3D Slicer RVXLiverSegmentation plug-in questions

[grojasy]

I am trying to use your 3D Slicer RVXLiverSegmentation plug-in (Windows 10), but I have some problems:

i) I specified all portal vein nodes. Why does the button "Extract Vessels from node tree" continue in gray color without activating it? ii) When I was trying to specify the nodes of the vessels, I tried to view the "node position help window". But, that window appears completely white color. Without any tree vessels. Why?

Sincerely,

Gonzalo Rojas Costa

[Thibault-Pelletier]

Hi @grojasy, Thank you for using our plugin.

i) Regarding your questions, the Extract Vessels from node tree is grayed out unless every point in the tree is positionned in the 2D / 3D view.

If one point or more is not placed in 3D then the button will remain locked. If one node can't be placed in the liver (for instance one of the optional branches) then you should remove it from the tree by clicking on the trash bin icon.

When every point is placed, the tree should look like this :

ii) Thank you for noticing this problem. It appears the help files are not properly packaged in the module at the moment. I will fix this issue right away.

[grojasy]

Ok:

i) I will test it. But, I loaded the data in 3D Slicer, but I will have to specify the points again because the module did not detect them. Why?

ii) When can I download the fixed version?

Sincerely,

Gonzalo Rojas Costa

[Thibault-Pelletier]

@grojasy I'm not entirely sure what you mean by loading the detecting the points.

At the moment, the plugin doesn't support reloading previous annotations generated by the plugin. You can view the results exported using conventionnal 3D Slicer tools (segmentations, markups and volumes)

For the points, you need to click on the name on the point in the branch node name widget before placing the point in the views. It will switch on the placement for the associated markups node and the name in the tree will switch to PLACING.

If you try placing points using a markup directly, the plugin will have no way to know which point you are currently placing so this feature is also not supported.

[grojasy]

I specified the node positions of portal veins. Then I pressed the button "Extract vessels from node tree". I got a large error window. Why?

[Thibault-Pelletier]

@grojasy thank you for your feedback on this. It appears you are using a preview version of 3D Slicer.

I tried the plugin on this version and there are a numbers of changes to the libraries we use including the image processing. We will have to investigate further to fixe this issue for the coming 3D Slicer version and the current one.

In the meantime, you can use the plugin in the official 5.0.3 3D Slicer release. I will keep you posted in this thread when the problem is resolved for version 5.1+

Please note also that the fix to the help icons has been solved and is now deployed in 3D Slicer's extension manager.

[Flex8786]

Hello Thibault, it seems that I have the same problem as @grojasy. I specified all node points of the portal tree, but the "Extract vessels from node tree" remains grey (not activated).

Is there any help for this problem?

Best regards and thanks for this great plug-in,

Felix

[grojasy]

Yes. I had a similar problem. The solution is that you must specify all the nodes, or you must delete it by pressing the trash icon. You should not leave any node undefined.

[Thibault-Pelletier]

@Flex8786 thank you for your feedback on the plugin and @grojasy thank you for your assistance on this subject.

As @grojasy said, all the nodes need to be specified before extracting the vessels from the tree. This behavior seems to be unexpected and not self explanatory so we may adapt how this information is reported or change how the vessels are extracted from partial tree definition in the future.

If removing or specifying the nodes doesn't resolve your problem, don't hesitate to reach out to us.

[Flex8786]

@grojasy and @Thibault-Pelletier Thanks for your response. However, as can be seen in the screenshot, I defined all nodes and deleted the optional ones. Nonetheless, the "Extract vessels from node tree" still remains grey. I tried several times doing everything again, but only one time it turned black. However, when I tried to extract the vessels from node tree, an error occurred. Unfortunately, I did not make a screenshot of the error.