I am working on the Automatic Lung segmentation in CT images. I have collected some Lung Ct images form the local hospital, Now i would like to create the ground truth of the collected images. But i don't know the exact procedure and open source software for ground truth creation. I would like to know how to create the ground truth and what are different open source software available for it.
Thanks in Advance
I entered this answer for a similar question previously. It may help you as well.
If you are looking for an out of the box solution ITK-SNAP is a good option. If you are a researcher in the area, you can also check out 3D slicer (http://www.slicer.org/) as a research viewer and ITK (http://itk.org/) as a toolkit for development. Both ITK-SNAP and 3d Slicer are built on ITK, so they should give you a feel for what is possible. You may also want to check out OSIRIX. It is an excellent viewer, but I a not sure if it has the ability to segment images.
If you decide to go down the ITK route, you might also be interested in looking up the Lesion Sizing Toolkit (LSTK -https://public.kitware.com/LesionSizingKit/index.php/Main_Page). I am not sure if it is still supported, but it was an ITK-based framework designed to decouple the different operations of lung cancer lesion segmentation and make it easier to do research on specific aspects of lung lesion sizing. 3D Slicer, ITK and the LSTK are all open source and free.
Ground truth in this scenario would just be a manual segmentation that accurately reflects the boundaries of the lung. I would not rely on an automated algorithm (even though they should be pretty good for the lung) as the 'truth'. You would then compare your segmentation results with the 'true' result obtained from the manual segmentation. At most I would use a semi-automatic technique so that you can see the boundaries in each slice and verify that they are 'correct', whatever that means in your use case.
@ Kent M Ogden
I would like to know the procedure for the manual segmentation & also want know the different semi-automatic technique & software use for marking the boundaries in each slice.
where can i get the ground truth marked images of the standard database.
Thanks in advance.
Another interesting ITK-based software for manual contouring is "The Medical Imaging Interaction Toolkit (MITK)" (http://mitk.org/wiki/MITK). Easy to use and you can perform manual contours at several orthogonal slices and then interpolate your 3D surface between them. In the end, you can extract the final surface, after smoothing, as a binary volume.
Hi all, also face the same problem.
How to label groundTruth for 3D/4D images dicom format??
Because imageLabeler or groundTruthLabeler in Matlab just for png/jpeg format can do the label.
Anyone can help me??
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