Slicer3:3.6 Final Issues

TODO: Issues to fix for the 3.6.2 patch release

• CompareView issues 929, 936 (Jim)
• CompareView + side-by-sideLightbox + Widescreen CompareView problems 995
• Resolve EMSegmenter related issues: (Kilian & friends)
  • vtkHTTPHandler is creating broken files 955 (Wendy)
• Import of XNAT xcat files not working 996 (Wendy)
• Integrate SPECTRE plugin as an extension (Nicole)
• in the editor module replace the words "Check Points" with the word "Undo" and compress saved label maps into stencils (Steve)
• Several tweaks to the Editor Module (Steve)
• 983 FetchMi crashes when deleting entry (Wendy --status: wendy could not reproduce; kilian has provided mrml file that demonstrates problem)
• Katie will create a 32 bit linux version of the modules in the Extension Manager for the release (Katie)
• Failed memory allocation dialog box (Steve) - in slicer3 trunk
• FetchMi does not store path names correctly 998

DONE: Issues fixed for inclusion in Slicer 3.6.2

• CompareView + Crosshairs issue 928 (Jim)
• Cannot change the window/level on color-by-orientation dti volumes (Alex [1]).
• Ron's requested changes to the volume rendering transfer function (email from 8/20) (Alex->Steve: implemented and checked in trunk for testing):
  • add thumbnails to show effect of the transfer functions,
  • remove unneeded ones, correct a typo.
  • Materials are in drop box in Ronsexamples in a zipped folder called Transferfunctions.
• 971 Scene import does not work correctly (Alex: fixed on the trunk, Slicer3.6, SLicer4)
• Fiber bundle display GUI issue (Alex) [2] NOTE: there is a MRML scene compatibility issue, see comments in [3]
• Color-orientation display for DTI volumes crashes Slicer when trying to save scene 976 (Alex)
• Diffusion Tensor Glyphs not showing (Demian)
• Diffusion Tensor Tractography having a strange no-tracking through high FA areas case (Demian)
• Make shift-leftbutton-drag be shift for slice viewers (Steve) (Committed to trunk -sending a binary to Ron for testing)
• volume rendering: sampling rate and a few other tweaks (Yanling)
• CompareView issues 927
• Bug when volume rendering volumes with smooth gradients [4][5] (Steve)
• Import scene does not update 3D viewer (Nicole, Wendy) http://na-mic.org/Mantis/view.php?id=840
• Loading a scene that contains a fiducial seeding node breaks fiducial seeding if the node points to an invalid fiducial node (Nicole)
• missing quick timeout if connection to web resource is blocked 969
• 954 EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build
• 948 + 958 Segfault during segmentation when saving intermediate results
• 970 EMSegmentMRMMLanager cannot handle two taks
• 973 MRML file does not read nrrd files correctly when the files are located in different directory
• Ordering of the series by number in DICOM browser 965 (Steve)
• Create robust pipeline for 3D MRI brain images 972 (Kilian)
• It seems that the camera does not transform correctly under transform node (Steve). 957 fixed and checked in.
• Reading fiducial lists with .txt extensions. 991 (Nicole)
• add the --tmpdir option to the start up allowing one to specify slicers temporary directory (Dominique)
• Fix the leaks in the nightly tests [6] (Dominique)
• Issue 968: LD_LIBRARY_PATH screwewd up when no network connection (Steve with Kilian)
• Relative paths in volume storage nodes 993 (Nicole)
• VTK GPU Ray Cast issues (Julien)
  • Flickering has not been improved since 3.6.1.
  • Crash on MAC: the 2 Apple bug reports from Francois Bertel and James Barabas are still open (rank #1). Apple didn't contact them.

DONE: Issues included in 3.6.1 patch release - in Slicer-3-6 branch by 2010-08-03 6pm

• make sure all BRAINS and Registration fixes are in the 3.6 branch (Hans and Jim with help from Dominik)
• 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"
• Scene save/restore crash for dti tutorial (Steve/Alex). [7] and [8]
• 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 [9] (Steve) - in trunk, need to move to branch
• KWWidgets issue with "%" in file names produced by DICOM browser -- fixed in trunk, need to make sure propagated to 3.6 bug 886 (Steve)
• Tractography display modes issue with Data module (FiberBundles have 3 display nodes but the Data tree has only one eye icon). (Alex) (Steve disabled the eye icon for in the Data tree for any displayable with more than one display node)
• Fix for crash after Save Island operation on windows (Steve) [10]
• EMSegment command line works now with BRAINS (Kilian)
• Removed KWWidgets that do not work under Windows (Kilian)
• fixed warning for some bad image spacing geometries http://www.na-mic.org/Bug/view.php?id=951 (Steve)
• fixed editor error dialog when editing on rotated volumes with some geometries (Steve [11], [12])
• Snapshot issue [13] (Alex)

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.