Engineering:TCON 2008

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Slicer 3 Dartboard

Link to the Slicer 3 Dartboard here


  • Attendees: Jim, Tina, Katie, Curt, Will, Daniel, Vince, Wendy, Xiaodong, Nicole, Allen, Luca

Agenda: to discuss potential external collaborations.

  • Daniel H - vessel segmentation collaboration with Luca and Raul
  • Python and NiPy Collaboration Opportunities - Luca, Steve, Matthew Brett, Fernando Perez
  • residual item from last week's call: jhu DBP - gabor, allen, katie
  • Breakout session:
    • Meshing Tutorial (Nicole, Vince, Curt, Steve)
    • Python Modules (Demian, Luca?)
    • GUI Testing and Developing Test Modules for Slicer (Sebastien)
    • How to use NITRC and slicer(Steve, Terry)
    • how to use batchmake and xnat to process larger studies (Julien and Dan Marcus)
    • DTI (sonia, randy, others?)


  • Attendees: wendy, sebastien, Tina, vince, jim, steve


  • Which external collaborators need to be contacted for next week's tcon?
    • daniel haehn at bwh - vessel seg project
    • berkeley numerical python
  • JHU didn't make last week's call
  • Breakout session:
    • Meshing Tutorial (Nicole, Vince, Curt, Steve)
    • Python Modules (Demian, Luca?)
    • GUI Testing and Developing Test Modules for Slicer (Sebastien)
    • How to use NITRC and slicer(Steve, Terry)
    • how to use batchmake and xnat to process larger studies (Julien and Dan Marcus)
  • Grok?


DBP Projects Planning

Attendees: Martin, Cedric, Clement, Jim, Steve, Nicole, Will, Curt, Katie, Mark, Dan, Jeremy

  • MIND team: Jeremy, Mark, Ross, Steve
    • Agenda Items for discussion
      • status of co-registration
      • status of brain extraction
      • status of bias field correction
  • UNC team: Heather, Jim, Martin, Clement
  • JHU team: Gabor, Katie, Allen
  • PNL team held on Monday Nov 3, 3pm ET
    • Attendees: Marek, Polina, Brad, Guido, Jim, Steve, Tracy, Sylvain, Tina
    • Q to dbp team: what are good alternatives to compare with, and what is a good way to compare?
    • Q: how best to cover all the projects of DBP beyond the roadmap.
    • Suggestion: increase tutorial time to 1 hour to allow coverage of projects with tutorials that have not been covered in DBP presentations

Call Notes:

  • UNC Visit Dates: December 15th visit for Will, Steve, and Julian
  • AHM Planning: All participants need to start updating the Wiki. Tina wants to remind all the DBPs that they have a timeslot for presentations during the AHM in January. The Wiki pages for projects need to be filled out. There will a presentation that is an overview of NA-MIC before the DBP. This is under discussion on what it will contain. Ross gave a NA-MIC overview at the NCBC meeting which could be a good guideline. There is a new format for the DBP presentations where each team has 10 minutes.
  • Each roadmap project needs to have a tutorial that walks users through reproducable results.
  • There is a contest for tutorials with the possibility of a prize awarded to the best tutorial. The message to NIH should be about generating tools that help users to generate answers and results, not just new algorithms. There is a focus on what are people doing with it.

Specific Questions by the DBPs

  • How should the cortical thickness module be integrated with Slicer? An atlas is needed. Should it be stored on NITRC, on the pub-db on SPL, or where? NITRC is attractive because of its download support. The Slicer modules are external modules. The module would be on the Subversion archive on NITRC, the atlases would be additional files (not in SVN). Discussion of how to make the module and the users aware of the atlases.
  • Discussion on Slicer integration: The Cortical Thickness Module is currently a single external module, which calls external application with a separate GUI. These applications call other applications during processing. There are five different modules. For this AHM, users will have to download all required modules, but we should look at how to bundle them together later (via dependencies) or create the concept of a package of modules. Details of how to organize the modules and store them in NITRC was discussed.
  • Tutorial Datasets and Tutorial document should be placed on NITRC next to the module. Add a link to the Slicer Tutorial page referencing the NITRC page.
  • BatchMake is used by Slicer modules. How to create the BatchMake .bmm files so that the modules will initialize the BatchMake config files. This is solved by the two-step Slicer initialization process. The environment variables should be queried to find appropriate paths.



Attendees: Jim, Will, Tina, Steve, Ross, Marcel (for Guido), Allen, Martin, Nicole, Katie, Dan Marcus, Vince


  • AHM agenda suggestions:
    • increase Ross' talk to 30 minutes and add materials to it to ensure that highlights of activities beyond the core 3 roadmap projects are also included in the meeting
    • Ross will circulate his talk to the group and solicit input+updated materials (an earlier version was presented in AUgust to all NCBC mtg)
    • Include training and dissemination slides (a couple) into the same talk, and a couple of slides on the NA-MIC Kit
    • Next week will be DBP specific talks: Monday 3pm ET PNL DBP, and Thursday 3pm ET JHU, UNC, MIND


Attendees: Jim, Chris, Brad, Katie, Tina, Vidya, Noby, Vince, Dingang, Kevin, Ziv, Dan Marcus

External Collaborators:


  • Dingang w/ Jim: two types of software development. MR-image registration algorithm will be extended and added to NA-MIC Kit. Second is for white matter lesion segmentation in MR images. Kickoff mtg will take place within team before January to identify which infrastructure changes need to be made to ITK and Slicer. This will get coordinated with visit to Martin. Team will also look at synergy with Lupus DBP.
  • Chris: EM segmenter is working well. At project week, would like to make it an all-slicer workflow. Dan Marcus will help before project week to get data into xnat central server (data is public).
  • Ziv: work has been divided into IGT Project Week (Dec 8-12) and NA-MIC Project week. The goal is to get a workflow prototyped in Slicer.
  • Vince: meshing is more than likely to be integrated by the time of the project week.


  • Kickoff TCON. Discuss Infrastructure Projects.
  • Attendees: Will, Steve, Ron, Jim, Tina, Nicole, Vince, Wendy

Core 2 lead Project Proposals

  1. Fluid mechanics tractography and visualization (Nathan Hageman UCLA)
  2. UCLA BrainLab/Slicer Neurosurgery Preoperative Tumor Planning - using Slicer and its link to BrainLab to investigate whether different tractography methods aid in preoperative planning of tumor resection.(Nathan Hageman UCLA)
  3. Development of FEM / FVM solver library in ITK/vTK(Nathan Hageman UCLA, Vince, Luca, Steve)
  4. Transform Management(Jim Miller)
  5. Interactive 3D Widgets - Introduce new interactors into Slicer (Karthik)
  6. VTK-ITK Pipeline (Jim, Steve)
  7. User Interface Flexible Layouts (Wendy, Jim, Steve)
  8. Packaging Python Interface - Fortran and openssl problems(Luca, Steve)
  9. xnat and batchmake integration (Julien, Dan Marcus)
  10. Automated GUI testing (Sebastien)
  11. Slicer Colors Module update (Nicole)
  12. Volume Rendering Debug (Alex, Curt)


Attendees: Steve, Katie, Tina, Jim, Dan Marcus, Nicole, Sebastien, Yumin, Ron

  • CTest for Teem (Gordon Kindlmann, Steve Pieper, CTest Expert TBN): we'd like to do this one before the AHM if possible.
  • Q for Kitware: VIsualStudio bug in ITKLandmarkTransformInitializer (in the RegisterImages module)
  • Wendy working on XNAT UI
  • Who's going to claim the .xcat extension? Let's have the Wiki specify the correct MIME-TYPE for xcat files, so that at least the file is downloaded automatically, and let the user which application to use (note that Slicer3 should open a .xcat file on the desktop).




Attendees: Xiaodong, Katie, Steve, Tina, Curt, Ron


  • Unstructured Grid support to be added to Slicer trunk soon - vtkUnstructuredGrid datatypes are a subtype of slicer models. There will be some changes to the slicer model viewers and hierarchy viewers to allow display and control over these datatypes. This was put in to support the finite element meshing module to be incorporated in Slicer in advance of the January 2008 All-hands meeting.
  • Meshing Module into Slicer - Curtis is working on integration of the standalone Univ. of Iowa meshing application as a Slicer module. Integration is working through MRML but the GUI is not integrated in Slicer's window yet. Sebastien has offered debugging help. Curt will be delivering a code sample to Sebastien during the next week for assistance in KWWindows integration.
  • GPGPU RayCasting - There is an open-source ray casting algorithm using OpenGL shaders that is experimentally being integrated with Slicer. If this is successful, the algorithm will be integrated into the Volume Rendering module and be available for use by the NA-MIC community.


Attendees: Jim, Xiadong, Steve, Vince, Sebastian, Tina, Wendy, Ron


  • Breakout session Ideas for Winter Project Week
    • Meshing (Nicole, Vince, Curt, Steve)
    • ITK (Luis)
    • IGT (Noby)
    • Setting up Development and Testing Environment (Kitware)
    • Python Modules (Demian, Luca?)
  • Conference calls for project week prep:
    • December 18: Loose Ends
    • December 4: Other Projects
    • November 20: New Collaborations
    • November 13: New Collaborations
    • November 6: DPB Projects (2)
    • October 30: DPB Projects (2)
    • October 23: Funded External Collaboration Projects
    • October 16: Kickoff TCON. Discuss Infrastructure Projects.
  • Review of recent python development. See Demian Wassermann's slides and examples from his recent lecture series at Harvard
    • For example, here's a Hausdorff distance between to fiber tracts:
dist2 = lambda i,j : numpy.sqrt(((i-j)**2).sum(j.ndim-1))
dist_hausdorff_asym_mean = lambda i,j: numpy.apply_along_axis( lambda k: dist2(k,j).min(),  1,i).mean()
dist_hausdorff_min = lambda i,j : numpy.min(dist_hausdorff_asym_mean(i,j),dist_hausdorff_asym_mean(j,i))
  • Download modules from NITRC by an end user
    • Where does this stand - Sebastian has committed the code to the Slicer3 tree.
    • Sebastian will be happy to help someone push this forward
    • How to pack modules to have Slicer3 install and find the modules?
    • What infrastructure is needed- particularly for Windows to check for the proper compiler and build type. Possibly have CPack generate keys that check this.
    • Slicer3 should provide the user with a list of modules that can be downloaded and installed.
    • Sebastian will work with Modules to create their own package for installation.


Attendees: Jim, Sebastien, Tina, Curt, Dan Marcus, Will, Ron, Wendy


  • Curt - Working on the integration of a standalone KWWidgets/VTK application as a loadable Slicer module. This standalone application does lots of callbacks to the RenderWindow and creates its own KWWindow and KWUserInterfacePanel. Therefore, this is a complicated example to integrate into Slicer's Module panel. At the current time, the widget creation seems to occur without warnings, but the panels never show up in Slicer. Sebastian and Wendy indicated that the management of the InterfacePanels and Slicer's UserInterfaceManager is intricate and that there is probably a relatively easy fix, but Sebastian would have to review some of the source code to comment further. Curt will make the source code and screenshots available to Sebastian for a follow up call later.
  • Sebastian - Evaluation of GUI-testing for KWWidgets and QT is ongoing. Sebastian is working on this as well as the requested tree control widget.
  • VTK bugs (Will) There were three VTK bugs reported last week in the TCon. Karthik solved all of the bugs. Kitware has fixed these and the fix is in the VTK CVS head already. The bug information is listed below:
  • Work is beginning on the planning for the All-hands Meeting in January. There will be another party. Ron and Will are working on the agenda already. We should put up the draft projects template soon.
  • XNAT visit followup discussion. The Web Services API is stable and it will be tested as the Slicer use case (written by Wendy) is implemented. There was discussion of the use of Slicer tutorial data to populate the use case. Wendy is developing a Slicer module to query the XNAT Desktop Services. There are is a set of minimal, required tags. The required ones are all that is necessary at first for the use case, unless there are others needed by the Use Case requirements.
  • MICCAI comments - One of the Slicer images received second place in the Visualization competition. There was a Slicer plug-in workshop offered and an IGT workshop given at MICCAI. Vince was helpful in making the Slicer tutorial possible.


Attendees: Dan, Xiaodong, Wendy, Vincent, Curtis, Nicole, Tina

  • VTK Bugs in 5.2 - These are issues with the integration of the meshing tools
    • 0007518 - vtkDataReader Memory Errors causes a seg fault
    • 0007511 - Bug in vtkSmoothPolyDataFilter causes a seg fault
    • 0007512 - vtkPlaneWidget Sphere Resizing - This is simply an annoyance
  • Slicer/XNAT update
    • Reading multiple files from a single data needed in Slicer
    • Building out the UI and workflow for talking to XNAT
    • Expected to have prototype Slicer/XNAT File Repository integration by October
    • Expected to have prototype Slicer/XNAT Enterprise integration by January, 2009
  • Sadness all around at the lack of a Kitware representative to disucss VTK bugs
  • Great joy at being set free after only 20 minutes


  • Plan for XNAT/Slicer interaction: 9: Sebastien, Katie, Wendy, Nicole, Jim, Vince, Steve, Curt, Dan
  • XNAT Desktop, Web Services Use cases (Wendy review of last weeks meeting notes)
    • Web services file repository api is currently on XND, but will also be supported on XNAT Enterprise (by January).
    • Sebastien and Yumin are working on the current save dialog box and will think about how the remote repository should look for that.
    • discussion of how extra data file names are handled in ITK (which files are actually written when you save a particular archetype).
      • idea: save to temp dir to get file names. Rather than changing all ITK io factory code to keep track of which files it wrote, the slicer code can keep track of what files are in the save directory before and after the Write method executes (this assumes that each factory will only save files in the single directory, but that seems like a valid assumption for all known code).
    • discussion of refining upload uri also how to keep track of metadata to store with derived data
      • how much can be kept track of automatically in mrml? Maybe a lot...


Attendees: Xiaodong, Steve, Curt, Ron, Nicole, Marco, Katie

  • Ron: Atlas generation for the EM segmenter. We need to develop an end-user capability to create atlases to drive the EM segmenter.
    • what is the right approach?
    • where is leverage with existing infrastructure?
    • what needs to be done
    • who will do it?
    • Need to schedule a followup discussion with Brad, Kilian, Polina, Guido, Stephen, Jim, Ross (possibly at MICCAI)
  • Report on NCI Slicer Course by Curt
    • NIST BioChange 2008 challenge may be suitable for Kilian's change detection module
  • NIH personnel told Ron that the wiki pages are not as up to date as they expected
    • Everyone should be sure the wiki reflects the current state of their NA-MIC work
  • Update from Marco on BatchMake coordination with GWE
    • Plan is to wrap GWE for use with BatchMake and Julien is working on it
    • Waiting for Kilian's updates for scripts
    • Ron says we need users to be actively using tools so we have a clear story for renewal - Marco to look at the NA-MIC DBP projects and see which are good fits with GWE and Ron can help facilitate connection


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

  • Filebrowser update by Steve.


Attendees: Tina, Jim, Steve, Katie, Nicole, Wendy, Vince


  • CompareView questions about slice layer logic and slice nodes
    • Nicole notes that switching to compare view loses FG, BG, Label settings she expects to have. Jim says this is the preferred behavior for now but is open to ideas.
    • Compare view aspect ratio? Check problem with panning, zooming in 3D view and changing the compare view fov by mistake. Compare view Field of View. Also lightbox seems to have broken in conventional layout (maybe after compare view).
  • Slicer 3.2 release
    • CLI load time on Mac
    • ModelMaker bugs - string memory problem, maybe in model storage nodes.
    • Xcede / Xnat catalog loading/importing bug
  • Slicer Developer Meetings
    • Many new people working on new Slicer stuff and have requested slicer developer meetings -- may also join tcons in the future. More face to face meetings will be helpful to get them up to speed.
    • James Ross is now working on the COPD project, will be porting an airway inspector tool ( to slicer3.
    • New PNL person (Julien) working on stochastic tractography with Sylvain.
    • New SPL students in town
  • Vince would like to add new pages to application settings menu specific to their module. Discuss a slicer-level API to the app settings for individual modules. Should this stuff be saved in the registry? Vince will spec it out a little and we'll discuss putting methods in Slicer base classes that create and delete app settings page for a module.
  • VTK disappearing actor fixes? (Karthic is working on this fix.)


Attendees: Nicole, Xiaodong, Steve, Ron, Wendy, Vince, Sonja, Jim, Dan, Will


  • Upcoming training tutorials at NCBC, NCI, Stanford, MICCAI
  • Plans for improving Slicer towards RSNA event
    • Data Saving / File browser See here for some info
    • Xnat download
    • Bug fixes needed before these events
    • Branch Slicer a ~month prior to RSNA and BWH workshops (10/15/2008)
  • Dicom browser
    • Subseries groupings are not accessible from vtkITK
    • Tags now available from vtkITK
    • Steve to build GUI
    • Can we use xnat desktop to cache series/subseries information?
  • xnat desktop
  • VTK bug?
    • Fiducials + 2D slice plane disappearance
    • Turn backface culling off?
  • Transforms requiring inversion between Slicer and CLI
    • Built in module to delegate to CLI modules?
  • Non-linear transforms, resampling DTI
    • vtkITKBSplineTransform, itkDeformationFieldTransform
    • Need extension to itkTransform to support encoding/compressing parameters.


Attendees: Xiaodong, Tina, Ron, Vince, Steve, Marco



  • Color image will work with Editor module (not there yet).
  • Four working days (due July 30, 5PM) till the response to 2008_Progress_Report_NIH Questions due.
  • Contest to encourage people to make more tutorial. More details will be work out in the next two weeks before it is announced.
  • Slicer 3.2 release is scheduled soon.


attendees: jim, nicole, wendy, katie, dan, xiaodong


  • Wendy has nearly fixed the packing issue introduced with the Compare View.
  • Xiaodong has added capabilities to vtkITKArchetype..Reader to identify "sub-series". This is necessary for time series data where the all the timepoints are stored in one series. Steve to build a UI to select sub-series or load them all. Perhaps XNAT desktop can help in storing meta data of registered data for fast browsing.
  • Selecting models and volumes for manipulation. Can we tie "active viewers" to the module panel (so the modules show information from the "background" volume, etc.)?
  • Release date? Before NCBC meeting?
  • Jim is off the grid the next week :)


attendees: jim, nicole, tina, steve, ron, wendy



  • Discussion of DICOM options for time series and other situations where directories contain files from multiple series.
  • Xenios from Yale is looking a visiting BWH for a day in late July to work on OpenIGTLink and VVLink in collaboration with NA-MIC and NCIGT.
  • One or more of Dan/Misha/Tim from WashU are looking to come to BWH to work on XNAT Desktop and XCEDE Web Services.
  • The USA will be 232 years old tomorrow!



Agenda: Discuss NEW EXTERNAL Collaboration projects for project week

  • 3:00-3:15pm Rutgers (Jinghao)
  • 3:15-3:30pm UIowa (Gary Christensen)
  • 3:30-3:40 GAP - NAMIC ENGR Core business
  • 3:40-3:45 Mario Negri Institute & Univ of Verona (Luca Antiga)
  • 3:45-3:50 Upenn (Ragini Verma from Christos Davatzikos' group, UPenn)
  • 3:50-4:00pm regular NAMIC engr business

Attendees: Brad, Jim, Katie, Raul, Tina, Will, Nicole, Gary, Alex, Andrey, Dimitri, Jhingao, Paul, Stephen, Luca, Ragini+2 students, Xiaodong


  • Rutgers group project: Lung cancer detection and segmentation. Will be ported to NA-MIC Kit. Page will be create for project week. Jim Miller will be on team.
  • Iowa Christensen group: 9 people attending the week! All project pages in place. Need to schedule two focus-groups for them: one with Sebastien for Kwwidgets, and one with Bill/Julien on setting up CDASH.
  • Non-rigid registration breakout: Luis to run. Topic suggested: regression testing of registration algorithms using cmake and cdash.
  • William and Mary: project is non-rigid registration for neurosurgery. Interested in focus session on validation, and access to non-rigid neurosurgery data from BWH. Dan Markus, Tina Kapur, Gary Christensen will be on team. Graz paper on validation from Insight Journal should be reviewed and discussed.
  • Mesh discussion next week 3-3:30pm.
  • Verona: vmtk integration with Slicer. Dan Blezek will be on team.
  • UPenn: will be present on Tuesday. Working on fixing a bug in Slicer at CF's request, and integrating their 5yr+ sw as a command-line module. Will create a page. Need a session with Steve Pieper.


Agenda: Discuss FUNDED EXTERNAL Collaboration projects for project week

  • 3:00-3:15pm Meshing Collaboration (Iowa)
  • 3:15-3:30pm RF Ablation Liver Collaboration (Georgetown)
  • 3:30-3:45pm Vervet EM Segmentation Collaboration (WFU/VT)
  • 3:45-4:00pm regular NAMIC engr business
    • Mesh discussion requested by Core 1. Core 1 would like to start working with meshes seriously and would like to assess mesh infrastructure in ITK with Will Schroeder and Aylward. The goal is to figure out what's there and what needs to be done to make meshes usable for algorithm development. When can this discussion be held?
    • 95 project week participants signed up already. No more room left. Please send checks in time for Donna to get them before Friday, June 13th.
    • (Steve:) Any vista users who can test the slicer3.2 release candidates? We have one test machine that cannot run it, but also reports from Sebastien that an earlier build (very similar) worked for him.

Attendees: Brad, Ron, Steve, Katie, Vince, Jim, Tina, Nicole, Alex, Xiadong, Chris Wyatt, Dan Marcus, Marco, Kilian, Kevin Cleary.


  • Iowa mesh code will be checked in at Project Week by Curt. It is built primarily in VTK.
  • We will schedule mesh tcon with core 1 and relevant folks in Core 2 including vince, andrey fedorov.
  • Georgetown - Ziv will attend project week on Wed/Thurs. 50 liver data sets that gp will consider making public using XNAT.
  • Wakeforest/VT -
    • Kilian and Vidya have been exchanging parameters for EM seg
    • Kilian needs faster registration - Ron's suggestion to try AFFINE with less than 10s runtime for volumetric data (256 cube)
    • Kilian will work during project week with Carlos to install van Leemput bias correction method into EM Segmentation. Will need input from MIND team as well.


Agenda: Discuss ALGORITHM CORE lead projects for project week

  • 3:00-3:15pm
  • 3:15-3:30pm
  • 3:30-3:45pm
  • 3:45-4:00pm
  • Status of Slicer 3.2: Steve Pieper et al.
    • Status
    • Bug squashing

Attendees: Casey, Marcel, Will, Sebastien, Nathan, Nicole, Katie, Vincent, Alex Steve Jim M., Polina, Tina, Sonia, Tom, Ron, Dan M., Michael, John M.,


Core1 people go over projects listed on Summer Project Week page: MIT, Utah, GATech, UNC. Polina (MIT) will work with on Brad Davis and Dan Marcus. John (GATech) will need more core2 help on the optimal transport registration project... will add additional titles to the project week page.

  • Need chaining and workflow session at project week. Feedback from core1 - core 3 meeting: Chaining, batch processing strongly discussed at the meeting. Core1 and Core 2 should address these topics.
  • Tina wants a title for all projects on the project week page by end of day today.
  • Sonia is preparing for the Germany Training event. Made a munich2008 branch of Slicer3 subversion repository. Still fixing bugs on main trunk. Will create a release branch tomorrow end-of-day.
  • Slicer3 release: developers should check mantis and squash as many bugs as possible in prep for release.
  • Steve encourages all to include impressive pix on the announcements page where people will be directed.
  • Request for a stable KWW target that Slicer can build against. --Sebastien will tag it.
  • Discussion of HelloWorld (Tutorial) and HelloSlicer (for testing)




  • A round of applause for Sebastian, Steve and all the code freezers
  • documentation assignments and schedule for the 3.2 release:
    • Outstanding issues in release
      • EM Segment Wizard - Button Issues
      • EM Segment Command line is in the wrong directory - should be put in bin
      • EM Segment Template Builders
        • First, second and 3rd steps do not work correctly - pull down list
        • Possible issue with MRML manager changes
      • Feature Request
        • Can not changes the name of the parameters because it references the node ID and not the name
        • EM Segment simple - images are specified by XML type file and not image - requires reloading and does not use images loaded within Slicer3
        • Loading parameter set - Add a hierarchy of the nodes for better visualization of parameters
    • registration,
    • loadable modules,
    • interactive editor,
    • volume rendering
  • New Slice Control Widget added by Wendy - last GUI based change
  • Issues with Resize of Slicer and 3D Widgets
  • Discuss Engineering Core Projects for the Project Week
  • Discuss Jeremy's request to add Support Vector Machine library to NA-MIC Kit.


  • Attendees: Will, Sebastien, katie, tina, brad, steve, xiadong, vince, jim, nicole, dan marcus, Ron, Sonia.



  • DBP II update and plans for project week. 2 DBPs and engr+algo core liaisons should attend.
    • 3-3:20 Harvard. Marek, Brad, Polina confirmed.
    • 3:20-3:40 UNC. Heather confirmed. Jim, Martin, Heather, Clement held offline mtg already.
    • 3:40-4pm regular NAMIC engr business
      • Slicer code freeze and release
      • Focus during the upcoming months on "ruggedizing" Slicer

Attendees: Tina, Katie, Nicole, Vince, Will, Marek, Sylvain, Polina, Clement, Brad, Ron, Alex, Sebastien


  • Harvard DBP projects for Project Week
    1. Probabilistic Tractography - on hold since Tri left
    2. Slicer3 - Need bug fix for why Slicer 3 can't load and run UNC data that Martin tried
    3. EPI Distortion correction (Sylvain, Tauseef GATech)
    4. Eddy CUrrent distortion correction (Sylvain, Ran Tao Utah)
    5. Parcellation - need help parametrization (Sylvain, Brad)
    6. fmri - apply polina's algorithm to Marek's data (Marek, Bryce Kim)
    7. Finsler method (John Melonakos, Eric Melonakos)
    8. Group Analysis on DTI (Casey Goodlett, Marek)
  • Code Freeze: scheduled for tomorrow
  • RSNA Demo
    1. editor, lightbox, data fusion
    2. Sonia is developing the curriculum for course
  • UNC DBP Projects
    1. Cortical thickness pipeline
    2. workflow module
    3. NITRC - need to talk to Steve pieper
    4. batchmake pipeline in Slicer
    5. use Bspline module in ITK



  • DBP II update and plans for project week. 2 DBPs and engr+algo core liaisons should attend.
    • 3:00-3:20 MIND. Jeremy, Ross, Steve Confirmed.
      • Testing lots of methods. None working well.
      • Bayesian labeling seems to be working the best.
      • Close the look on itkEMS method
    • 3:20-3:40 JHU. David G, Allen T., Katie H. confirmed.
      • Prostate really difficult task
      • Delphine's work was originally on prostate.
      • Optimal mass transport registration project at project week
    • 3:40-4pm: regular na-mic engr core business
      • Short update on UNC DBP needs: registration, module chaining
      • Discussion on plans for chaining. Prototype for project week?


Attendees: Steve, Jim, Will, Tina, Xiaodong, Katie, Danielle, Sebastian, Sonia,

  • Slicer 3 stable release schedule planning (Slicer 3.2)
    • We would like a stable version before the Mid-June German training event that includes all the latest namic technology (CMake 2.6, ITK 3.6, VTK 5.2, Tcl/Tk 8.5, KWWidgets...). Some problems were fixed this week for ITK3.6 and VTK 5.2; Slicer3 was successfully built using CMake 2.6 against VTK 5.2, ITK 3.6, and Tcl/TK on Linux, Windows, and Mac (by Sebastien). Need more coverage on Slicer. TODOs: Developing tutorial material for the new Slicer release. Testing, automated part plus user interaction part.
    • Project Week projects can go into the trunk after the release is branched. GUI changes to show "axial", "sagittal", "coronal" slices in the acquisition orientation.
    • Proposed schedule:
      • May 16: Feature Freeze of the trunk followed by group debugging/testing
      • May 23: Create Release Branch for Slicer 3.2
  • Danielle Pace @ Robarts Inst. joined NCIGT/SNR to develop Slicer IGT Tutorial.


Attendees: Steve, Katie, Nicole, Tina, Nathan, Jim, Vince, Brad, Louis, Marco


  • Slicer3D Wikipedia page discussion. Check it out here.
    • Need to tone it down a little so it sounds less like ad copy.
    • Needs more pawprints on it from unique editors/authors for Wikipedia to keep it online.
  • Nathan
    • Helical phantom available to LONI web service.
    • Should we make the link available through Slicer or not?
  • Project pages need to be updated.
    • Deadline: May 15th for NA-MIC, a week earlier is preferred
    • Progress report link
    • Project week pages need to be linked off the progress report (indirectly)
  • Waiting for CMake and ITK releases to be finalized
    • Probably will be cut tomorrow
  • Set up special T-con time for Oz
  • What's the deal with the CMake Policy Change warnings?
    • Copy three lines before CMAKE_MINIMAL_REQUIRED
    • Ask the CMake list


Attendees: Jim, Dan Marcus, Xiaodong, Nicole, Tina, Steve, Katie, Jeff, Sebastien, Vince


  • 2008_Annual_Scientific_Report
  • 2008_Summer_Project_Week
  • VTK (5.2) and CMake (2.6) release schedules
    • VTK Plan on branching next week
    • CMake is on RC8, guessing will branch in 1-2 weeks
  • VTK (5.2) performance issues when rendering
    • In the meshing project we have seen a significant reduction in the rendering of a large number of vtkSphereSource and vtkPointWidgets in 5.2 as compared to 5.0
      • 100x performance hit in debug mode on Linux
      • Jeff added code to make sure the check doesn't happen more than once/sec.
      • Still 25% slower, but not 100x slower
    • Rendering time has been increased by an order of magnitude
  • OK for Kitware to put Slicer3 screenshots on Flickr? (see Kitware's Flickr account)
    • => I (Seb) did a quick pass at the files uploaded in 2008, and copied them to a Slicer3 photoset.


Jim, Curt, Tina, Nicole, Wendy, Steve, Brad, Xiaodong, Vince, Ron, Nathan


  • CMake 2.6 release candidates have been cut with .rpm and .deb output targets!
    • Will will work with Katie on this
  • Jim is going to visit Kitware to talk about BSpline registration


Attendees: Steve, Will, Xiaodong, Nathan, Katie, Wendy, Tina, Nicole, Marco, Sebastien

  • Nathan will discuss presentation of fluid mechanics projects.
  • Update from Core 1 + Core 2 meetings in Utah earlier this week.
  • Discussion of Module Chaining (Marco and All)
    • Requested by Core 1 to systematize common use case
    • Need several steps in an analysis process to act like a single command
    • Would like something akin to the EMSegment workflow wizard, but as command line module rather than built-in module


Nathan's overview: discussing visualization options for his fluid velocity vector fields for tractography algorithm. Steve mentions a few options:

  • A LDDMM module in Slicer2 that does animated vector field visualization (work done in collaboration with Johns Hopkins: Anthony Kolasny, Mike Miller, et al.).
  • Another option would be to try using ParaView as a way to flesh out specifics, and then build a more custom tool for tractography later. Will will point Nathan to documentation for file formats, data formats, etc. or help with any questions, and Nathan will try this out.

Discussion of these topics at the engineering review in Utah:

  • chaining modules together
  • grid wizard (Marco) for grid and batch computing
  • Bspline registration
  • setting up repositories for collecting slicer modules (as technology transition mechanism)
  • how this will fit into the slicer build process
  • diffusion weighted imaging, shape analysis, and segmentation
  • dicom to nrrd converter...

Milestones were set for April-end, Project week, and AHM.

Module chaining discussion (see link above):

  • Java version as first goal -- eventually C++ implementation.
  • Discussion about module discovery process and how will chained modules be packaged: (c++ stub programs? or

or discovery find chain-descriptor xml files? shell scripts? (cross-platform issues)...)

  • Goal: By project week in June we would like to be able to chain modules developed by Core 1.

Sebastien's update on module building: Wiki will be updated today with status. (link)


Attendees: Tina, Jim, Will, Wendy, Xiaodong, Nathan, Martin, Marco

  • Progress Report - read over the assignments. We will look for progress from June 1, 2007 to May 30, 2008.
  • June 23-27 is the summer project week. We will make first pass on projects in late April.
  • Module discussion: Martin wanted to understand the state of module creation and usage within Slicer. Sebastien is working on modules that are built against an installed module. Terry is working on built-in modules for Slicer. Jim is working on modules using CMake in the NTRIC repository.
  • Nathan- write a command line, Slicer module that is a wrapper to a web service. Nathan thinks he can get this done prior to the June AHM. We referred to Jim's presentation at the Utah SLC Core 1/Core 2 meeting.
  • We will talk about grid wizard next week at SLC


Attendees: Jim, Nicole, Dan, Xiaodong, Vince, Sebastian, Alex, Curt, Steve, Will, Terry


Attendees: Steve, Jim, Katie, Nicole, Tina, Xiaodong, Marco, Ron



  • Attendees: Jim, Steve, Wendy, Katie, Tina, Jeff, and Marco (Grid Wizard Guy)
  • Discussion on time series analysis (viewer, scene markup). Initial viewer will be a general tool for comparing images.
  • Avalanche of new features in grid wizard and GSlicer3
    • Proxy around Command Line Modules
    • Extends command line with specifications for ranges of values as well as specify remote resources (data) that need to be transferred to/from the grid.
    • Uses Velocity for parameter template engine
    • Grid selection and authentication still being refined for Slicer
    • Could be extended to other grid types (LSF, etc.)
    • Lots of information on the website. Instructions for installation. A bit daunting for non-grid people. Some of us will have to work through the instructions step by step to evaluate.


  • Attendees: Xiaodong, Jim, Katie, Nicole, Will, Steve, Nathan, Tina, Ron, Padma, Marco

- Nathan brought us up to date on fluid mechanics tractography

- Padma Sundaram: SCIrun environment supports EEG processing

- Marco is releasing Grid Wizard alpha version

- Nathan brought up the helical digital phantom web service. Currently the thinking is that it can be accessed through a web service. We suggested that Nathan write a wrapper, consistent with Slicer's execution module, to invoke the web service. However, since it is not available in source form, NAMIC cannot accept it as part of the NAMIC Kit proper. We can guide Nathan in the execution of this module.


  • Attendees: Xiaodong, Katie, Will, Sebastien, Steve, Mike, Wendy, Haiyi, Dan, Curt, Tina

Other NA-MIC Projects

16 - CPack (Katie): Slicer3 compiles and packs using the new C-tools with some bug fixes. Using CMake to select desired modules, using something similar to cygwin. Official Slicer3 snapshot tagged. Different Tcl/Tk versions are currently used for different platform. This need to be addressed.

17 - Slicer GUI Style Guide and Cookbook {Wendy}: This will be a long term effort. During the programming week, the design and implementation details were discussed. The Cookbook will be launched from Slicer, act like KWWidget tour.

18 - Volume rendering (Steve): UI is fairly stable.

19 - Volume rendering using Cuda (Steve):

20 - 3D W Widgets and Picking (Will): found a list of candidates of widgets for Slicer. A few bug fixes for VTK.

21 - XNAT Integration (Dan): Requirements were gathered for a XNAT application that organizes files and caches files from XNAT repositories. Some XML format issues have been addressed.

22 - KWWidgets Roadmap (Sebastien): Gathered requirements. Been working down the list of the feature requirements.

External Collaboration

1 - Astronomical coordinate system support [Harvard IIC] (Mike): Astronomical datasets are quite different from medical dataset. Wendy helped with re-centering data. Made progress in converting between coordinate systems (Cartesian to Spherical).

2 - New Meshing Techniques into NA-MIC [Univ. of Iowa]

3 - Meshing Workflow into Slicer [Univ. of Iowa] (Curt): Will be integrated into Slicer soon. Command line program using VTK.

4 - Evaluating NA-MIC Tools for Small Animal Imaging Workflows [NCI] (Curt):

5 - IGSTK-Slicer [Georgetown] (Haiyi): Successful tracking data using IGSTK.

6 - Japanese Intelligent Surgical Instrument Project [AIST]

7 - GoFigure:High-Level Microscopy Image analysis Application and Algorithms [CalTech-Harvard Medical School]

8 - Doing microscopy image analysis with Slicer3 [The Ohio State University]

9 - fMRI Analysis with Slicer 3 [The Ohio State University]

10 - Resampling DTIs with Slicer 3 [BWH]

11 - Analyzing fMRI and concurrent EEG with Slicer and SCIRun [BWH]

12 - Bayesian hierarchical models for fMRI variance components analysis [BWH]


  • Attendees: Ron, Will, Steve, Wendy, Nicole, David G, Mark S., Casey, Sebastien, Curt, Luca


1 - Stochastic Tractography in Schizophrenia (need to be invited to follow-up TCon)

2 - Cortical thickness analysis - testing EM segmenter to their data. They estimated parameters and tested during the week. The goal now is to compare ITK-MS and EM segment module to see how these two tools compare for cortical thickness. They are reviewing the tools using the same patient data.

3 - (Mark Scully) Legion segmentation using EM segmenter and other options - worked with Brad using 2 channels of data. Flare as 3rd channel caused problems. Desired to have T1/T2/Flair together as three channel dataset. Marcel is going to deliver his segmentation algorithm software to them to compare results.

4 - Robotic Prostate Interventions - (David Gobbi) Working on transrectal biopsy module for Slicer. They had a previous module for transcranial biopsies. One of the most exciting developments was a new prototol "open IGT-Link" which will replace navitrack inside Slicer. Image transfer is working over this protocol. A simulator is being developed for the robot. A few VTK bugs may have been discovered during this process, but it isn't on the top priority list right now.

5 - Prostate Cancer - Wrote new ITK filter that has been submitted to the Sandbox. They are looking at spherical wavelets for shape segmentation. The wiki page will be updated soon.

Other NA-MIC Projects

1 - Groupwise Registration - (Casey) New Bspline registration method is being developed here. It has been used for another project by Casey (#6). Page needs to be updated.

2 - (Need to be invited to follow-up TCon)

3 - (Need to be invited to follow-up TCon))

4 - (Need to be invited to follow-up TCon). Page needs to be updated

5 - Incorporating DTI tools into NAMIC toolkit - They are gathering a dataset that has both structural and DTI data in agreement. Previous dataset was missing part of cortex. UNCDB2 dataset has full coverage of the brain. Resolution is a bit lower, but full coverage is an advantage. Page is close to up to data. Just submitted a paper to ISBI 2008 and working on MICCAI paper, as well.

  • NITRIC is g-forge and would be a good place for automated build process for Slicer modules. This could make it easier to configure Slicer in client labs without need to build from source. This is still being developed by the NA-MIC core team. There is an entry on the collaboration section of the NA-MIC website. Also link.

6 - (Casey) Worked with Serdar using groupwise registration tool. They are currently evaluating results of this study. More images will be added.

7 - (John Melanakos) Spent last week working with collaborators on the MICCAI paper. Project page is well filled.

8 - (Need to be invited to follow-up TCon)

9 - (Need to be invited to follow-up TCon)

10 - MRML scenes for execution model. Some of the issues Brad was having have been resolved. Alex is making adjustments to MRML library as needed for the EM segmentation model.

11 - (Curt) Unstructured Grids in Slicer - Finite Element modeling process was originally in a standalone VTK application. The first Slicer module integration did not use MRML based storage. We are now creating subclasses of Model and Unstructured grid data for storage and display in Slicer. Some minor issues need to be worked out, but the MRML extensions for UnstructuredGrid datatypes are working.

12 - Python (Luca) MatPlotLib plots are close to happening within Slicer. Steve believes it is 80% complete. Python command line modules are working now. Multiple arguments had to be worked by Luca. He has developed Python-based CLI modules. The event broker is discussed here because it affects the interaction with Python, because a Mutex lock has to be placed on the MRML scene. Dan has been helping with metamodules - a single Python module which calls other mothers (hierarchical execution, recipes, etc.).

  • Ron asked about using this scripting technique for the ModelMaker. Some of the parameter setting, etc. could be set in the top module. Nicole will look at this. Kilian said that he wanted to call the "modelmaker" from another module.
  • A need was identified for new wiki pages: (1) scripted modules, (2) metamodules, (2) python scripted modules

13 - (Luca) Transform hardening - Sometimes images are not XYZ alligned. How will command line modules treat an object if it is the child of a transform. The module needs to be able to apply xforms to data (after hierarchy is flattened) to get xformed data. Jim and Steve talked through this lately becomes of the transforms access two-directions (from parents / to parents, etc.) They are looking at how to change the model.

14 - (Steve) MRML support for out-of-core processing - Steve put a link to a new page. Dan, Jim, Wendy, Steve, etc. working through NAC renewal grant (5 years). Multiresolution and asynchronous data are likely targets for this effort, but it will be a long-term effort.

15 - Event Broker discussion - Steve has made process on this, but this wiki page is older. See the event broker page. (look at link under Objective). New term "observation" : completely introspectable. A full dependency between objects is implemented. When a subject issues a "modified" event, Delete events are maintained. Complete "relationship" management of the interaction between objects. This helps by allowing asynchronous event processing. MRML has been converted to use the event broker with asynchronous events managed by the Slicer GUI (async events invoked after GUI events are done). This hasn't broken anything so far, but should improve scalability. Dot logfile format can be generated for inter-object dependencies. This can be used to help provide "who called who" traces. Some special magic is done in MRML Display nodes. They set "observation nodes"

Next Week

Continue through project review. Request missing project members to attend. Review wiki pages.


Attendees: Jim, Steve, Stephen, Wendy, Xiaodong, Nicole, Katie, Ron

  • Project week follow-up
    • Half of tcon on Feb 7
    • Half of tcon on Feb 14
  • Registration
    • Viola-Wells optimizations need to be enabled
    • Stephen needs to check-in and publish recent changes
    • Stephen needs to update the wiki
    • Luis continues to make optimizations (main focus is memory reduction)
  • BatchMake
    • Grid Wizard - meeting on Monday
    • Integration with Slicer delivered via getbuildtest2
  • New webpages
  • Slicer-specific wiki
    • Migrating appropriate info from Na-mic to slicer
    • Hold off on adding to Slicer-wiki until notified
      • Continue using Na-mic wiki
  • New Nitrc project
    • Jim Miller is leading
    • "Slicer3 plug-in examples" project
    • - search for slicer3
      • Includes demo/stub for ITK filtering data, etc.
    • Collection associated with an ITK course being taught
    • Requires CVS version of ITK
    • Works with Slicer build and Slicer install
    • Steve P is the liaison with NITRC
  • Slicer tutorial at UNC, April 14th
  • User-level Slicer training - Feb 20 at BWH
    • 1249 Boyleston
    • Release version of Slicer3


Attendees: Jim, Steve, Wendy, Xiaodong, Nicole, Katie, Alex, Luis, Ron, Will

  • Project week follow-up (Next week?)
    • Will will send email invitations for first half of projects for next week's tcon
  • Loadable modules
    • Alex and Terry are rearranging Slicer3.cxx to support loadable modules
    • Separate branch for built-in module discovery process
    • Sebastien is working on build issues for modules whose code is outside Slicer3
  • GenerateCLP - Thanks Hans for changes to support building modules
    • Hans is running a class this semester where the students will build Slicer CLI modules.
    • Jim is working on an ExampleModule for people to use as a template for building modules outside of Slicer3. Perhaps NITRC.
  • XML library
    • What to do with libaries that are too big to include in the source directory?
  • AHM 2009, Jan 5-9, 2009
  • Summer Project Week, Jun 23-27, 2008
  • New server architecture for wiki, svn, publication database


Attendees: Jim, Katie, Sebastien, Stephen, Luis, Steve, Wendy, Will

  • Luis and Bill Hoffman are making progress in making ITK installation relocatable. This is needed to finish the work on building plugins from an installation.
  • What's in VTK 5.2?
    • Infovis - Tables, Graphs, Views, IO
    • Refinements to WWidgets. Client/Server connections within the widgets. Event translation. New widgets (text, caption, affine, checkerboard, rectilinear wipe, annotation, key frame, contour, measurement, point/placer, plot)
    • Build now? Or wait until 5.2 released?
    • Repository freeze in March
    • Release on April 1, 2008
  • ITK release
    • Patches to ITK 3.4
      • Nine component/six component tensor conversion in IO has been patched to ITK 3.4
    • 1/19-2/1 moving contributions on Insight Journal for ITK 3.6
    • Move items from Review directory to main tree (QuadMesh, TransformIO) for ITK 3.6
    • Freeze repository 2/29 for ITK 3.6
    • Slicer3 will need to build against the Review directory.
  • CMake release
    • Version 2.6 on the horizon - release candidate in 3 weeks.
  • Tcl/Tk 8.5
    • Sebastien has a Windows build
    • Steve will try it out
    • Wait to switch to 8.5 until we have a good reason
  • Loadable modules
    • Sebastien - working on CMake issues on building modules as loadable modules
    • Terry - working on loading modules and reworking Slicer3.cxx
  • Slicer3:EventBroker | Event Broker
  • DWI DICOM as part of the Load Volume. Xiaodong is working on it.
  • ITKFactories directory in build and installs to hold ImageIO plugin libraries. Should increase the speed of executable plugins on the Mac.
  • OpenIGTLink
    • Protocol on the wiki (message format)
    • Put code in Sandbox, SourceForge, NITRC, Google Code???
  • Will schedule a time to go over the Project Week results


No tcon due to AHM


  • Attendees: Jim, Steve, Will, Brad Davis
  • Topics:
    • Jim and Will talked about leading the Monday and Friday sessions, and who would do what.
    • We are going to send out reminders to the project leads to ensure that their project descriptions are up to date
    • We discussed the software process project to make sure that we have a chance to address the Slicer build process, dashboards, etc.
    • We decided not to hold the project wrap-up presentation at AHM; we will do that later at subsequent TCons. (We decided that we needed the time to actually work. We are concerned that we are starting to see too many break-outs and not enough time to work.)
    • We keenly missed Tina and hope that she and her family are doing well.