Imaging Protocols for Stereotactic Navigation

For CT and MRI techs and schedulers preparing a scan for image-guided surgery.

Printable version. A one-page reference with every parameter in a single table — for the control room wall or the scanner.
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A navigation scan has requirements a diagnostic scan doesn’t. A study that reads perfectly can still fail at registration — and by then the patient is on the table. This covers what navigation systems need and the handful of things that most often make a scan unusable.

Every navigation scan

  • Contiguous slices. Slice spacing must equal slice thickness — no gap, no overlap. This is the most common reason a scan can’t be used.
  • Constant slice thickness through the entire series.
  • Scan at 1 mm or less. This is the setting that most affects how the case goes. The maximums below are limits, not targets — a 3 mm study will register and navigate, but the reconstructions are coarse, planning off them is harder, and accuracy degrades with every millimeter. If the scanner can give you 1 mm, give us 1 mm.
  • Square matrix, 256 × 256 or 512 × 512, with square pixels.
  • Smallest field of view that covers the region of interest. Circular or square both work. Size depends on the application.
  • Axial slices preferred. MR may be acquired axially or reformatted into axial slices.
  • Contrast may be given before scanning if the case calls for it.
  • Remove any mask or head covering before scanning.

CT

Standard soft tissue algorithm · no gantry tilt · axial or helical at 1:1 pitch, checking reconstructions for artifact.

MR

No oblique slices. Scan along the axial plane.

Cranial and stereotactic

Maximum slice thickness: 3 mm. Same parameters for both — what changes is how much you capture.

Cranial navigation — FOV up to 25 cm. Scan from the superior aspect of the horizontal mandible through the vertex, with an air gap above the head. Include every fiducial marker, the ears, the maxillary teeth and the tip of the nose. The nose must be the most anterior point in the scan.

Stereotactic and DBS — FOV 28–32 cm, wider because the frame must be captured. Include the AC/PC structures, the target region, the entry region for frameless cases, and the frame itself on the registration scan.

If anchors are implanted for a stereotactic platform, they carry their own scan requirements — check the manufacturer’s instructions for those.

ENT

Maximum slice thickness: 2 mm — tighter than cranial. A 3 mm scan that would pass for cranial will be rejected here.

FOV up to 25 cm, including the top of the head, the skull base and the nose. If the study will be merged with another, leave an air gap around the head.

Typical procedures: anterior skull base, endoscopic sinus surgery, transsphenoidal and endoscopic pituitary approaches.

Spine

Maximum slice thickness: 2 mm.

FOV up to 18 cm — considerably tighter than cranial. Completely encompass every vertebra of interest, including the spinous and transverse processes. Clipping the processes costs you registration landmarks.

Scan region: half a vertebra above and half a vertebra below the region of interest.

Typical procedures: pedicle screw placement, posterior and transforaminal lumbar interbody fusion, cervical and thoracic fusion, minimally invasive approaches.

What makes a scan unusable

  1. A gap between slices — spacing set larger than thickness
  2. Gantry tilt on a CT — not recoverable
  3. A 3 mm ENT or spine scan — fine for cranial, rejected by both
  4. Cropped anatomy — the nose on cranial, the transverse processes on spine, the frame on stereotactic
  5. Slice thickness varying through the series
  6. Oblique slices on MR

Unsure before you scan? Call us — two minutes on the phone beats rescanning a patient.

Compiled by PRONAV from current manufacturer specifications. Confirm against your system’s documentation before scanning. Last reviewed September 2026.