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DCBIA-OrthoLab / EasyClip-Extension

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Flipped orientation #13

Closed luciacev closed 3 years ago

luciacev commented 4 years ago

When surface models (stl or vtk format) are loaded into Slicer 4.11, we can orient them in the Slicer Coordinate system following our protocol described by Ruellas in 2016. When the oriented files are saved and later uploaded back in Slicer, we must now select the coordinate system as RAS. However, if we edit the surface model files with EasyClip and save them in Slicer, when we upload them once again in Slicer they are flipped 180 degrees (anterior shows as posterior) and it does not make a difference if we upload them as LPS or RAS orientation, they are always flipped.

Please see video recording saved to google DCBIA/KitwareSlicerextensionswork/VIDEOS on BUGS

cc: @jcfr @bpaniagua @jehoctor @aruellas

allemangD commented 3 years ago

I'm not able to reproduce on the current stable version of Slicer (4.11.20210226) on Linux or Mac. I'm using the oriented file from https://github.com/DCBIA-OrthoLab/CMFreg/issues/29#issuecomment-645412387 A1MxT1oriented.vtk

These are the steps I took

  1. Load A1MxT1oriented.vtk in Slicer (with RAS option) image
  2. Cut the model in half with EasyClip image
  3. Rename the model to A1MxT1oriented-clipped
  4. Save the model
    • Saved as A1MxT1oriented-clipped.vtk with default options image
  5. Delete all models from the Slicer scene
  6. Load A1MxT1oriented.vtk and A1MxT1oriented-clipped.vtk (both with RAS option) image

The screenshots were done on Linux, but I also tested on a Mac and the results are the same. @luciacev, could you try this again and see if the issue has been resolved by updates to Slicer? If the problem persists, could you share the problematic files?

luciacev commented 3 years ago

Hi David Issue 13 has been solved incurrent version , ok?

On Friday, July 23, 2021, David Allemang @.***> wrote:

I'm not able to reproduce on the current stable version of Slicer (4.11.20210226) on Linux or Mac. I'm using the oriented file from DCBIA-OrthoLab/CMFreg#29 (comment) https://github.com/DCBIA-OrthoLab/CMFreg/issues/29#issuecomment-645412387 A1MxT1oriented.vtk

These are the steps I took

  1. Load A1MxT1oriented.vtk in Slicer (with RAS option) [image: image] https://user-images.githubusercontent.com/10702931/126788780-ce270e88-a2de-40cc-9df1-b6d73098b02f.png
  2. Cut the model in half with EasyClip [image: image] https://user-images.githubusercontent.com/10702931/126788883-b24b0942-8448-44e2-b091-1e340ec8fadc.png
  3. Rename the model to A1MxT1oriented-clipped
  4. Save the model
  5. Delete all models from the Slicer scene
  6. Load A1MxT1oriented.vtk and A1MxT1oriented-clipped.vtk (both with RAS option) [image: image] https://user-images.githubusercontent.com/10702931/126789545-0fc9051c-0c22-4b8b-8f05-c468f858365e.png

The screenshots were done on Linux, but I also tested on a Mac and the results are the same. @luciacev https://github.com/luciacev, could you try this again and see if the issue has been resolved by updates to Slicer? If the problem persists, could you share the problematic files?

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allemangD commented 3 years ago

In that case I'll close the issue. @luciacev if you find there is a case where it is still broken, please reopen the issue and, if possible, share the problematic file.

Thanks!