[Bug] Use Segmentation tools with Stack Viewport

[1isten]

Describe the Bug

This documentation link is broken: https://www.cornerstonejs.org/docs/tutorials/basic-segmentation-tools/#read-more

https://www.cornerstonejs.org/live-examples/segmentationRendering.html

Steps to Reproduce

Checkout above link

The current behavior

The segmentation rendering example is broken, can't find any example of using segmentation tool for stack viewport.

The expected behavior

Please give an example of using segmentation tool for stack viewport. In my case, I render single dicom file from my local filesystem (using stack viewport like this example). But I can't figure out how to add segmentation tool then

OS

macOS 13.3

Node version

16.17.1

Browser

Chrome 115.0.5790.114

[sedghi]

sorry about that it is wrong. I will edit it Stack Viewport segmentation is not ready yet unfortunately but we are working on it

[1isten]

@sedghi So currently we can only use segmentation in volume viewport?

If that's the case, may I ask another question (sorry I'm not familiar with cornerstone...)

Can I create a volume viewport to display just a single dicom file from my local filesystem?

[sedghi]

yes currently only in volume viewports. I haven't tried it it might work

[1isten]

May I know if it is possible to load a single local dicom file such as this example: https://www.cornerstonejs.org/live-examples/local.html, but use volume viewport instead of stack viewport?

[JiaBob]

I also have such questions. The example shows how to load data from a server. What if I just want to load local dicom or nifti files? Could you also let me know how to create a server to provide such files? Thank you very much!

[sedghi]

You can look into our dicomImageLoader package for more infor on how to load.

Nifti -> still in progress PR #696

DICOM ->

• Using WADO-RS and dicomweb standard https://www.dicomstandard.org/using/dicomweb and using open source pacs such as orthanc or dcm4chee. Most examples in the repo are this type which is our server in cloudfront (but you can achieve the same with other pacs)

see for instance example here

 const imageIds = await createImageIdsAndCacheMetaData({
    StudyInstanceUID:
      '1.3.6.1.4.1.14519.5.2.1.7009.2403.334240657131972136850343327463',
    SeriesInstanceUID:
      '1.3.6.1.4.1.14519.5.2.1.7009.2403.226151125820845824875394858561',
    wadoRsRoot: 'https://d3t6nz73ql33tx.cloudfront.net/dicomweb',
  });

Then imageIds are the path to the data that is created by cornerstone3D. Read more about imageIds here

• Using WADO-URI, example here
• Using dicomfile itself either hosted or as a drag and drop

[sedghi]

May I know if it is possible to load a single local dicom file such as this example: cornerstonejs.org/live-examples/local.html, but use volume viewport instead of stack viewport?

You can convert stack to volumes and vice versa if you need, look at this example

[sedghi]

Could you also let me know how to create a server to provide such files? Thank you very much!

If you don't want to deal with all these you can look into OHIF which handles these complexities. For instance https://docs.ohif.org/configuration/dataSources/dicom-web#running-orthanc

[JiaBob]

Thanks for your answers! It takes time to dive into them. Let me try.

[1isten]

Now I've used the orthanc server to retrieve metadata and successfully created the volume viewport to render some dicoms

But I found that even if the dicomweb server is used, cornerstone's volume viewport still cannot render some dicoms (such as US dicom files) which missing below tags:

• 0020,0037 - ImageOrientationPatient
• 0020,0032 - ImagePositionPatient
• etc...

when those tags metadata is missing, creating volume viewport causes below error:

I think the error is raised because imagePlaneModule metadata is missing some required value:

So does that mean the volume viewport cannot be used for such dicom files or do you have any other solutions? @sedghi

Btw, may we know when Stack Viewport segmentation would be ready? Thanks

[sedghi]

No you are correct, if that metadata is missing you can't reconstruct a volume. We are pushing on making the stack segmentation work soon #666

[sedghi]

https://github.com/cornerstonejs/cornerstone3D/pull/670