of displayed paths per bundle.
A streamline can represent a model trajectory without corresponding one-for-one to an axon.
Explain before revealing
Does twice as many displayed streamlines mean twice as many axons?
Explanation
No. Seeding, reconstruction, selection and display sampling affect the count. The atlas caption describes sampled paths; it is not a histological measurement or a measure of functional reserve.
In a surgical discussion
Do not use a thicker-looking rendered bundle as a direct explanation of greater functional reserve. A quantitative claim needs an appropriate measurement model.
Pathway colour represents local orientation; cortical and network colours have separate legends. Opacity controls visibility, line count reflects sampling, and a trace sweeps along shape. None measures conduction, velocity or fibre density.
Ask the learner to answer before opening the explanation. Compare the answer with the named structures and the cited method. Teaching point: No. Seeding, reconstruction, selection and display sampling affect the count. The atlas caption describes sampled paths; it is not a histological measurement or a measure of functional reserve.
This relationship draws on 4 cited sources.
Relationship 3 of 4 · model metric
A model weight is not a truth probability
Orient
SIFT2 adjusts streamline contributions to make a tractogram agree more closely with a diffusion-derived fibre-density model. That is a different quantity from the chance that a connection is anatomically correct.
Rotate the atlas until you can name what lies in front, behind and beneath the displayed structures.
Compare
Inspect the sample without assigning significance to brightness. State what extra measurement would be needed to make a quantitative claim; no SIFT2 values are installed in this atlas.
Read the neighbours
SIFT2 weights belong to a model fit and its tractogram.
The atlas display provides geometry and sampling information, not a probability of functional preservation.
Explain before revealing
Can a high SIFT2 weight be read as a high probability that an entire connection is true?
Explanation
No. It is a model-derived contribution to the fit, not a calibrated connection-truth probability. It also does not measure an individual pathway’s functional integrity. This atlas supplies no such weights to inspect.
In a surgical discussion
When a tractogram includes a numerical metric, ask what it measures before incorporating it into a clinical explanation. A familiar-looking score can answer a different question from the one you need.
A quantitative model-derived weight answers a different question from displayed line count or opacity. SIFT2 fits streamline contributions to a fibre-density model; neither a weight nor an attractive render is a probability that the entire connection is true.
Ask the learner to answer before opening the explanation. Compare the answer with the named structures and the cited method. Teaching point: No. It is a model-derived contribution to the fit, not a calibrated connection-truth probability. It also does not measure an individual pathway’s functional integrity. This atlas supplies no such weights to inspect.
This relationship draws on 1 cited source.
Relationship 4 of 4 · reconstruction
Report an unresolved reconstruction honestly
Orient
Teaching vignette: a tract is expected anatomically but appears short and sparse. Describe the discrepancy and identify the next kind of evidence needed, without turning absence on screen into absence in the brain.
Rotate the atlas until you can name what lies in front, behind and beneath the displayed structures.
Compare
Inspect OR from two views and alter transparency once. Separate a visibility finding from an unresolved question about the reconstruction.
Read the neighbours
Tracking near complex fibre configurations is sensitive to the orientation model and method.
An absent reconstruction can coexist with anatomy or function that requires another form of assessment.
Explain before revealing
What is a better conclusion than “the tract is absent, so there is no risk”?
Explanation
“The pathway was not adequately demonstrated by this reconstruction.” State the method and discrepancy, then reconcile them with individual structural and functional evidence. The statement preserves uncertainty without hiding the actual observation.
In a surgical discussion
A useful report says what was reconstructed, where it was incomplete and which limitation remains unresolved. It should not declare tissue expendable from a failed visualization.
Pathway colour represents local orientation; cortical and network colours have separate legends. Opacity controls visibility, line count reflects sampling, and a trace sweeps along shape. None measures conduction, velocity or fibre density.
Ask the learner to answer before opening the explanation. Compare the answer with the named structures and the cited method. Teaching point: “The pathway was not adequately demonstrated by this reconstruction.” State the method and discrepancy, then reconcile them with individual structural and functional evidence. The statement preserves uncertainty without hiding the actual observation.
This relationship draws on 3 cited sources.
Recap
A tract looks short and sparse. How do you describe the discrepancy without declaring it absent?
Check whether visibility and cortical opacity explain what is missing on screen.
Displayed lines and vertices are sampling choices, not axon counts.
State the unresolved reconstruction question and the evidence needed to investigate it.
Review the final explanation
“The pathway was not adequately demonstrated by this reconstruction.” State the method and discrepancy, then reconcile them with individual structural and functional evidence. The statement preserves uncertainty without hiding the actual observation.
Provenance for the HCP1065 population-averaged bundles rendered here. Every displayed line is an average-space reconstruction sampled for display; it is not a patient’s pathway and carries no direction of conduction.
Neurosurgical comparison of tensor and higher-order fibre-orientation models. Demonstrates that the orientation model changes which pathways appear; a rendered bundle inherits its model’s failure modes.
Challenge dataset with a defined ground truth and many submitted pipelines. Its false-positive findings motivate caution; its error figures belong to that challenge and are not an error estimate for this atlas.