Slicer cli

slicer-cli — drive 3D Slicer over HTTP

slicer-cli is an agent-first wrapper around 3D Slicer's in-process HTTP server (default http://127.0.0.1:2016). This skill teaches you when to invoke it and how to do so safely.

Tool: this skill drives the slicer-cli tool at https://github.com/Lightbridge-KS/slicer-cli. Install it from there.

When to use

Invoke this skill when the user:

• Asks to interact with a running 3D Slicer instance, the MRML scene, or any Slicer node.
• Wants to load, list, inspect, export, or delete volumes inside Slicer.
• Asks to render a slice viewer or 3D view from a volume currently loaded in Slicer.
• Wants to query Slicer's DICOM database via DICOMweb (QIDO/WADO) or pull a study from Orthanc into Slicer.
• Asks to switch Slicer's GUI layout or grab a screenshot of the Slicer window.

Do NOT invoke this skill for:

• Parsing raw DICOM files outside of Slicer (use pydicom or similar).
• Writing image-segmentation algorithms (Slicer modules do this; the CLI does not).
• Launching the Slicer GUI itself (the user starts Slicer manually).
• DICOM DIMSE protocol work (C-STORE, C-FIND, C-MOVE) — that is a separate domain.

First contact (do this on every fresh task)

slicer-cli --json status

• On ok: true → proceed.
• On ok: false with code: E_NOT_RUNNING → stop. Tell the user Slicer is not reachable. Do not fabricate Slicer state.

Optionally cache slicer-cli --json doctor once per session to know which capability probes (render, dicomweb, power-tool-endpoint, …) are green. Do not re-run status / doctor between every command.

Output contract — always pass --json

Every invocation should pass --json. Output is one JSON object per call.

Success envelope:

{"ok": true, "<key>": "...", "<key>": "..."}

Failure envelope:

{
  "ok": false,
  "error": {
    "code": "E_HTTP_5XX",
    "message": "...",
    "hint": "...",
    "endpoint": "/slicer/...",
    "http_status": 500
  }
}

Branch on error.code, never on error.message. Codes are stable public API; messages may be reworded between releases.

Exit code summary (full table → references/errors.md):

Exit	Meaning
0	success
1	bad CLI input (E_BAD_INPUT)
2	Slicer-side HTTP error (E_HTTP_4XX/5XX, E_BAD_RESPONSE)
3	network (E_NOT_RUNNING, E_NETWORK, E_TIMEOUT)
4	config (E_CONFIG)
5	exec disabled (E_EXEC_DISABLED)
6	destructive guard fired (E_DESTRUCTIVE, E_EMPTY_SELECTOR)
7	not yet implemented (E_NOT_IMPLEMENTED)

Safety rules (non-negotiable)

1. Never run these without explicit user instruction:

   • slicer-cli scene clear --confirm (wipes the entire MRML scene).
   • slicer-cli system shutdown --confirm (kills the Slicer process).
   • slicer-cli exec --code '…' / --file … (arbitrary Python in Slicer's process).

2. Hard-stop error codes — surface, do NOT retry, do NOT "fix" by adding flags:

   • E_DESTRUCTIVE → the user did not authorize the destructive action. Surface it; ask the user.
   • E_EMPTY_SELECTOR → an empty <id> was passed. Don't substitute --all. Ask.
   • E_NOT_IMPLEMENTED → the feature lives in a later phase. The hint says which. Don't emulate via api raw or exec unless the user explicitly asks.
   • E_EXEC_DISABLED → don't auto-pass --i-understand-the-risk. Ask.

3. Binary commands require --out: volume export, dicom instance, render slice|threed|screenshot|gltf, and api raw … writing non-JSON. Pass --out - only when piping into another process. In --out - mode the success envelope routes to stderr; stdout is pure binary.

4. Read references/safety.md before touching anything destructive or before invoking exec.

Common commands (the 80% surface)

Command	One-line example
status	slicer-cli --json status
doctor	slicer-cli --json doctor
scene nodes [--class C] [--name N]	slicer-cli --json scene nodes --class vtkMRMLScalarVolumeNode
scene ids	slicer-cli --json scene ids | jq -r '.ids[]'
node show <id>	slicer-cli --json node show vtkMRMLScalarVolumeNode1
node delete <id>	slicer-cli --json node delete vtkMRMLScalarVolumeNode2
volume list	slicer-cli --json volume list
volume show <id>	slicer-cli --json volume show vtkMRMLScalarVolumeNode1
volume export <id> --out PATH	slicer-cli --json volume export vtkMRMLScalarVolumeNode1 --out /tmp/mr.nrrd
volume import <path> [--name N]	slicer-cli --json volume import /data/img.nrrd --name MyImg
render slice [--orientation …] [--offset MM] --out PATH	slicer-cli --json render slice --orientation axial --offset 12 --out /tmp/ax.png
render threed [--look A|P|L|R|I|S] --out PATH	slicer-cli --json render threed --look A --out /tmp/3d.png
dicom studies [--patient PID]	slicer-cli --json dicom studies --patient 12345
dicom series <studyUID>	slicer-cli --json dicom series 1.2.840…
dicom instance <study> <series> <sop> --out PATH	slicer-cli --json dicom instance … --out /tmp/cxr.dcm
sample load <name>	slicer-cli --json sample load MRHead
api routes [--method M] [--destructive]	offline route inventory
api raw <method> <path> --out PATH	escape hatch for unwrapped endpoints

For everything else (gui layout, markup *, exec, config get/show, system shutdown, full flag lists) → references/commands.md.

Worked examples

Example 1 — Render an axial slice from MRHead at offset 12 mm

# 1. Probe.
slicer-cli --json status

# 2. Find the MRHead volume id.
MR_ID=$(slicer-cli --json volume list \
  | jq -r '.volumes[] | select(.name == "MRHead") | .id')

# 3. Render.
slicer-cli --json render slice \
  --orientation axial --offset 12 --out /tmp/ax.png

render slice uses a named view (--view red/yellow/green, default red); --orientation and --offset set the slice plane within that view.

Example 2 — Export a volume to NRRD on disk

slicer-cli --json volume export vtkMRMLScalarVolumeNode1 \
  --out /tmp/mr.nrrd
file /tmp/mr.nrrd        # → "NRRD0004 ..."

--out is mandatory. Use --out - only when piping into another process; in that mode the success envelope ({"ok": true, "bytes": N, …}) routes to stderr.

Example 3 — DICOMweb QIDO (list studies for a patient)

slicer-cli --json dicom studies --patient 12345 \
  | jq '.studies[] | {patient_name, study_date, study_description}'

If the result is [], Slicer's DICOM database has no matching studies — dicom pull populates it from a remote DICOMweb peer. See references/dicomweb.md.

Example 4 — Cleanup pattern after sample load

When loading throwaway sample data and you need to clean up afterwards, capture node ids before AND after, then delete by id:

BEFORE=$(slicer-cli --json scene ids | jq -r '.ids[]' | sort)
slicer-cli --json sample load CTAAbdomenPanoramix
AFTER=$(slicer-cli --json scene ids | jq -r '.ids[]' | sort)

for id in $(comm -13 <(echo "$BEFORE") <(echo "$AFTER")); do
  slicer-cli --json node delete "$id"
done

Don't try to find new nodes by name — sample loads create multiple nodes with version-dependent names. Diffing ids is robust.

Example 5 — Capability check before render-heavy work

slicer-cli --json doctor | jq '.checks[] | select(.ok == false)'

• empty output → all probes green; proceed.
• name: "render" failing → render commands will fail with E_BAD_RESPONSE and a hint mentioning GALLIUM_DRIVER=llvmpipe.
• name: "dicomweb" failing → /dicom/* endpoints unavailable.
• name: "power-tool-endpoint" failing → scene save, dicom pull, markup line, and exec will 5xx.

If a probe is red, surface that to the user before falling back.

Discovery — learn the surface, don't guess

slicer-cli --json api routes                  # offline route inventory
slicer-cli --json api routes --destructive    # routes that need --confirm
slicer-cli --json api routes \
  | jq '.routes[] | select(.note != null)'    # routes with known caveats
slicer-cli --json doctor                      # live capability probe

api routes is offline — it works without Slicer running. Use it to pick the right command/endpoint for a task. The note field flags Slicer-side bugs and CLI workarounds (e.g., accessDICOMwebStudy is bypassed via /exec).

When to load a reference file

Situation	File
Need a less-common command (gui layout, markup line, config, all flags)	references/commands.md
Hit an unfamiliar error.code or want the full code ↔ exit map	references/errors.md
About to do something destructive, or the user asked to use exec	references/safety.md
Working with DICOMweb / Orthanc / dicom pull	references/dicomweb.md
A command failed unexpectedly and the error doesn't tell you why	references/troubleshooting.md