Internal:Student Reports

Eleni, Thomas , Angelos

Angelos

Joi

Image-to-Mesh (I2M) Conversion Tool

In mid –June, I began gathering the code for the Image to Mesh Conversion tool and gaining a better understanding of the tool’s capabilities. Before I could start changing the code, I needed to understand how to build the tool in Windows by using QT, ITK, and VTK. Kevin gave me a step by step Readme.txt file that explained how to build QT, ITK, VTK, to generate the files needed to build the Image to Mesh Conversion Tool. There were a few errors, that I encountered when I first compiled the code, but I asked Kevin about the issues and we came up with a temporary fix. Root has granted me local admin rights, and I am now able to download and install any other software that I need to continue my research.
In late June, I started creating a test loading bar for the Image to Mesh Conversion tool to track the progress of mesh generation. The loading bar pops up in the middle of the screen and shows the progress in percentage based on the time it takes it read the input image, generate the mesh, warp the mesh, compress the mesh, and write the output mesh. I would like to change the position of the loading bar to the bottom right of the screen instead of having it popping up in a new widget in the middle. I will be finding out a way to change the position of the loading bar and I will be researching ways to implement a feature to display a multi-tissue labeled mesh using different colors, and ways to implement a feature that will allow the user to cut a cross-section of a mesh to view its interior. I will also start learning about machine learning, so that I will be able to experiment with CBC3D in the future.

3D Slicer CBC3D extension

In late June, I began working to integrate the current versions of the CBC3D extension into 3D slicer. I received the older multi-tissue version of CBC3D code that Fotis used to create the CBC3D extension, and I added it to my repository on Github. I made the changes suggested by Jean-Christophe Fillion-Robin to fix the issues that were preventing the CBC3D extension from being built and packaged. I then changed the Slicer Extensions Index file to point to my repository with the changed code. The Slicer Extensions Index file is used by the Slicer Extensions build system to build, test, package, and upload the extension to the extension server, so that it can be installed using the extension manager. He also suggested that I add a license file to the repository. Github had a copyright template for BSD License, so I used this template to add a License.txt file to the CBC3D Github repository. I updated the documentation page on the Slicer Wiki.
I am currently testing out the code to make sure it would work with the upcoming release of 3D Slicer version 4.9. I built the Slicer source code for the 4.9 version using cmake and QT5. I had some problems building Slicer with Qt in the beginning, but I eventually was able to build it successfully. Once the slicer code was built, I built the current CBC3D extension using the Body Centric Cubic Mesh and Mesh Compression modules. I was able to build the extension binaries on cmake. I then used visual studios 2015 to create the library executables for the Body Centric Cubic Mesh and Mesh Compression modules to be used on 3D Slicer. The Mesh Compression module creates a mesh, but I encountered some problems with displaying the mesh for the Body Centric Cubic Mesh. I am still working on improving the code to make sure everything is working properly.