MRI Cutting — Final State

Branch

MRI-Cutting

Current Approach

MRI spherical cutting is geometric / coverage-only, rather than using CT-style intensity gating.

Regular Cut and Plane-Guided Cut share the maskInsideSphere path.

Policy	MRI	CT
Voxel eligibility	Sphere coverage only (minValue: null)	Iso / skull threshold (minValue = cut-time iso)
Erase / background write	eraseValue: 0	Default 0
Boundary	Soft anti-aliasing (binaryCarving: false)	Same
Do not use	Display iso, MRI tissue threshold, fixed MR intensity floor	—

Stage 1A Implementation

Stage 1A is implemented in:

• sphereCutMaskParams.js
• Cursor3D live cutting path
• Cursor3D rebuild path

Cut History stores the cut-time mask fields:

• eraseValue
• minValue
• binaryCarving
• continuousScooping
• modality

This allows replay to use the saved cutting behavior rather than re-reading the current iso slider.

For MRI spherical and plane-guided cuts:

minValue: null
eraseValue: 0
binaryCarving: false

The cut is therefore based on geometric sphere coverage rather than MRI intensity.

Contour / Path Cuts

Contour/path cuts are outside Stage 1A scope.

Their current behavior is unchanged.

Contour cuts erase voxels to:

scalars.getRange()[0]

rather than using a hardcoded 0.

MRI Clinician Note

Plan displays the MR-specific clinician note:

MRI signal intensity is sequence-dependent…

This reinforces that MRI intensity should not be treated like a fixed CT/HU tissue threshold.

Supporting MRI Work

Additional work on the branch includes:

• Plan NIfTI loading fix
• MRI transfer-function path restored in Plan and View
• applyMrIsoTransferFunctions is used when modality/profile is identified as MR

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Final State

MRI Datasets Tested

A formal cutting-specific dataset test matrix has not yet been recorded on this branch.

Available library MRI samples include:

• MRI Cardiac 3D and Cine
• MRI PROSTATEx

Related MRI transfer-function work exercised:

• T1 series
• T2 series
• Modality tag MR

Cutting-specific dataset pass/fail results still need to be recorded from manual Plan testing.

Erase Value 0

eraseValue: 0 is wired as the Stage 1A default for:

• Regular spherical cuts
• Plane-guided spherical cuts

This behavior is also covered by unit tests.

However, consistent visual success across different MRI datasets has not yet been confirmed in the repository.

For now, 0 should be treated as the working erase-value experiment rather than a final validated rule for every MRI dataset.

Cases Where Removed Regions May Remain Visible

No dataset-level failure list has been recorded.

Residual visibility may still occur when:

• The dataset background/air value is not near 0.
• Writing 0 places the erased voxels inside an opaque part of the MRI transfer function.
• Soft anti-aliasing leaves partially blended intensities around the cut boundary.
• Modality detection fails and the volume falls back to CT-style rendering behavior.

In the modality fallback case, a narrow CT-style white band can make a valid carved region appear visually incomplete or weak.

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Interaction With MRI Transfer Functions

MRI cutting changes the underlying scalar values.

The visible result is then determined by the MRI transfer function.

The MR transfer function currently uses:

• A warm-tinted appearance
• Opacity concentrated around the selected intensity region
• Approximately zero opacity near the lower end of the transfer-function curve

Erasing to 0 produces a visually clean hole only when 0 lies in the transparent portion of the transfer function for that MRI series.

Changing the intensity slider or other display settings can therefore change how visible a cut appears without changing the actual carved voxels.

Contour cuts currently use:

scalars.getRange()[0]

This may better represent a transparent background than a fixed 0 when the MRI volume minimum is not zero.

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Live Cutting vs Save Plan Replay

Live cutting and Save Plan reconstruction are designed to use the same Stage 1A spherical-cut behavior.

Live Cutting

Live cutting uses:

buildSphereCutMaskParams

Rebuild / Load Replay

Rebuild and Plan replay use:

resolveSphereCutMaskParamsFromHistory

The stored cut-time mask fields are used during replay.

For MRI, replay forces:

minValue: null

so replay does not reintroduce current-iso gating.

Legacy Cut History entries that do not contain the newer mask fields also receive coverage-only MRI defaults.

There is no intentional Stage 1A code-path difference between live spherical cutting and Save Plan replay.

If a visible difference appears between live and loaded cuts, likely areas to investigate include:

• MRI transfer-function state
• Intensity/display state
• Older Cut History created before Stage 1A
• Modality/profile detection

rather than the sphere-carving rule itself.

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Recommended Next Experiment

If MRI holes still appear incomplete:

1. Load the failing MRI series.

2. Compare:

   scalars.getRange()[0]

   with:

   0

3. Retest spherical and plane-guided cuts using:

   eraseValue = scalars.getRange()[0]

4. Compare the result with the current eraseValue: 0 behavior.

5. Confirm that modality/profile during the cut is:

   MR / mr

   and that the renderer has not fallen back to CT behavior.

6. If the boundary still appears incomplete, compare:

   binaryCarving: false

   against:

   binaryCarving: true

This will help determine whether the remaining visibility comes from:

• The erase value
• The MRI transfer function
• Modality detection
• Soft anti-aliasing at the cut boundary

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Branch Status Summary

Item	Status
Stage 1A geometric MRI sphere / plane-guided cut	Done
eraseValue: 0 initial experiment	Wired; empirical consistency TBD
Cut-time mask fields	Done
Rebuild / Save Plan replay support	Done
Contour MRI carve policy	Unchanged; uses data minimum
Formal MRI dataset test matrix	Not recorded yet