Engineering:TCON 2010

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2010-06-17

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

Agenda:

2010-06-10

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

Agenda:

  • 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

2010-06-03

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

Agenda:

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

2010-05-27

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

Agenda:

2010-05-20

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

Agenda:

2010-05-13

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

Agenda:

2010-05-06

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

Agenda:

  • 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)

2010-04-27

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

Agenda:

  • 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.

2010-04-22

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

Agenda:

  • 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.

2010-04-15

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

Agenda:

  • 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

2010-04-08

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

Agenda:

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

2010-04-01

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

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

2010-03-25

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)

Notes

  • 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

2010-03-18

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

2010-03-11

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.

2010-03-04

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.

2010-02-25

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

2010-02-18

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.

2010-02-11

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

Agenda:

  • 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!)

2010-02-04

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

Agenda:

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.

2010-01-28

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

Agenda

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

2010-01-21

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

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

2010-01-14

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

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