Slicer3:3.6 Final Issues

Issues to include in 3.6.1 patch release

• Fixes for EMSegment command line working with BRAINS (Kilian)
• Fixes for color table preview icons showing up in node selectors (Wendy and Nicole)
• OpenIGTLink reslice performance (Junichi)
• VTK GPU Ray Cast flashing (Julien)
• Crosshair traking modes (Jim); also see bug #861
• Updated meshing module (Curt)
• DicomToNrrd issues reported by AlexZ and Sylvain (Xiaodong)

Done (in branches/Slicer-3-6 after June 10):

• fix for Python programming tutorial (Steve, Luca)

3.6 Release issues

Final punch list for slicer 3.6 release:

Finalized June 10 for 3.6 binaries and Announcements:Slicer3.6

• VTK GPU ray-cast clipping issue
  • bug fix:[Non axis aligned volumes]
  • bug fix:[ROI on Non axis aligned volumes]
  • 90% of the flickering when the camera is inside the volume is removed
• compare view + crosshair issue when loading a scene, the crosshair does not appear in all viewers until the slice location is changed, (Jim)

Done:

• Remove unused color and glyph options from fiber bundle display (Alex)
• fiducial behavior
• fiducial behavior/3D viewer behavior: (Steve, Nicole, Wendy met Jun 7)
  • saw one example of persistent place mode being stolen by pick mode. I think this has to do with inappropriate initialization of modes. It is possible for pick mode to take over until transient-pick mode is explicitly chosen. (FIXED)
  • tractography updates not happening during drag - fixes checked into SlicerVTK and Slicer3 branch
  • tractography updates slow when drag stops (Steve confirmed this was due to update only happening when mouse was moved after button released - made it seem extra slow)
  • widget issues (Nicole putting fixes in SlicerVTK)
• making sure mouse-modes work same in 3D/2D (Wendy and Nicole) Let's call it DONE!
  • done for 2d, Andras has tested it and says it's fine
• editor volume merge feature clarification (Steve meeting Sonia June 2, fixes committed June 3)
• getting BRAINS tests to pass (Hans is working on it)
• tracking down what is making that crash on Mac OsX when several PET volumes are loaded into Slicer (Wendy).
• are there extra pick operations going on? There seems to be a delay after clicking mouse before camera begins to rotate when large models are present in scene. could not replicate - tried 2.5 million triangle model on slicer and paraview and performance is the same
• should picking of fiducials in 3D be disabled unless user explicitly chooses 'pick mode'? Not a good idea to change behavior at this point
  • should parallel behavior be implemented in 2D for consistency? Stevie votes no, Wendy votes yes. Not a good idea to change behavior at this point
• roundtrip to xnat desktop --OK: confirmed that Ron was using dirty files in cache; checking 'always re-download' in the Cache and DataI/O Manager GUI caused fresh download and successful load into slicer. Sometimes, even when you delete cached files thru the GUI, some applicaiton is holding on to files still there and they don't get cleared out. I'm adding a little code to check for remaining files after a ClearCache() is called; if so, we'll warn user that not all files were removed, and to select 'always re-download' to ensure proper data loading.(Wendy)
• view control gui: (Wendy) this guy isn't always updating anymore. He may be a casualty of multiple view nodes in the scene. He was a casualty but is fixed now!
• The diffusion tensor estimation module is using defaults that are not good and partially incorrect. Can the defaults be as follows:
  • for Output DTI volume: DTI Volume
  • for Output Baseline Volume: Baseline DTI Volume
  • for Otsu Threshold Mask: Otsu Threshold Label Volume
• new default color table (Nicole and Mike)
  • Mike working on creating a LUT from this hierarchy this subset, by Jun 7
  • Steve and Nicole to meet June 9 to integrate default editor color table
  • Jun 10: checked in new color files, one from GenericAnatomyColors, and one based on that but with names set to integer values and the color for 255 changed to blue. Wendy making new drop down menu icons.

Issues that cannot be fixed (or aren't crucial to fix) should be listed in the slicer 3.6 release notes.

• finishing up the DICOM file copy on remote upload, also close (Wendy) (DONE)