Segmenting Bone and Volume Rendering CT Datasets

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Hi Everyone,
I have hit a brick wall with segmenting and volume rendering CT DICOM data. Would love some help.
My input is a raw CT Abdo dicom I have converted into a 3D matrix (512x512x118 double). The output I would like to achieve is a 3D rendered volume of the skeletal components of the scan, which I can then manipulate the viewing position / orientation axes (IE. save JPEGs of the skeleton from multiple viewing angles). My aim is to then feed the JPEGs into a neural net.
I can produce an adequate isosurface volume rendered image of the skeleton using the Volume Viewer App, see below. Is there a way to work with the Volume app through command line inputs only? (I have a lot of CTs to process). For each CT volume rendered image, I want to save a JPEG from a pre-set viewing angle (ie. 45*, 90* so on around the Z-axis), which would not be possible using the app on its own. Alternatively, is there a way to save the volume-rendered image to workspace, so I can then manipulate the volume viewing axis?
Thanks for input!
  1 Comment
Alexander Juall
Alexander Juall on 8 Apr 2020
I am a biomedical engineering student at Rowan University. My capstone project surrounds the task of finding the volume of a spatious gap within subchondral bone. I have tried several volume rendering toolboxes including, the image processing toolbox, volume viewer, and color thresholder. These can all segment a dicom image based on a manually set threshold. However, these toolboxes cannot creat ROIs, meaning that when an image is segmented, due to the grayscale nature of dicom files, the entire image is highlighted. I am yet to find a program that can perform these three tasks, create a ROI, threshold the ROI, and produce an output volume for the ROI. Does anyone know of a file exchange or toolbox that could assist? I have tried creating my own code to perform these tasks. However, I have been unable to interact with dicom images on my own. I have only been able to create a video player that displays my dicom directory. Any help is greatly appreciated!

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Accepted Answer

Sharan Paramasivam Murugesan
Unfortunately the ability to work with Volume Viewer app programmatically or to manipulate the volume viewing axis via workspace variable is not available yet in MATLAB. However, our developers are aware of this feature request and are planning this for a future release.

More Answers (2)

Adi Vainiger
Adi Vainiger on 7 Nov 2018
Edited: Adi Vainiger on 7 Nov 2018
hey Is this feature already available in 2018b? I wish to set the exact viewing angles of the volume , and not by mouse movement . Also , how can I add more features to 3D view - as scale intensities next to the intensities bar ? scale of axes ? etc.

Sailesh Sidhwani
Sailesh Sidhwani on 28 Nov 2018
In R2018b, Image Processing Toolbox added a new standalone volume viewing component called 'volshow'. You can access all the properties from the command line.
The Camera Properties viz. 'CameraPosition', 'CameraTarget', 'CameraUpvector' can be used to set the viewing angle during contruction and no mouse interaction would be needed.
The following doc page also has an example on how to save the current frame:

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