This bug is only reproducible when OpenIGTLinkIF is set as start-up module in the application settings/module settings.

Some more info:

It's not necessary to set the OpenIGTLinkIF module as startup module. It's enough if you just switch to the OpenIGTLinkIF module at any time, and after that if a model is generated the slices disappear from the 3D view.

If I skip the import of the MRML scene that the model maker generates, then the problem doesn't occur.

The implementation of MRML scene import from CLI results is very messy, so there may be some issues there. But probably the main culprit is the OpenIGTLinkIF module, as if it is not opened, then the issue doesn't occur.

Thanks for reporting. I could reproduce this with the latest build on Mac OS X (10.7).

I could not reproduce the problem, when I comment out the code inside qSlicerOpenIGTLinkIFModule::setMRMLScene(vtkMRMLScene* scene). I suspect that the bug is related to mrml event handlers in qSlicerOpenIGTLinkIFModule class.

I would suspect that the issue is not related to event handlers as they cannot really change classes. For me it seems more probably that the Qt MVC classes (qMRMLSceneModel-derived classes) have some problem, because these classes are only instantiated when the module GUI is created, they are able to modify the nodes, and they are very complex (therefore easy to make mistakes in the implementation).

That is possible. I tracked down my previous finding, and found that the qMRMLSceneModel::setMRMLScene(scene) call in qMRMLIGTLConnectorTreeView::setMRMLScene(vtkMRMLScene* scene) caused the issue.

I could reproduce the same bug with Annotations instead of OpenIGTLinkIF. Annotations also uses qMRMLSceneModel.

Tractography Display module also reproduced the bug.

Wow. I think it's time to notify the others on the slicer-devel list. Looks like we found an important bug.

I agree! I updated the category and assigned this issue to Jc.

On Ubuntu 13.10, using a Debug build of Slicer r22924, I am not able to reproduce the issue following the same sequence as the video.

Unfortunately, the problem is still the same (just tried on the latest Win64 nightly build).

How to reproduce:

• Start Slicer
• Open the Annotations module (or open the OpenIGTLinkIF module, or probably other module with a GUI that has a scene model based widget)
• Go to the Sample data module and download MRHead
• Go to the Editor module and paint with 2 different labels
• Go to the Model maker module and create models from the labelmap
• Click the eye icon of the red slice in the 3D view => red slice appears in the 3D view
• Click the eye icon of the yellow slice in the 3D view => ERROR: yellow slice does not appear in the 3D view
• Click the eye icon of the green slice in the 3D view => ERROR: green slice does not appear in the 3D view

I confirm, the problem is still there with today's nightly.
What I didn't know at the time of reporting this issue was that it's not OpenIGTLinkIF specific. Annotations module does the same. Maybe the bug should be renamed.

There is only one thing I see different. With today's version, when I open/close the eye icon of the green slice, the green model does not change its color.

But the slice still cannot be visualized, the slice intersections are not visible, and there are those contours around the segmented areas in the red slice.

I confirm this an issue. I will be looking at this in the coming days.

Wonder if this is related to 0003707

The problem is still there with the latest nightly build

Reproducible after updating the slice intersections code:
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23495

I can get to an error state (non updating slice intersections) with these steps:

• start slicer
• download sample data MRHead
• enter Annotations or Markups or Models module
• turn on Slice Intersections from Crosshairs drop down

If you move the slice offest slider, the slice intersections don't update. I toggled visibility on the yellow slice, it did show up and update the slice intersections on sliding, but the red and green sliders don't update slice intersections. Toggling the red and green slices visible updates the slice intersections in 2D and the slices do show up in 3D.

It might possibly be related to bug 0003783 in that the annotations or model hierarchy is over riding the slice model display settings?

I am unable to reproduce the problem. Please, re-open if this is still a problem.

Unfortunately, the problem is still the same (just tried on the latest
Win64 nightly build).

How to reproduce:

• Start Slicer
• Open the Annotations module (or open the OpenIGTLinkIF module, or probably other module with a GUI that has a scene model based widget)
• Go to the Sample data module and download MRHead
• Go to the Editor module and paint with 2 different labels
• Go to the Model maker module and create models from the labelmap
• Click the eye icon of the red slice in the 3D view => red slice appears in the 3D view
• Click the eye icon of the yellow slice in the 3D view => ERROR: yellow slice does not appear in the 3D view
• Click the eye icon of the green slice in the 3D view => ERROR: green slice does not appear in the 3D view

If I skip the scene import step when model maker processing is finished then there is no issue.

If Annotation module is opened after the model making then there is no issue.

So, probably mini-scene import at the end of CLI execution and qMRMLSceneModel initialization has some interference. Both are large and complicated code, so it is not surprising, it's just very difficult to track down the issue.

On windows 64-bit, downloading latest nightly (2014-08-15), I was using the default parameter for ModelMaker.

Here is a list of updated steps leading to the problem:

1) Start Slicer
2) Open the Annotations module
3) Go to the Sample data module and download MRHead
4) Go to the Editor module and paint with 2 different labels
5) Go to the Model maker module
6) Create a new model hierarchy for the output
7) Click Apply
8) Click the eye icon of the red slice in the 3D view => red slice appears in the 3D view
9) Click the eye icon of the yellow slice in the 3D view => ERROR: yellow slice does not appear in the 3D view
10) Click the eye icon of the green slice in the 3D view => ERROR: green slice does not appear in the 3D view

As of 2015-09-22, after following steps reported in note 12389 I confirm this is still an issue.

Menu -> file -> Close scene .. leads to a crash.

From JC, these commands in the console also lead to the error state:
m = slicer.qMRMLSceneDisplayableModel()
m.setMRMLScene(slicer.mrmlScene)

Fixed in r24723
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24723

This issue has been fixed quite a long time ago. Status of ticket was not updated.