OrthoMesh3D. Plan orthopaedic surgery in 3D using Blender

After completing this lecture you will be able to open DICOM CT scan in Osirix and Convert it into a Mesh Model file that Meshmixer and Blender can read.

In this lecture, the import OBJ and STL file format options are enabled in Blender. Using this file format Blender can read the 3D model that you have created in the DICOM software of your preference such as Osirix for Mac Users or Vesalius for PC users.

Autodesk meshmixer is a fantastic free software for creating and manipulating 3D files for 3D printing. Whether you need to clean up a 3D scan, do some 3D printing or design an object, meshmixer can help. In this lecture the 3D model created in OsiriX is cleaned up, and prepared to be imported in Blender

DICOM2Mesh is an addon for Blender 2.8 that allows to convert DICOM volumes to 3D meshes and import them to Blender in the form of a Mesh Model. YOU CAN DOWNLOAD the script from the WEBSITE orthomesh3d.com It is based on a command line tool used to transform a DICOM volume into a 3d surface mesh (obj, stl or ply). Several mesh processing routines can be enabled, such as mesh reduction, smoothing or cleaning. Works on Linux, OSX and Windows. The add on depends on this command line tool to import convert DICOM volumes to 3D meshes

Install the OrthoMesh3D Blender Addon through the Preferences section of Blender. The Addon is given for free and can be downloaded through the "Resources" section of  this lecture. Download the file or the source code, one or the other, both are the same. For the Boolean operations of the OrthoMesh3D to work, it is a REQUIREMENT to have the JMesh tool installed first. Please refer to last lecture of the Introduction Section of the Udemy lecture on how to get and install the JMesh tool.

Use the OrthoMesh3D toolbar in blender for 3D surgical planning. The first step is to import the Meshmixer STL or OBJ file into Blender, set the correct size of the Grid of the Viewport in Blender and the desired measurements units, "X-ray" your model and understand the size of it in Blender.

Separate the Radius from the Ulna. You can positioning the forearm in the position that you wish, pronation or supination. I prefer to have it in supination.

3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. It can be downloaded for any computer platform - Windows, MacOS, Linux- from www.slicer.org. Documentation for the 3D Slicer can be found at https://www.slicer.org/wiki/Documentation/4.10/Training. In this bonus section a fast simple and reliable method of creating high quality models is demonstrated. Using this method, in one stage using the 3D slicer software you can segment the bone from the CT scan, utilizing the DICOM data, create the 3D models of the bones, separate the models - for example radius and ulna - and export them in the STL file format which can be inserted in Blender for surgical planning. This process eliminates several steps and minimizes processing time while getting better quality 3D models

Decimate Modifier. The Decimate modifier allows you to reduce the vertex/face count of a mesh with minimal shape changes. This is not usually used on meshes which have been created by modeling carefully and economically (where all vertices and faces are necessary to correctly define the shape)

This Updated version of the OrthoMesh3D has the following fixes/updates:

1. Grow selection of Mesh for Segmentation - automation of the selection process of areas of interest on the bone for later separation

2. Automated Separation of the osteotomy, ie after the osteotomy is made, the osteomized bone can be separated into two three or more fragments depending on the number of osteotomies with the press of a button

The new version (1.1) has some additional features which are outlined or described below:

1. Set up scene function has been added that allows to set up the scene ready for planning. This is a 3 in 1 function: (a) remove the Cube from the scene, (b) set the grid scale to mm instead of meters that it is the default in Blender (Under Scene Properties the scale is set to 0.001 from 1.000 and (c) change the reporting Length from meters to mm

2. Add plane function: generate a section plane object at the bone that allows to see a cross section of the bone. This plane can be moved anywhere in the bone and the section plane will update automatically

3. Undo and Redo buttons added at the suggestion of students that allow you to undo and redo steps in your plan

The new script is given for FREE under the resources of this Lecture. To install the new version you need uninstall the old version. To do that go to Blender – Edit - Preferences and search for OrthoMesh under Add-ons. Once you find it, click on the arrow to expand the options and click Remove. Then click install and install the new script as described in the original lecture on how to install OrthoMesh3D.

Thank you everyone for your feedback. If you have problems with the new version or questions please feel free to contact me.

Respectfully,

Anastasios Papadonikolakis, MD, PhD

Using the Animation capabilities of Blender -called "Bones" or Armature - you will learn how to animate the forearm, simulate the forearm pronation supination. In this section Forward Kinematics is used to achieve the animation

Learn how to use Boolean operations to create osteotomies for deformity correction. The OrthoMesh3D add on helps speed up this process in Blender.

In this section you will learn how to superimpose the normal bone to the pathologic for analysis of the deformity. The normal radius and ulna are provided to you for free. You can download them and practice this method of analyzing the deformity of the forearm. Under the Resources link of the this lecture, you will find the file that you need to download, the name of the file is Archive.zip

Using Inkscape and knowing the dimensions of your hardware, in this case the size of the plate, you will learn how to import the 3.5 mm DCP ulnar Synthes plate in Blender. Inkscape will allow you to convert the picture of the plate from pixels to a curve - in other words from Bitmap format to SVG file.

In this lecture the creation of the 3D cutting guide for the deformed ulna is explained. This is done using the Boolean operations within Blender - OrthoMesh3D script

This cutting guide serves as a cutting jig, and is designed with  screw holes of the plate as a reduction guide for the correction of the deformity. The 3.5mm Synthes plate that was designed in Blender in Lecture 17 is used for the fixation of the osteotomized ulna

In this lecture you will learn how to animate the corrective osteotomy. The animation can be used for demonstration purposes. You can use it in your Powerpoint presentation or conference presentation

Model in 3D a humeral stem using 2D photos of the stem

Draw in 3D the Prosthetic Humeral Head

Draw in 3D an All poly glenoid component from 2D Photos

Create a library of the 3D All poly glenoid implants

Draw the Glenospheres of the Reverse Total Shoulder Replacement

Draw in 3D the Baseplates of the Reverse Total Shoulder Replacement

Draw in 3D the Humeral Tray and Polyethylene Inserts

Add the Scapulothoracic Motion and animate the scapulohumeral Rhythm to the Reverse Total Shoulder Replacement

Animate the Reverse Total Shoulder using Armature Bones

Implement Auto Inverse Kinematics and scapulohumeral rhythm

Plan the anatomic total shoulder replacement

Surgical planning of a hemiarthroplasty for a shoulder with severe glenohumeral arthritis and a Walch type C  retroverted glenoid

This is a method of growing a segment from a CT scan using Slicer. The grow from seeds is a good method for separation of joints or segments that are highly arthritic or have similar image intensity and they are very close to each other (or even fused together in some places). The island method cannot separate them easily. In the past, “Grow from seeds” effect ignored masking settings.  Region growing can be restricted to certain areas by using “Masking” section in the Segment Editor. Masked area can be defined by image intensity range and/or existing segments.

• Included in this section is a CT DICOM data set for practice. The name of the patient on the CT is factitious