Difference between revisions of "Engineering:TCON 2010"

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*migration of Slicer and Na-mic websites
*migration of Slicer and Na-mic websites
** Currently on Solaris machine, moving to Linux machine
** Currently on Solaris machine, moving to Linux machine
** Ron will be sending email when this happens
*Need to fix the slicer dashboards:
* factory.slicer.org
* Need to fix the slicer dashboards:
** split slicer4 to dedicated dashboard with superbuild and Qt
** split slicer4 to dedicated dashboard with superbuild and Qt
** fix remaining failing tests (EMSegmenter, SparseFieldLevelSet, other sporadic failures...)
** fix remaining failing tests (EMSegmenter, SparseFieldLevelSet, other sporadic failures...)

Revision as of 19:19, 30 September 2010

Home < Engineering:TCON 2010
Back to TCON:Main, Events


Attendees: Ron, Will, Stephen, Steve, Wendy, Daniel, Casey, Nicole, JC, Dominic, Tina

photos of Barcelona

NA-MIC renewal

  • Barcelona - brief description of CTK DICOM/Slicer integration
  • Short term activities
  • Slicer 3.6 debugging
  • migration of Slicer and Na-mic websites
    • Currently on Solaris machine, moving to Linux machine
    • Ron will be sending email when this happens
  • factory.slicer.org
  • Need to fix the slicer dashboards:
    • split slicer4 to dedicated dashboard with superbuild and Qt
    • fix remaining failing tests (EMSegmenter, SparseFieldLevelSet, other sporadic failures...)
    • fix test machines with no X server (thurmite)


Attendees: Steve, Wendy, Tina, Jim

  • DBP meeting (Monday ~11am at AHM) will be sent out by Katie M. this week
  • Slicer and OpenIGTLink featured in NDI booth at MICCAI 2010 (See slicer visual blog)


Attendees: Jim, Tina, Wendy, Nicole, Dan, Dominik


Attendees: Jim, Stephen, Steve, Daniel, Nicole, Tina, Katie

  • discussion about 3.6 versus 3.7 versus 4.0
    • move to GIT will be deferred.
    • discussion about svn for slicer 4
Host  	TTL  	Numeric IP
www 	7200
@ (None) 	7200
* (All Others) 	7200
ext.slicer.org 	7200
i2b2.slicer.org 	7200
mi2b2.slicer.org 	7200
svn.slicer.org 	7200
viewvc.slicer.org 	7200
xnd.slicer.org 	7200 

Plan for Slicer4 nightly builds:

  • Funding will hopefully resume next week
  • Zack will create a new Slicer4 svn repository
  • The Slicer3 trunk will become Slicer 3.7
  • Nightly binaries will be built from the Slicer3 trunk
  • Nightly builds will eventually switch over to Slicer4
  • A dashboard for both Slicer3 and Slicer4 builds will be set up


Attendees: Jim, Steve, Nicole, Wendy, Tina, Vince, Ron, Jay

  • Discuss additional slicer layout options (Wendy, Jim, Steve, Ron)



  • Discussion of slicer 3.6.1/2




Attendees: Xiaodong, Tina, Steve, Wendy, Nicole, Vince



Attendees: Steve, Jim, Nicole, Tina, Xiaodong, Wendy,


  • discuss how to correctly remove display nodes if they become not needed after CLI invocation (this is just a hint for Nicole, we talked about this today, I will try to join around 3:45 --Fedorov 17:48, 29 July 2010 (UTC))
    • usability level: what if there was something set on the output volume already? (Field of View)
    • copy the input reference display node values inot the current output display node rather than creating a new one (if type is same)
    • display node management is done when load volume back in
    • if create new volume node (from a node selector), it doesn't create default display node automatically
    • in command line module logic, store the information about what do you want to hook up (input volume display node id), and then in vtkSlicerApplication logic, when read things in set them up (around line 1570).
    • if a display node should only be used by one thing (current implementation), in this rare case where change the type of the display node, remove the old display node node
    • add method vtkMRMLScene to check if any displayable node references a given display node? Not necessary yet...
    • every node has to be able to report everything it references (on vtkMRMLNode, see also UpdateReferenceID there)
    • update the read data request with the reference display node and then put logic in the Slier application logic to deal with it, extend ReadDataRequest in vtkSlicerApplicationLogic.cxx


Attendees: Xiaodong, Steve, Ron, Tina, Vince, Wendy, Katie



Attendees: Jim, Xiaodong, Steve, Tina, Dominik, Vince, Wendy, Katie

  • slicer 4 planning continues. next mtg+training session scheduled for aug 12-13 in chapel hill. details to appear on wiki soon.


Attendees: Jim, Stephen, Nicole, Tina, Junichi, Xiaodong, Vince, Harini, Wendy


  • Generalized plotting infrastructure in Slicer?
    • Have DCE plotting infrastructure
    • Also have CTK transfer function widget plotting
    • Need generalized base class for plots, upon which other specialized plotting can be based?
    • 3D Slicer 4D Analysis Module has 2D plotting
    • Nicole's wish list, based on use of scatter plots in population studies (one brain surface geometry file will have multiple scalars defined at each vertex) (see pages 70 and up here where BLT was used):
      • highlight on mouse over a plotted point
      • toggle plotted point, or data set, visibility
      • legends: change text, colour, font, position for data set name, axis labels, chart title
      • print/save image to disk, export as table, postscript, pdf
      • set x/y axis variables (for example: input file has 10 values, allow selecting two to plot, and allow changing this at run time)
      • support plotting from multiple data sources
      • set plot symbol/colour/style to plot each data source
      • programmatic add/remove points from plot
      • on hover over a plotted point, pop up extra information about it (be able to associate extra info with a plotted point, for example if have a file that has an index, id, gender, age, val2, val1, when plot age versus val1, pop up id when hover over the point)
      • calculate average line through scatter plot
      • allow user to see values for all points


Attendees: Xiadong, Nicole, Tina, Dominik




Attendees: Katie, Jason White, Jim Barabas, Tamas, Xiaodong,Tina, Nicole, Steve, Vince, Luis, Sudhir Pathak (U Pittsburgh), Ron, Karl, Jim Miller, Marco, Hiro Yoshida



Attendees: Jim, Tina, Dan, Tamas, Nicole, Wendy, Vince, Dominik, Jim Barabas, Katie, Luis, Hans


  • project week review
  • jim b's project
  • Slicer 3.6 release
  • http://www.slicer.org/
  • Tutorial contest entries are due to Sonia Pujol on Monday


Attendee: Jim, Tina, Wendy, Vince, Xioadong, Steve, Dan Marcus, Katie, Dominik, Sean Megason, Arnaud Gelas, Isaiah, Michel


Notes (discussing projects):

  • community effort to make NA-MIC tools accessible to microscopy IA (Sean)
  • Paraview: link via MRML or scene description file format w/o VTK dependencies. Which MRML node types should be supported.
  • BrainLab-Aurora HybridNav (Isaiah Norton, A.Golby Lab): optical tracking system -> trying hybrid with AURORA, have both optical and EM tracking. Tool position history to track/document resection progress. -> add Dan Marcus (STEALTH -> openIGT) to project.
  • Groupwise registration: (Ryan Eckbo); porting Matlab/C code into ITK -> Jim, Luiz
  • removed Python & Execution models as project categories, fused into NA-MIC Kit Internals
  • Computer Aided Photodynamic Therapy: contacts?
  • Slicer 3.6 release: last fixes: Editor, BRAINS, mutiple volume loading, DICOM series & XNAT, color LUT for generic use. New release scheduled June 10. If you know of critical issues please submit to http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:3.6_Final_Issues


Atendees: Dan Marcus, Misha Milchenko, Tina, Nicole, Jim, Steve, Lorent, Greg, Wendy, Andre, Xiaodong, Leslie Holton, Tamas, Ron, Dominik



Attendees: Jim, Tina, David Fuentes (MD Anderson), Dieter Hahn (Erlangen), Katie, Dominik, Xiaodong, Stephen, Andrej, Harini,Andrew Elliott (MD Anderson), Alex Z, Luis, Curt, Tamas (Queens), Nicole



Attendees: Sonia, Wendy, Ron, Tina, Katie, Haiying, Xiaodong, Nicole, Dominik, Vince, Marek, Andras, Tamas, Andrew Rauch, Ryan Eckbo (PNL), Mark Scully, Curt, Clement, Stephen, Harini, Isaiah, Luis Ibanez, Stuart



Attendees: Jim, Steve, Curt, Tina, Xiaodong, Nicole, Vince, Harini, Dominik, Ron


  • http://wiki.na-mic.org/Wiki/index.php/2010_Summer_Project_Week
    • registration via credit card available, make sure to book hotel before June 1
    • updated project page Wiki template [1], includes "Delivery Mechanism" section
    • Tuesday: Slicer Handson workshop from 10-12
    • Wednesday: QA training session
    • new Projects
      • registration:promote unsolved registration problems as project: e.g. Stanford group & knee MRI
      • connect Python tools with execution model (NiPYPE)
      • Slicer 4
      • femur fracture classification (Karl from Prof. Schubert's group), project placeholder added (Analysis)
      • category for meshing efforts
  • prospective first-time AHM attendees are welcome to attend the TCon, feel free to invite
  • NA-MIC renewal: Supplemental Information needed: latest software releases
    • Slicer 3.6
    • ITK 3.18 (fixing DICOM parsing)
    • VTK 5.6 (integration of GPU ray casting)
    • XNAT 1.4 (webservices API)


Attendees: Jim, Tina, Xiadong, Steve, Nicole, Ron, Wendy, Dan, Katie


  • Please note that there will be two project-week specific tcons:
  • Discussion of help text of command line modules.
    discussion topic
  • Review of slicer3.6 release plans and bug tracker.


Attendees: Wendy, Nicole, Steve, Sonia, Ron, Dan, Dominik, Adam, J2, Jean-Christophe.


  • QT tutorials/discussion with Adam Weinrich, Nokia.
    • Review of Slicer tutorial structure (Sonia)
    • Adam works on strategic accounts (advanced development for new applications) and on university outreach to encourage creation of new developers
    • Kitware is a key account for Nokia
    • Review of current state of Qt with Slicer (Steve, Jc, Julien)
    • Best to stick with first hands on session on Monday afternoon (Adam).
    • Topics to cover:
      • Adam: Motivation (examples of other applications), Designer, available widgets, signals&slots, coding style, implicit representation
      • J2/Jc: how to make a simple module, working with the rest of the slicer application (Tuesday afternoon).
    • Qt Q&A lunch on Tuesday. Adam will check with Boston-based Qt developer group about attending.
    • TODO: get a lecture hall for Monday afternoon? Tina will check with Donna.
  • Note: May 27th is the OpenIGTLink discussion, led by Junichi Tokuda.


Attendees: Xiadong, Harini, Tina, Steve, Dan Marcus, Vince, Ron, Dominik, Luis, Dave P, Katie, Alex Z, Marco


  • Project Week Kickoff Call for Engineering
    • 2010_Summer_Project_Week
    • Start listing Engineering Projects
    • Project Page Template: Add Delivery Mechanism (Extension-cmdline or loadable, Built-in)
    • Ideas for handling Project Week Planning/calls


Attendees: Jim, Dan, Nicole, Tina, Wendy, Ron, Stephen Aylward


  • Slicer Training Course in Iowa city tomorrow.
  • Added breakout sessions/talks for the project week


Attendees: Curt, Nicole, Katie, Wendy, Tina, Dominik, Vince, Steve, Dan Marcus, Luis

  • Slicer 3.6 Feature freeze
  • Project Week breakout session: QT, ITK, git,...


Attendees: wendy, nicole, dominik, vince, tina, jim, dave, luis, katie, steve, ron, xiaodong, stephen, jj, jc, j2

  • MIDAS Feedback from John M./Tina
  • Slicer 3.6
    • Documentation
    • testing and code coverage
    • VTK status
  • Slicer 4.0
    • Community process (Stephen Aylward)
      • Superbuild status (Dave)
      • qt status (Julien)
      • Module acceptance process
        • From Nitrc
        • With Slicer
    • Educating the community about the benefits of Qt (Steve Pieper)


  • Slicer Extensions
    • Reuse Statistics functionalities from MIDAS to report on downloads from
    • http://ext.slicer.org/ext/trunk/
    • Building Slicer extensions and submit them to the Slicer Dashboard
    • Where are they located ? (it is described in the .s3ext files:)
    • Maybe build them only when their source code is actually modified ?
    • Label extensions by a level of compliance with NAMIC practices ?
      • E.g. Gold, Silver, Bronze,... Coal.
        • Gold: have > 80% coverage, 0 Valgrind errors, documentation and tutorial
        • Silver: have > 70% coverage, < 10 Valgrind errors, and tutorial
        • Bronze: have > 60% coverage, < 50 Valgrind errors, and tutorial
        • Coal: have < 10% coverage, > 1000 Valgrind errors, no documentation, no tutorial
    • Web of trust
      • Have gatekeepers who review the extension and label them accordingly.
      • Define a Testing procedure for Slicer 4.0. (Check lists)
    • Community Support
      • Provide User Ratings (based on the Insight Journal / MIDAS functionality)
      • Use current MIDAS C++ API to Upload/Download data.
      • Create MIDAS Plugins to manage data / code for Slicer extensions
  • Slicer Release 3.6
    • VTK Release 5.6 : March 26th 2010
    • Immediately after, switching Slicer to use VTK 5.6.
    • Sorting out KWWidget issues on Windows 7 with VTK 5.6 (VTK CVS HEAD).
  • Slicer Release 4.0
    • Git: Conversion of CMake, VTK, Paraview
    • Moving Slicer to Git ?
    • ITK 4.0 will move to a clean Git repository (full reset of the history)
    • Moving only Slicer modules that satisfy the Gold criteria.
    • A2D2 Idea : port CLI modules to ITK 4.0
    • Question about CLI modules in CTK for Slicer 4.0: Discovery process; making it cleaner by using Qt methods. But raise the concern of forcing a dependency on Qt (that not everybody may want).
      • Have specific mechanisms of discovery based on : Python, Qt, C++.
    • MRML Refactoring ?
      • Jim suggests to add a dictionary-like organization to be able to query MRML nodes {by type,...}.
  • Slicer Superbuild
    • Dave reported on progress
      • Dealing with patches that getbuildtest.tcl applies to the third party libraries.
        • Difficulty of applying patches. Need for a multi-platform way of applying patches
        • Hosting git repositories with the patched versions of the third party libraries.
        • Use github ? create a "Slicer" user-account ?
        • CMake-ifying Python source tree ?
  • Testing Modules and Extensions
    • Hosting them in MIDAS
    • Setting up Dashboard configuration to test modules as Slicer sub-projects
    • Some CDash/CTest work is needed.
    • Currently, sub-projects must be run from a common CTest script (the same of the host project).
    • Needs to manage dependencies between extensions. (this can be done today with an XML file on CDash).
  • Testing Submission Grouping
    • Grouping {configure/build/test} submissions by Library and / or subdirectory
    • Using CMake for generating labels that can be used later for grouping


Attendees: Andriy (ran out of the room before he could take notes) Nicole, Dominik Wendy, Steve, Stephen, Jim, Katie


Attendees: Dan, Tina, Vince, Xiaodong, Wendy, Nicole, Katie, Kurt, Dominic, John

  • Updated Download page
    • Do we want to add images?
      • Yes, please. And also to format this into a table. Thanks.
  • OpenIGT and Medtronic Navigation
    • Consider a joint grant to fund the development
  • Ron can kill 18 birds with one stone.


Attendees: jim, ron, nicole, vince, dan, katie, wendy, dominic, tina

  • GetNodesByName leaking the collection from Tcl ( set foo [$::slicer3::MRMLScene GetNodesByName bar] )
  • VTK GPU Mapper - Mac driver issue. But otherwise is working well with compositing. Dual 3D issue tabled for now.
  • Store the Collapse of the SliceController in the Layout node?
  • Should the layout of the modules (left verses right) be stored in the scene? Not for now.
  • DICOM databases. See discussion on mailing list.
    • DICOM Schemas. Jim tried searching for Osirix's schema. What about the XNAT schema? What about ClearCanvas?
    • Extend Schemas for MRML, Project views, NRRD, VTK files, etc.


Attendees: john, marco, dominik jim, steve, wendy, tina, nicole, ron, vince, dan, katie

  • MIDAS handles - fixed
  • GWE's RSE ("Record Set Explorer") version 0.6.1.alpha released:
  • Slicer Release 3.6 Feature Freeze on April 1
  • Japanese Slicer workshop in 2 weeks
  • CTK workshop last week - went well


Attendees: Jim, Steve, Wendy, Dan, Dominik, Katie, Nicole

  • Discussion of whole body CT/MR data (Dan)
  • Discussion of the "Spit Kidney"
  • Dominik's registration case library data for download
  • Discussion of download data for each module (like in ChangeTracker currently)
  • Tutorials and Datasets
  • Discussion of slicer 3.6 release schedule.


Attendees: Jim, Katie, Curt, Casey, Tina, Xiaodong, Steve, Wendy, Dan, John, Dominik, Nicole


  • NA-MIC data migration is complete and the Downloads page has been brought out to the Wiki sidebar (http://www.na-mic.org/Wiki/index.php/Downloads)
    • Feedback is requested on the sidebar
    • Feedback is requested on the Downloads page
    • Feature request to track the downloads like it is done on the publication database. (Julien reports it is already available to administrators).
    • Curt will work with John to add Meshing Module tutorial.
    • Dominik will try putting some data in midas to see how much context can be added.
    • John will check with Marek about Harvard data that had been on BIRN.
  • Review of DBP2 webpages, which need updating
    • Ron has contacted the parties directly
  • Dan: XNAT workshop this summer (possibly June 28, 29, 30 in St. Louis)?
  • Discussion of entry behavior on
  • New Volume features from Xiaodong for viewing image sets in a directory (cool!)


Attendees: Xiaodong, Tina, Casey, John, Dan, Vince, Stephen, Nicole


DBP Tutorials should be listed at the top. Software should point to Slicer and the NA-MIC Kit. Data hosting is available on XNAT and Midas.


Attendees: Xiaodong, Tina, John M, Katie, Nicole, Dominik, Vince, Casey


  • data update (john m): Discussion of Data & Tutorials on the following page. Discussion of where to put the data (XNAT or Midas).


Attendees: Jim, Katie, Nicole, Wendy, Curt, Ron, Dominic, Steve, Dan

  • Update wiki pages in preparation for the review of the NA-MIC renewal


Attendees: Katie Ben Casey Yin Tina Vince Jim Satra Nicole Lauren Hiro Fernando Chris Brian Dominik Ron