Dear Fahime Rezai,

have you tried ImageJ software? It is freely available, with a lot of plug-ins to read the various file formats. Often CT scans are stored in a proprietary format, with the option to save them as DICOM format files. In ImageJ, one can write a scipt to do the contouring. But a lot of libraries with these functions are freely available.

Hope this helps. Kind regards, Harrie Verhoeven.

Dear F. Rezai,

Generally speaking this is area of research in CT imaging as the low and nondescript contrast of organ systems make it difficult to contour CT image data of organs. 

https://www.ncbi.nlm.nih.gov/pubmed/24821646

https://www.ncbi.nlm.nih.gov/pubmed/24593731

https://www.ncbi.nlm.nih.gov/pubmed/21940543

These groups may be willing to share software with you.  Another 3D volumetric program that you may find useful is ITK-SNAP, www.itksnap.org.

Also you can try a more modern version of ImageJ, Fiji, fiji.sc.  Fiji has many additive functions included which you will find helpful.  One of the more powerful is the Weka classification engine which can be used to build image classification models of the type you want.  

Good luck with your project,

Doug Morris

http://www.itksnap.org

http://fiji.sc

Dear Fahime,

The Eclipse planning system (commercially available for radiotherapy planning) has tools which allow for automatic segmentation of soft tissue structures, without the need for a contrast scan. Some structures such as the lung can be done with very little manual input, but others can be done semi-automatically based on manipulations of the CT data (window levels, geometry, VOI boxes) . I assume other commerically available treatment planning systems have similar functions.

Lloyd

Dear Fahime,

as Mr. Smyth mentioned, several software used for radiotherapy treatment planning is feasible for automatic segmentation of soft tissues based on CT scans. As far as I know, software such as Ecplipse (Varian), Pinnacle (Philips) and RayStation (RaySearch Lab.) has such tools for atlas-based or model-based segmentation.

You can have a look at this link, where RayStation's abilities regarding contouring are explained (also with demonstration video):

https://www.raysearchlabs.com/contouring-organs-at-risk/

And I found a literature, that could be interesting or you:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971890/

Off course, you will find a lot of more publications searching for keywords such as "automatic conturing", "Atlas-based segmentation", "model-based-segmentation", etc.

Good luck and have fun. Best regards