Is there API documentation or source code to describe how to save and load Annotation and Segmentation? What Annotation and Segmentation data structure are?

[longerking]

Prerequisites

• Which version are you using? (Is it latest?)
• Are you reporting to the correct repository?
• Did you search existing issues? (Were any related?)

Description

Steps to Reproduce the issue

1. When I do add Tools such as LengthTool, FreehandScissorsTool
2. Then I want to save Annotation and Segmentation parameter that I drew on the element to database of vuejs-dicom App. Attempt to load them the next time user open the application
3. Is there API documentation or source code to describe how to save and load Annotation and Segmentation? What Annotation and Segmentation data structure are?

Expected behavior: (What you expected to happen)

Actual behavior: (What actually happened)

CodeSandbox With Reproduction of Issue:

I've added FreehandScissorsTool，but I'm confused about what to do next of saving the Segmentation.

• FreehandScissorsTool

[JamesAPetts]

IO using open source libraries is still a work in progress.

Using dcmjs, a library for DICOM manipulation in JavaScript, its possible to interoperate between cornerstoneTools toolState/labelmaps and DICOM representations.

There are live examples of writing labelmaps to DICOMSEG and annotations to DICOMSR (sources here).

Although DICOMSEG support is relatively good so far, support for all cornerstone annotations in DICOMSR is lacking, see an open issue here.

[longerking]

Thanks, @JamesAPetts . I think I need to explain my problem specifically. I have some data in nii (NIFTI) format, and I want to convert it into segments, and overlay them on the dicom element. is it possible? Is there any way to help me achieve my goal. Can you give me some advice?

[longerking]

Here is a solution

https://codesandbox.io/embed/priceless-newton-ib1m3

[zhihli]

Thanks, @JamesAPetts . I think I need to explain my problem specifically. I have some data in nii (NIFTI) format, and I want to convert it into segments, and overlay them on the dicom element. is it possible? Is there any way to help me achieve my goal. Can you give me some advice?
@longerking I have the same problem as you，Have you solved it？

[longerking]

Thanks, @JamesAPetts . I think I need to explain my problem specifically. I have some data in nii (NIFTI) format, and I want to convert it into segments, and overlay them on the dicom element. is it possible? Is there any way to help me achieve my goal. Can you give me some advice?
@longerking I have the same problem as you，Have you solved it？

can you make your question clearer? if your problem is like mine, here might be the solution

https://codesandbox.io/embed/priceless-newton-ib1m3

[zhihli]

@longerking yes, I hava a nifti file containing segmentation data，I have seen your example，But I don’t know how to get the required data from nifti and draw it, Can you give me some advice?

[longerking]

@longerking yes, I hava a nifti file containing segmentation data，I have seen your example，But I don’t know how to get the required data from nifti and draw it, Can you give me some advice?

cornerstoneTools load labelMap or segmentation source as an array, so ,the first thing you need to do is convert the nifti(nii or nii.gz) data into numpy array. You could do it via python module NiBabel

https://nipy.org/nibabel/installation.html

[zhihli]

@longerking Thank you for your reply，I will try. A digression, are you from China?

[longerking]

Yes and hope my answer will help you.

@longerking Thank you for your reply，I will try. A digression, are you from China?

Yes and hope my answer will help you.

[zhihli]

@longerking 你好，能加个联系方式吗, 想请教下具体实现，谢谢

[longerking]

@longerking 你好，能加个联系方式吗, 想请教下具体实现，谢谢

可以，这是我的邮箱： [email protected]