Introducing Osteotomy Planner: A 3D Slicer extension module to simulate bone cutting, remodeling and repositioning

This blog describes the Osteotomy Planner extension module that was developed for osteotomy simulation. This module was presented at the SPIE Medical Imaging conference recently held in Houston, TX [1]. This extension is available in the 3D Slicer nightly build.


The Osteotomy Planner is a 3D Slicer extension for arranging and cutting closed surface mesh models that represent bone structures.  It can be used for the planning of surgical procedures and analysis of the resulting structures. The input models for this module would typically be generated by segmenting a CT/MRI/etc dataset.  This pre-processing should also include registering the model to a fixed space, in order to allow for direct comparison with reference models.

Data representation

The mesh models are grouped into a model hierarchy (the “Bone Group”).  Each model within the group represents a piece of the overall structure.


The Planner module in the extension allows the user to execute four different types of operations on the bone group: arrangement, cutting, bending and analysis.


Each bone in the model hierarchy can be rotated and translated in 3d space to change its position relative to the rest of the bones.  These rigid transforms are applied using an interactive GUI. The module displays a box representing the orientation and position of the bone, and the box can be moved with click-and-drag movements.


Each bone can be cut using an arbitrarily placed and oriented planar surface.  The cutting surface can be manipulated in 3D in the same manner as the transform box.  The Planner allows the user to preview and adjust the before finalizing. When a model cut is finalized, the original model is removed and replaced with the two resulting pieces.  They then behave as any of the original bone pieces, and can be arranged and cut again.


Bones are bent by placing fiducial control points to define the bending axis.  Once the points are placed a slider is used to adjust the magnitude of the bending transform.


The Osteotomy Planner can generate a number of metrics for analyzing changes to bone structure.  There are currently two types of metrics: volume and surface distance. The enclosed volume of the final state of the model hierarchy is compared to references, the initial state of the hierarchy and an external reference model.   Surface distances are computed between the model hierarchy and the external reference. These distances are displayed as scalar overlays on the models.

Use cases

1) Frontal orbital advancement osteotomy procedure

Craniosynostosis is a birth defect caused by the premature closing of one more sutures on a child’s head. This results in an abnormal skull shape that can potentially cause excessive intracranial pressure. Frontal orbital advancement is one of the surgical treatment procedure. The figure below shows simulation of an orbital rim advancement. In this procedure, the fused frontal bone is separated from the rest of the skull, and advanced to increase the volume.  We also show bending actions applied to the craniosynostosis case. Control points are placed to define the direction and axis of bending, and typical inward and outward bends are shown.



2) Femoral osteotomy procedure

The purpose of this procedure is to correct the angle between the ball joint and the long axis of the femur.  Using a femur model, we simulated a femoral osteotomy as shown below.  First, the joint is separated from the femur (b). A second cut is then made to create a new attachment surface for the joint (c). Finally, the joint is re-positioned at the corrected angle (d).


Video Tutorial



How to access the extension module?


$ git clone git://

Instructions for building and installation can be found here.


[1] Sam Horvath, Beatriz Paniagua, Johan Andruejol, Antonio R. Porras, Marius George Linguraru, Andinet Enquobahrie, “Osteotomy planner: an open-source tool for osteotomy simulation,” Proc. SPIE 10576, Medical Imaging 2018: Image-Guided Procedures, Robotic Interventions, and Modeling, 105762R (13 March 2018)


The project provides just one example of how Kitware partners with clinicians  to build powerful applications using open-source solutions such as 3D Slicer. To learn more about how Kitware can tailor its solutions to meet your research needs, please contact


This work was supported by the National Institute of Health (NIH) Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) grant 5R42HD081712-03 (Image-guided Planning System for Skull Correction in Children with Craniosynostosis: Phase II).

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