Slicer3:3.6 Final Issues

Issues to include in 3.6.1 patch release

• Fixes for EMSegment command line working with BRAINS (Kilian)
• VTK GPU Ray Cast flashing (Julien)
• make sure all BRAINS and Registration fixes are in the 3.6 branch (Hans and Jim with help from Dominik)
• Import scene does not update 3D viewer (Nicole, Wendy) http://na-mic.org/Mantis/view.php?id=840
• brackets in filenames (Steve - fixed in trunk, migrate to branch if tests well) http://www.na-mic.org/Bug/view.php?id=851
• changes to avoid error messages when using single-slice volumes (Steve) - in trunk, need to move to branch
• Editor rounding issue [1] (Steve) - in trunk, need to move to branch
• Snapshot issue [2] (Alex)
• CompareView issues 927, 929, 936
• CompareView + Crosshairs issue 928
• KWWidgets issue with "%" in file names produced by DICOM browser -- fixed in trunk, need to make sure propagated to 3.6 bug 886 (Steve)
• Diffusion Tensor Glyphs not showing (Demian)
• Diffusion Tensor Tractography having a strange no-tracking through high FA areas case (Demian)

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

• check for duplicate filepaths when saving data (Alex) http://www.na-mic.org/Bug/view.php?id=925
• tractography seeding issue (Alexy) http://www.na-mic.org/Bug/view.php?id=885: Changed Tracttography/LabelMapSeeding module: 1. added UseIndexSpace option for seeding placement. 2. Also found that IJK indexes used for traversing the label volume were floats. Changed them to doubles that may crate slightly different tracts, but it is less prone to error accumulation (Alex).
• Added multi-label selection to Tractography/ROISelect module (PNL request for Slicer2 compatibility, Alex)
• Added more scalar options to Diffusion Tensor Scalar Measurement module (PNL request for Slicer2 compatibility, Alex)
• fix for Python programming tutorial (Steve, Luca)
• Fixes for color table preview icons showing up in node selectors (Wendy and Nicole)
  • svn 1377
• DicomToNrrd issues reported by AlexZ and Sylvain (Xiaodong)
• Crosshair traking modes (Jim); also see bug #861
• Wizard page transition error in ProstateNav. The issue was fixed by Haiying.
• OpenIGTLink reslice performance (Junichi) (fixed by Steve)
• Updated meshing module (Curt) - checked in trunk for contest; needs merge to branch if all is well.
• "Change island" effect of Editor is not functioning when the Scope is set to "all"

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)

• Picking NCI GPU Raycasting on machine that doesn't support it causes lockup. Not able to reproduce the problem (Yanling).

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

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