Dear greatest community of all,
I am having issues displaying models whilst segments are looking just fine in 3D view. I am running slicer on linux on a calculation server, never had this kind of troubles before…
affects both slicer 10 and 11.
You need to explain your issue a little better. It is not clear from the screenshot.
My apologies Murat,
when visualising a model, the light projected on the model seem to be coming only from one direction.
If I am looking from a certain angle, model appears:
but as I am changing angle, the model start loosing illumniation:
And eventually becomes completely black upon a full 90° rotation:
This issue is happenning on both slicer10 and 11. To clarify, we are operating on a Linux-based system. I connect to our calculation server cluster interactively using NoMachine for remote access.
This issue is only on .vtk models, whereas .obj and segmentations are looking fine.
More information. I just uploaded some old .vtk files produced via slicermorph or slicermorph+distance to distance models and they loaded fine. So neither slicer 10 or 11 or my environment settings are to blame I think.
However, tt seems that it is only the most recent .vtk files I created via slicermorph that have been affected. I think those would have been created on the latest build (version 11).
I’m now trying creating a .vtk model on slicermorph slicer 10 to see if that works.
I have run into this before, but unfortunately I don’t remember the details of what the problem was or what made it go away. I haven’t ever used SlicerMorph, though, so that can’t have been the source of the problem when I ran into it. Try turning off “Shadows visibilty” in the 3D view settings. I think the most likely source of the problem is that there is something wrong with the surface normals on these models in particular. Is it possible that the surface normals for these models are unset, or all in the same direction? I think that would lead to the type of behavior you are seeing (i.e. uniform illumination from a single direction across the entire model, which disappears completely at 90 degrees to the normal vector). You could try Surface Toolbox to recalculate the surface normals and see if that fixes the issue.
As @mikebind said this is probably related to surface normals. Are vtk files generated the same way as the obj? Why do you have two different formats?
Hello, and thank you for your answers.
Shadows visibility was set to off. I tried to set it to “on,” and that crashed Slicer 11 on my server. I restarted it, and it was back to the default “off.”
I started looking into the Surface Toolbox, and using the “Splitting” function in Compute Surface Normals worked. I also tried: 1) auto_orient normals, which had no effect; and 2) flip normals, which had the expected effect: the model lighting effect turned on, until I rotated the model by 90°, and then it went black again.
So, splitting works. I set the feature angle for splitting at 90, and I have a good result (not sure what I’d need to change it to but 90° seemed to give the best result). This model is the result of a model-to-model distance computation, and I can tell the end result is correct, so it is purely a display problem that is only apparent in Slicer 11, not Slicer 10.
An important note also: I only used SlicerMorph GPA to create these models, so I don’t know yet if it is specific to SlicerMorph or to Slicer 11 in general on my setup. What is clear is that if I run a GPA in Slicer 11 and load/create a model via the interactive 3D tab, I get those “black” models: the original model and the warped model, even though my original model, if loaded separately, appears normal.
So, things go awry when I use SlicerMorph on Slicer 11 only. Slicer 10 is okay.
Why I use .vtk and .obj is possibly only because I use different modules to export models and they are set by default to either .obj and .vtk. I should probably have enforced using only .obj only ?