Engineering:TCON 2007

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Project Week Final Discussions

  • Tina - discussion of re-binning of the projects
  • Discussion- review of project week projects and Core 2 participation
  • Discussion of Interest Groups
    • Discussion of fMRI Interest Group - can set-up a birds of a feather session at Programmer's Week
    • Raghu discussed the idea of a Microscopy Interest Group
  • Discussion of re-casting MICCAI workshop

No meeting on 2007-12-27


Finalize all Breakout session agendas.

  • 3pm: Tractography (Randy)
  • 3:10: EM Seg (Brad)
  • 3:20: Slicer Plug ins (Sonia)
  • 3:30: Geometry/Meshes (Alex G)
  • 3:40: Registration (Guido)
  • 3:50: Batchmake (Stephen for Julien)


NA-MIC Winter Project Week TCON#2 w/ all participants.


  • Projector inventory for the project week:
    • We need 4. Two bright (~2000 lumen or better) for the main mtg room, and one each for the breakout rooms.
    • We have: Rons (2000), Tina will buy one, Randy's (?), Will (1), Jeff (?), Ross has a backup
  • NA-MIC Winter Project Week Activities Kickoff TCON - this is the first tcon to plan the project week w/ the engineering team.
  • Discuss NAMIC-Kit paper: where to submit (must be in MedLine or IEEE)
  • Testing Slicer: what is the minimal set of platforms?
    • Slicer3 supported platforms:
      • Win32 (not Win64 due to vtk/cmake limitation - confirm with Bill H.?)
      • Mac 10.4, 10.5 (we need to test that 10.4 build runs on 10.5)
      • Linux x86 and x86_64 (linux is highly fragmented these days and there are issues with c, c++, and X libraries and even /bin/sh across distributions)
      • Ubuntu CPack issue
    • Testing needs/wishes:
      • Continuous builds on all platforms (need)
      • Human testers
      • Tests of packing and installing (need/wish?)
      • GUI Tests (wish)
  • Execution module distribution as binaries
    • Mixing different versions of ITK? (cvs -vs- release)
  • Cool NA-MIC image of the week
  • Attendees: Tina, Jim, Seb, Brad Davis, Stephen, Will, Steve, Nicole, Vince, Jeff, Ron


Gobble, gobble. T-con resumes next week, 11/29.


Attendees: Steve, Jim, Katie, Will, Nicole, Tina, Sebastien, Vince, Kevin, Steven, Brad, Kilian, Luis, Noby, David


  • 3-3:30pm: NA-MIC Slicer Topics
    • Feature freeze
      • 46 minutes!
    • Feedback from MICCAI/ open source workshop
    • Next mtg we start discussing the project week in January
    • AHM_2008
      • BatchMake presentation schedule (Jomier)
      • EM Segmenter End User Breakout Session??
  • Starting 3:30pm - Slicer IGT Call#2.

No T-con next week due to Thanksgiving



  • Slicer3 release plans
    • Last feature in (LFI) by 11/15
      • Re-evaluate deadline/status next week
    • Features that we are trying to add by LFI
      • Color storage nodes, Transform storage nodes
      • CLI modules from a Slicer installation
    • After LFI, put new development on branches
  • Side topic: have a look at - it is mediawiki based but has a nicely integrated wysiwyg editor.
    • Can we upgrade our wiki to have these

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



  • Proposal for AHM 2008 Breakout session (Tue, Jan 8th 1-2pm): Geometry and Topology processing of Meshes by Alex G of Caltech:
    • 30 mn Prof. GU: Discrete Algorithms for Surface mesh processing
    • 05 mn Alex G : curent and future ITK Implementations (QuadEdge, Param., ..)
    • 05 mn Luca : curent and potential uses in his research
    • 20 mn : interactions

Attendees: Steve, Will, Dan, Nicole, Jim, Jeff

  • Steve has started putting together a page for debugging command line modules
  • Nicole is having a problem with sending fiducials to command line modules when the fiducials are from a scene loaded from disk
  • Dan is proposing a macro recorder for running data through a series of command line modules interactively
  • How to test Slicer? One dashboard? One dashboard for the base and separate for modules?
    • How to test interactive modules?
      • VncRobot
  • OrientImageFilter bug
  • Tensor 9 to 6 conversion in ITK. 1 ITK test failing with changes to DoConvertBuffer



  • Review of Training plans
    • Update: 3 audiences: clinical researchers (app-users), biomedical engineers (app-users and developers), algorithm researchers (developers)
    • Sonia has first pass user training for slicer3 (working with Katie making builds on all platforms compatible with tutorial.)
    • First developer tutorial in the work (command line modules, working with Jim to make sure binary distributions can be used as platforms for devel tutorial -- so trainees don't have to build all of slicer to do the tutorial.)
    • Sonia would like feedback from developers on the tutorial content. Would be good if we tested it.
    • First programming example "Hello World" : will describe how to implement an ITK filter, and testing it with CTest.
    • How will course materials be distributed? Dataset is currently on wiki. Sonia will keep us updated on where to look to find tutorial and data as it develops.
  • Discussion of OSU experiments in fMRI preprocessing registration (Firdaus, Wendy, Steve, Raghu) Inter-slice_Motion_Correction_for_fMRI
    • challenge: correcting motion due to slice timing errors and motion between slice acquisition
    • comparing itk and spm's approach to affine registration, and finding problems with itk
    • images, 8-bit greyscale converted to float, EPI data (60 iterations, max 100)
    • discussion: how to make itk affine methods work?
    • Possibilities: parameters in metric are too strong; also need to set center of rotation for registration transforms;
    • Put src code into na-mic sandbox and a few slices for testing -- Luis will experiment to see if a good set of parameters can be found. May create a polynomial transform if necessary (such as is used in second stage of SPM's registration process).
  • Other Registration Things:
    • need for Slicer registration filters to output and input (linear and b-spline) transforms
    • approach: either new plugins for Slicer, or modifying current filters to give the option for resampling data or returning the xform instead?
    • Jim will be working on adding the changes -- will probably implement a VTK b-spline xform that's based on ITK b-spline xform.
    • NIfTI has subcommittee on spatial transform file formats, Steve is part of this: may want to look at how NIfTI is going to store the formats and be compatible with that. Tenative plan: to have Slicer represent linear trnasforms and non-linear ones a little differently: linear transform will still have a matrix attribute, and non-linear transform will have a storage node attribute...
  • Atendees: Dan, Jim, Tina, Steve, Sonia, Katie, Firdaus, Wendy, Vince, Luis



  • Separating Slicer Base from Slicer Modules
    • follow up to this discussion
    • dynamic linking of internal modules (similar to the way command line modules are loaded)
    • extensions repository (NITRC projects)



  • Jim updated the INSTALL_* CMake commands to the newer INSTALL() CMake command.
  • Slicer snapshot for BIRN will be Friday morning.

Attendees: Jim, Wendy, Nicole, Katie, Dan



  • - Dec 12-13-14 as candidate dates for Hands on Slicer/IGSTK/Opensource IGT Programming workshop. Is 1249 conference room available?
  • November 15 Slicer 3 Code Freeze. How is the notification being done - email and Slicer3 dev page? Core 1 developers of plug-ins need to be notified of this as well as updated on how this code freeze impacts them.

Katie,Steve, Dan, Nicole, Tina, Wendy, Jim,

  • Slicer3 code freeze will focus on the sections of Slicer3 code that Core 1 developers will rely to develop plug-ins
    • Jim will develop a UseSlicer.cmake to facilitate building plugins from a Slicer installation
  • NA-MIC Kit wiki pages
    • Will has started revamping the pages.
    • Needs to add BatchMake, Dart2, and CPack
    • NA-MIC Web page page should point to NA-MIC wiki sections?
    • How much of the content should transition over to
  • ImageActor and picking
    • Steve rolled back the code that switched to using ImageActor. ImageActors are not being processed correctly by CellPickers/PropPickers. Wendy needed the ImageActors rolled back to prepare the QueryAtlas for the fBIRN meeting.
    • Will will look at the ImageActor and picking issue and attemp to fix before the fall VTK release.
    • Another alternative is to write a vtkSlicerSliceOpenGLTexture class that incorporates some of the logic from ImageActor to avoid resampling textures to a power of 2 and simply reserve a power of 2 texture (if this is still a constraint) and use subtexture calls to load.
      • Another benefit of this approach is that we could bypass the error emitted in LightBox mode when our image data is 3D and simply grab the first slice to download to the texture engine (or any particular slice).


Agenda: Slicer IGT discussion: David Gobbi (Queens), Stephen Aylward (Kitware), Noby Hata (BWH), Sebastien Barre (Kitware), Luis Ibanez (Kitware), Kevin Cleary (Georgetown), Jeff Stoll (CIMIT) to join call.

  • Kevin: introduce NIH R01 to integrate IGSTK and Slicer for liver RFA, progress with IGSTK
  • Tina: wiki presence for this collaborator grant?
  • Steve Pieper: introduce mBIRN collaboration opportunity.
    • Overview page [1]
    • PAs:
      • Data Ontologies for Biomedical Research (R01) [2]
      • Sharing Data and Tools: Federation Using the BIRN and caBIG Infrastructures (R01) [3]
    • Workshop at NIH Thursday October 18, 2007
      • Schedule (Word Doc) [4]
      • Registration [5]
  • Pending Engineering Issues:
    • Loading ITK IO Factory shared libraries on Mac - need a way to rename libs in cmake
    • CPack adding to PATH on windows; need small cpack example for debugging
    • GUIs for applications with specific workflows: Workflow Phases in a Slicer GUI (David)
      (for reference, also check the GUI Workflow Wizard/Framework that was added to Slicer3 and used to implement the EMSegmenter Module; here is an animated GIF of an earlier version of the module)
    • Slicer3 Neuroendoscopy Module notes (Noby Hata); this is a private wiki (contact Noby for access?)
  • Workflow discussion from IGT Workshop [6]
  • Workflow tcon in 2006 [7]

Tcon Minutes


  • Tina Kapur
  • Ron Kikinis
  • Will Schroeder
  • Wendy Plesniak
  • Nobi Hata
  • Kevin Cleary
  • Steve Pieper
  • Jeff Stoll
  • Vincent Magnotta
  • Stephen Aylward
  • Sebastien Barre
  • David Gobbi
  • Katie Hayes
  • Nicole Aucoin
  • Jeff Grethe (UCSD)
  • Luis Ibanez


  • Tina: introduced the context of collaborations between multiple groups working on IGT projects
  • Steve: we should identify requirements for IGT systems, pursuing interoperability
  • David: from the DBP point of view
    • Interest in Workflows
      • Not enforced yet in Slicer at the top but available in the EMSegmenter module
    • Interest in customizing the Slicer GUI layout
      • Font sizes (should be bigger)
      • Arrangement of widgets in the front end
      • Two screens: One for Visualization and another one for medical information
  • Kevin:
    • Described IGSTK
    • NAMIC collaboration award for (IGSTK+Slicer) integration for radio-frequency ablation of liver tumors
  • Nobi:
    • MRI guided surgery
    • Neurosurgery
    • Endoscopy: Slicer module with workflow.
      • Lightbox in separate window
      • Status window for displaying information such as trackers, instead of having to navigate through menus
  • How flexible Slice3.cxx should be ?
    • Balance maintainability with flexibility and reuse for different clinical applications
    • Or having multiple Slicer3.cxx top applications.
    • One option was to hide the main panel and display extra information in the main 3D window (Steve).
  • Workflows
    • Defining the workflows
    • Running them
    • Can we simply restrict to a small set of workflows that are representative of common IGT situations ?
    • It may be too early to know, we may need to experiment more.
  • Jeff:
    • IGT in the gut.
    • Deformable registration need
    • Workflows are nice for final products, but they may be limiting in the research environment.
      • Workflows shouldn't be limited to linear wizards.
    • Memory issues
      • Multi-processing as a solution ?
    • Need for more flexibility in the Slicer front end GUI.
  • Some groups are working with Slicer 2.x, others are using Slicer 3.0
  • Reminder of the January Project Week.
  • Plan on an IGTK project week ?
  • Safety issues
    • Having different operating modes ?
    • Using the workflows as a mechanism for enforcing safety ?
    • Is user training enough for enforcing safety ?


Attendees: Jim, Steve, Will, Dan, Wendy, Nicole, Vince


  • Additional dashboard machines
    • Mac, Linux 64
    • Continuous builds
      • Need continuous build machines for each built type (Zack, Julien)
    • Builds that do installs
      • Nightly installations - need improved mechanisms to upload installations from Nightly Builds
    • Email when submission causes errors
  • build issues with curl
    • Errors when curl from within CMake build is found
  • possible collaboration with Dr. Claude Lechene from the National Resource for Imaging Mass Spectrometry
  • Webpages
    • Access to software tools from toplevel NA-MIC Website
    • Rendering/font issues on webpages


Attendees: Steve, Tina, Katie, Jim, Vince, Sebastien, Dan, Nicole


  • Michael Sherman from Simbios has agreed to be an invited speaker Thursday at noon at the AHM_2008. He'll be there all day Thursday - is there interest in a breakout session? If so, when would it work on the schedule?
  • Post kitware retreat followup
  • Figuring out caching
  • Supporting the end-to-end DBP projects
    • Possible modifications to VTK and ITK for tensor calculations
    • How to create a vtk convention for tensors, masks
    • Feasibility of adding a symmetric tensor to VTK



  • application specific executables as front ends to the na-mic kit
    • how best to provide clean user interfaces for things like IGT while being able to build on slicer3 infrastructure (possibly even invoke modules)
    • this is a request from the JHU/Queens DBP
    • possibly custom Applications/GUI code or different startup modes for slicer3
  • Plans for September 12, 2007, Engineering End of Summer Meeting
    • breakout sessions on batchmake, cmake, volume rendering, etc

Attendees: Dan, Wendy, Nicole, Katie, Steve, Tina, Jim, Julien.


  • Discussion on app specific front ends. We want to do this at an infrastructure level rather than clean up slicer.cxx file.
  • Set up IGT specific agenda on one of the upcoming tcons. Goal would be to talk about what is being with planned on endoscopy application at kitware, and how to coordinate it with the IGT support that the JHU group needs.



  • Training Discussion - will require Sonia to be linked with a Core 2 co-trainer to develop materials and/or present. Some suggestions below, subject to change. Questions include: can we cover all these topics? Over what timeframe? What venues will best reach our intended audiences? Is wiki+ppt still the best format? How much existing material can we re-use? Should we pull in Core 1 people for some topics?
    • User Training
    • Developer Training
      • Software Process (cmake, dart, svn, ctest, cpack, getbuildtest) (Will)
      • ITK (Luis)
      • VTK (Will)
      • vtkITK (Jim)
      • Teem (Gordon)
      • KWWidgets (Sebastien, Yumin)
      • Slicer Command Line Modules (Jim)
      • Slicer Internal Modules (Wendy)
      • BatchMake (Stephen)
  • Supporting Greg Sharp at MGH: Any clues from the email Steve forwarded?

Attendees: Wendy, Nicole, Steve, Will, Jim, Katie, Sonia, Steve, Sebastien


Attendees: Steve, Wendy, Tina, Dan, Jim, Vince, Katie, Will

  • NCBC program discussion
  • Project oriented DBP projects
  • Dan will be going to Mayo Clinic in October :(
  • Discussion of Mac issues
    • module startup times is biggest end-user issue
  • Discussion of Engineering:September_12,_2007
  • discussion of vtkITKLevelTracing and vtk and itk 64 int types


Attendees: Steve, Katie, Nicole, Stephen, Vince, Will

Announcements from Will

  • need to update the core 2 web pages (project pages will be assigned by Will)
  • brainstorming on the renewal
    • will start discussing in Sept
    • discussion at January AHM
    • writing will take place in 2008

Kickoff retreat Wednesday Sept 12 in Clifton Park

Mac Talk (postponed)

  • debugging with Xcode
  • slicer3 startup time (slow to discover each module)
  • passing arguments to applications launched with "open"
  • lots of link errors like:
symbol used from dynamic library /Users/pieper/slicer3/latest2/Slicer3-lib/Insight-build/bin/libitkvnl.dylib(vnl_matrix+uint-.o) not from earlier dynamic library /Users/pieper/slicer3/latest2/Slicer3-lib/Insight-build/bin/libitkvnl_algo.dylib.3.3(vnl_rnpoly_solve.o)


Attendees: Katie, Nicole, Stephen, Jeff, Vincent, Ron, Dan

Report by Vince on Steve and Curt's visit to Iowa

  • KWWidgets wrapping of meshing code
  • Allows instant incorporation into Slicer3
    • Initial application panel appeared in Slicer3
    • Need to have 3D widgets incorporated, some ready, some in progress, requires more recent VTK
      • Slicer3 will compile against VTK CVS Head, but some bugs need to be resolved

Exporting Transforms to CLI Modules

  • Need to have discussion on saving transforms
    • Nicole working on MRML export to be digested by CLI executable
    • Need to work out round trip
    • Nicole porting Slicer 2.6 modules as CLI Modules, all VTK-based



  • Programming Week - updates/questions

Attendees: Jim, Will, Brad, Stephen, Lucas, Wendy, Katie, John, Vince, Tina, Nicole, Randy, Clement, Alex


  • Tractography workshop. Randy provided update on the contrasting tractography project. Santa Fe Workshop October 1-2
  • Lucas' query about
    • transform/Slicer ... Jim will work with him and bring in Steve/Alex as needed.
    • is looking for 3D+T vascular data set to demo his work and submit to IJ. Jim will look into it.
  • Clement from UNC DBP - the segmentation/cortical thickness pipeline that was working during project week is no longer working now. Randy/Nicole pointed him to the freesurfer wiki where error messages/logs can be reported.
  • Will - starting September, we will use a few calls to start talking about the Core 2 competitive renewal.



  • Ubuntu nightly build problems & Coverage (Dan)
  • Possible dates for next mini-retreat (Dan/Steve/Jim)


  • Bspline status needs to go to Ron

Attendees: Dan, Tina, Steve, Nicole, Wendy



Attendees: Jim, Steve, Tina, Katie, Vince



  • Project week follow up
  • Interest from Europe

Attendees: Jim, Stephen, Brad, Tina, Steve, Vince, Ron


  • AHM 2008
    • Sunday Jan 6th is a site PI meeting
    • September will be a tcon of all site PIs to start prep
  • August 2nd will be the project week followup call
  • Slicer discussion
    • Problem with shared object version of "Simple Region Growing". Cannot reproduce error.
    • Discussion of new widget (not c++ wrapped) included in kwwidgets. See Slicer3:GUI_Experiments:TkTreeCtrl for how to test it.
    • Other general status discussions...


  • Project Week final q&a. wiki templates must be completed by now for all projects.


  • quick review of project week projects (10 min)

Attendees: Tina, Will, John M, Jim, Katie, Nicole, Brad, Stephen, Martin, Vince

  • Project week
    • limit to 70 participants
    • forum for Peter Kazanzides robot, 3D widgets problem: add-hoc session
    • review of break out session pages
    • Tina is disappointed with Windows Vista :)
    • discussion of long lead time items: competitive renewal meeting at project week
  • Misc
    • Slicer3 mesh support for META meshes: put on "the list" for Stephen
  • Action Items
    • Tina will send reminders to fill out project wiki pages


Attendees: Jim, Dan, Joseph, Brad, Stephen, Tina, Vince, Wendy, Steve, Nicole, Ron

  • 2007_Materials_for_NCBC_Program_Review Urgently needed for NIH
    • Discussed content for each of the questions
    • Established procedure for providing content, deadline for content Friday AM, Tina to revise and submit by 4pm Friday
  • Slicer discussions
    • ROI: Fei only checked in some of the ROI related files while he struggled with tabs in the source code. Resolved later Thursday afternoon.
    • Some leaks crept into the slicer code, causing some tests to fail
    • Brief discussion of Slicer3/Scripts/getbuildtest2.tcl which is a subversion-only version of the build script.


  • Project Week
    • review of project week breakout sessions(15 min)
      • Attendees for breakout session responsible for establishing the agenda for the breakout
      • Given the short duration of the breakout session, set reasonable goals for discussion points and priorities
      • Suggest gather numerous discussion points and then spending the first few minutes of the session prioritizing
    • projectors - who is bringing these?
      • Training Core has a NA-MIC projector
      • Steve Pieper has a 800x600 projector
      • Brad Davis can bring a projector from Kitware south
  • A Slicer module that runs BatchMake is illustrated HERE
    • BatchMake can generate a DAG script with is input to Condor's DAG manager. An illustration of a DAG from BatchMake is HERE




  • Summer Project Week Contd. Are all the core 2 expected attendees on the list?

Attendees: Casey, Alex G, Kevin T, Katie, Skip, Pat, Bryan, Lauren, Nicole, Brad, Stephen, Jim, Wendy, Steve, Dan, Jeff, Kilian, Will, Gary, Neil, Greg Sharp, Vince, Ron,David Gobbi, Clif, Jack Blevin, Gabor, Tina


  • Discussed projects



  • Summer Project Week Contd.
  • June 11, NCBC review?

Attendees: Jags, Wendy, Luca, Brad, Stephen, Nicole, katie, Steve, Haiying, Michael M (NCBO), Gary Christensen, Pat, Will, Ron, Dan, Tina, Jim.


  • Discussed projects of attendees, and added to the list.
  • Michael M. from NCBO attended and was given an overview of the NA-MIC software process.



  • Summer Project Week discussions Contd.

Attendees: Nicole Aucoin, Brad Davis, Tina Kapur, Jim Miller, Katie Hayes, Steve Pieper, Vince, Raoul, Sebastien Barre

  • David Gobbi is in NA-MIC
  • Update on Progress Report
    • "looking not so bad :)"
    • Tina pointed out the new format used to document Algorithm Core Activities

see and sub-pages

  • Summer Project Week
    • Projects placeholders need to be documented.
    • New projects listed: Display Optimization, MRML Scenes for the Execution Model, EMSegmentation Validation, Adding VTK Interaction Widgets to Slicer 3, vtkITK wrapper for rule based segmentation, Application of the Slicer2 module on DBP data, Conversion to Slicer3, Migrate Iowa Neural Net code to pure ITK, Support for Unstructured Grids, Python support in Slicer3, CPack, Ctest infrastructure improvements.
  • Status of EM seg in Slicer3
    • Testing and validation is in progress, Regression tests, command-line version are coming (by project week)
    • Intensity normalization
    • Bug fixes
    • Question arises: stick to VTK 5.0 CVS branch, or is there a 5.2 stable planned? Not to Kitware's knowledge, but that could be pushed?
  • Status of DTI in Slicer3
    • MRML part of DTI is in
    • Raoul taking care of moving from Slicer2 to Slicer3
    • Teem issues should be solved by project week
  • TIFF reader problem
    • Slicer issue where TIFF is a 2D format but coming back as 3D volume, confusion with scalar image, vector image, etc.
    • On the ITK side, ITK seems to read just the first slice of some volumes, the rest gets corrupted.
    • To be solved by project week.
  • KWWidgets
    • BoF at the project week
    • In the future, shared screen session with Sebastien to be setup, or even training course (to be discussed at project week)


Attendees: Nicole Aucoin, Brad Davis, Tina Kapur, Jim Miller, Madeline Miller, Skip and Pat from Nothwestern, Vince, Katie Hayes, Bryan Smith, Steve Pieper, Jeff Grethe, Jags


  • Report from Bryan Smith (UCSD NCMIR) on his visit to BWH to develop ITK-based command line modules for connected component and math morphology analysis of microscopy data.
    • Update on progress
    • Reading data into Slicer
    • Slice through surfaces, generate models
  • Review progress report progress
    • Voxel statistics from image data
    • Otsu contains connected components...problems on OS X
    • Reworking the wiki page hierarchy for progress report
    • Final pass on NA-MIC kit projects
    • How to handle projects which use GPLed code in Slicer extensions
    • Review the publications page to make sure all of your pubs are there
  • Slicer bugs
    • Problems reading 3-D TIFFs with RGB colormaps



  • A bug in TIFF IO. Given a high-priority rating by Ron. Volunteer needed.
  • There is an emerging slate of bioinformatics platforms for research: BIRN, XNAT, CaBig, I2B2 etc. Slicer3 will need to work with these environments.
    • We are already working with BIRN on XNAT, HID, and XCEDE
    • What kind of additional interactions should we attempt for the near term?
    • What kind of functional behaviour is realistic, given resources available?
    • Does this diagram accurately reflect our approach?
  • NITRC Administrative Supplements available (Steve)
    • See announcement [11]
    • Dave Kennedy plays a major role in the program
    • Applications are accepted any time, but there's a review coming up so getting proposals in by May 15th is a good idea
    • These supplements can support documentation and integration of tools into the NITRC (Neuroimaging Informatics Tools and Resources Clearinghouse)
    • NITRC is based to some extent on gforge.
    • Goal is for "modifying, documenting, and otherwise making more adoptable, interoperable, and usable existing neuroimaging informatics tools and resources."
  • Patching vtkImageReslice in Slicer-2-6 VTK, also do we want a Slicer-2-7 branch of VTK/ITK?

Attendees: Jim, Steve, Ron, Jeff, Nicole, Will, Stephen, Neil

  • TIFF Bug: Jim will ask one of his people to look into the TIFF bug.



  • Slicer2 RuleBasedSegmentation Module (for the DLPFC semi-automatic segmentation)
  • Further discussion of large scale experiment control (Dan, Steve, Sebastien)
  • Process for annual report (Tina, Jim)
  • Collaboration grant updates
  • fBIRN / BIRN informatics update (Steve)

Attendees: Jim, Dan, Sebastien, Brad, Tina, Vince, John, Ramsey, Nicole, Stephen, Jeff Notes:

  • (Pre meeting discussion of sunspots)
  • Rule-Based Segmentation Module
    • Marek would like to use it for his data
    • GATech provided info on work so far, Brad has reviewed
    • VTK/ITK implementation issues that can be easily resolved
    • Slicer2 module needs to be integrated with actual filter
    • Delphine and Ramsey wrote the interface and filters based on Jim Fallon's rules
    • Slicer2 implementation relies on subvolume and draw capabilities (discussion of slicer3 implementation).
      • possible new subvolume selector to add to slicer3
      • could use new editor in slicer3 for ROI
      • also need some kind of wizard or detailed instructions to help guide
      • then the rule based code could be a command line module
    • GATech is planning to do a project with Jim Fallon using the Slicer
    • At project week we can look at getting Marek up to speed on Slicer2 and the engineering group can work on a slicer3 implementation.
  • Issue with NAMICSandBox ability to commit? John may be specific to John.
  • Update on Neil's work on the GWiz (Grid Wizard) and discussions with Jeff and Steve at fBIRN meeting
  • Stephen update
    • Starting to do 'batchboard' tests on bspline registration
    • planning public face for registration optimized methods
    • integration of BatchMake and CMake for running tests on multiple platforms
  • Sebastien is doing timing tests on various machines at BWH
    • ITK timer class does the clocking (wall clock timing) but could look at performance timers at the processor API (build in the CPU).
    • Process priority is set high to get best guess of fastest behavior
    • may need an administrative approach to avoid multiple jobs running during night performance tests
    • new features being added to cmake/ctest/batchmake to help determine machine environment, could be extended
  • Progress report mechanics
    • The report describes just the current year (not the cumulative sum of all the years).
    • Tina is going to send email about the themes for the progress report
    • Need to be sure the pdf has clickable URLs for wiki page entries
    • Discussion of Impact for the highlights section
      • non-na-mic people at the programmer events and AHM
  • Update on XCEDE work at fBIRN AHM



  • Collaboration proposal Peter Y.


  • Attendees: Peter, Dan, Jim, Katie, Steve, Wendy, Nicole, Vince, Tina, Will, Sebastien, Stephen, Brad

Discussion of Peter Yim's plans for disseminating algorithms through the NA-MIC Kit.

  • Biomedical Engineering, UNC, NIH
  • Algorithms for MRA, vessel reconstruction
    • Segmentation, skeletonization
    • University of Medicine and Dentistry of NJ
    • Vascular diagnostics, quantifying angiogenesis, stroke...
  • Algorithms could be valuable, but aren't written in a way that can be disseminated (written in C for IRIS Explorer)
    • Peter needs to have collaborators to re-write the code
    • Peter can provide the clinical background and potential user community
  • Could be good candidates for integration into ITK
    • Need to review what it means for the NIH patented technology to be deployed
    • Some of the algorithms require close interaction and others are more automated
  • Discussion of the possible allocations of effort and collaboration




Attendees: Will, Jim, Wendy, Csaba, Marek, Nicole, Katie, Dan, Steve, Sebastien, Brad, Ron, Tina

  • Marek - vcsf data on 5 patients. familiar with software and algorithms available in na-mic. segmentation and fine tuning of algorithms is needed in slicer. Would like to use GeorgiaTech algorithm for automated segmentation of DLPFC.
  • Csaba putting details of JHU project on wiki. Will schedule himself into the tcon in about 4 weeks.



  • Progress Reports - the folks who lead the sections last time will be invited to do the same again this year, or to nominate someone else who they will help.
  • DBP-II - algorithms contacts added by Ross. (UNC: Guido, Harvard: Polina, MIND: Bruce Fischl, JHU: Allen)
  • Invitation sent to DBP2 for this call, with the following agenda suggestion:
    • Notes: Marek has conflict on 3/22 and will attend 3/29 tcon.
    • reminder that he would like your pages to be updated in March. Example of an updated page is:
    • introducing you to your namic engineering contact points and the role they will be playing. (we expect to introduce you to your namic algorithms core contact points at a later point as well).
    • summer project week at MIT (June 25-29). Ron's expectation is that by then (1) you will have identified a problem that can be solved with the na-mic kit in a 6-month timeframe and the results for which you will use in your work, (2) you will send an engineer and data to this project week, and the engineer will be able to articulate to the larger group what the problem is, and use that week to work on it with the na-mic team.

Jim has notes and attendees to add.



  • Heads up: 2007 Progress Report. Recommendations needed from Ron on section/theme leads.
  • Dissemination and Outreach for the rest of us (Will, Tina)
  • DBP2 Points of Contact (DBP, Engineering, Algorithm). Need contact information for DBP2s. Algorithm contact points still need to be added. (Update: email sent to Ross 3/1 and 3/15 with request to provide names in march.)
  • Performance analysis tools and strategies: ITK_Registration_Optimization, Slicer3:Performance_Analysis (Steve Pieper, Sebastian Barre, Stephen Aylward, Katie Hayes)
  • Slicer release schedule (Steve)
  • Question from Douglas Alan: At the January NA-MIC All Hands meeting in SLC, Mike Halle and I met with Bill Lorensen and Jim Miller to discuss how in Slicer we might pass a FITS world coordinate system transform (and its inverse) from an ITK FITS image reader to the resulting Slicer VTK image so that Slicer can then be enhanced to use the transform to properly display the world coordinates. The proposed solution was for me to define a subclass of itk::Transform (i.e., FITSWCSTransform) that would handle the WCS transform, and once I had completed this (which I have) for me to then modify my FITSImageIO reader so as to include a pointer to a FITSWCSTransform object in the FITSImageIO's MetaDataDictionary. As it turns out, there seems to be a snafu with this plan: the MetaDataDictionary of an ITK image appears to be stripped from the image whenever it passes through an ITK filter. Or so it is the case, at least, for the filters that I have tried. Any ideas on how we should proceed, in light of this?


Attendees: Jim, Steve, Will, Katie, Nicole, Raymundo, Stephen, Sebastien, Wendy, Tina, Jeff

  • Schedule for the progress report in on the wiki. Last year's report is also available. Assignments are imminent.
  • Need to update the NA-MIC web presence. Wiki to web will be used to author and publish the content. Ron will set the vision for the web presence statement (DBP focus? Theme focus? Core focus?). Everyone is responsible ensuring all NA-MIC activities and contributions are advertised.
  • Tina will get the contact info for the DBP2's
  • Stephen is pulling together a test application to run across systems to evaluate registration performance.
    • Note that only one optimizer is relevent to B-Spline registration (LBFGS-B?)
    • Torsten has a hierarchical B-Spline algorithm that Killian uses as the yardstick.
    • Brad developing proposal to evaluate EM pipeline soup-to-nuts for sources of errors.
  • Steve and Katie looking at Callgrind and Callgrind Control to track the overhead of observers and potentially the over-calling of callbacks.
  • Tracker performance okay but the images update slowly
  • Slicer3 release at the end of March
    • DTI tools availability gated by MICCAI deadline
    • Launchers work with getbuildtest but may have impacted CPack installations.
    • ModelMaker needs MRML read/write (Jim!)
    • Filebrowser will be available
    • Any features to suppress?
    • Any additional documentation needed?
  • Slicer 2.7 release at the end of March
    • Mostly bug fixes but a few new features
  • Jim will talk to Mike about the FITS needs for the MetaDataDictionary and the pipeline.



  • Question from Steve: best way to handle "neurological" analyze files (where right-is-right unlike radiological files where "left -is-right"). The oaisis brains data collection from mBIRN stores their data this way and the ITK IO factory doesn't have a way to know which kind of file these are.
  • Python in Slicer - project overview: Dan
  • Google Summer of Code - are there any project takers?


  • Update - it turns out analyze files are stored in radiological convention but displayed in neurological convention, so everything is as 'correct' as it can be for this file format. But the ambiguity remains about the real meaning of analyze files, so in the future oasis will supply nifti formated files.



  • Adding Engr+Algorithms core representatives to each DBP-II team: DBP2:MIND
  • Google Summer of Code
  • SIfTI effort to standardize spatial transform files. (login info will be given on the phone)
  • Technical Slicer3 item: command line executables


  • Eng contacts for DBP-II:
    • Katie Hayes for the JHU project
    • Jim Miller for UNC
    • Brad Davis for Harvard (Confirmed)
    • Steve Pieper for MIND
  • Summer of Code
    • Generally agreed to be a good idea if there's time
    • Check with Luis
  • SIfTI
  • Command Line Interface to EMSegmenter
    • Jim will work on making MRML scenes come as arguments to command line modules and give an example that can be used for EMSegmenter and other projects like the ModelMaker.


Attendees: Wendy, Jim, Nicole, Dan, Andy, Katie, Tina, Ron


  • match dbp-IIs to engineering core members (Jim and Tina to do offline)
  • contact dpbs regarding participation in project week (Tina)



Attendees: Jim, Nicole, Tina, Katie, Jags



  • Please note that we now use a new TCON#. If you don't have it, please send an email to
  • Review remaining Project Half-Week Updates




Attendees: Bill, Jim, Steve, Wendy, Nicole, Katie, Brad, Andy & Jags


  • Last call with Bill as the PI...
  • Next TCON (Feb 1) to review 4-block from project half week. Will use Jim's tcon #.


  • New phone number for TCON next week; email Jim for the number
  • Problem with region growing?
  • Bye, Bill! We'll see you in three weeks when you get bored with retirement.


Attendees: Bill, Tina, Steve, Katie, Sebastien, Zack, Jags

  • Slicer3 release schedule discussion
  • Which teem are we on?
  • Status of filebrowser?
    • Current unix browser does not allow for making a new directory
    • Does the new one support specifying a list of file types? (Yes)
  • Feb 1/8 for project half-week results 4-blocks review?


  • Feb 1 and 8 for project half-week results 4-blocks review
  • 12 days till Bill's retirement...
  • OHMB workshop agenda info by Steve: DTI tutorial for Slicer3 is a candidate topic.


No tcon this week. AHM_2007 in progress.


Agenda and Highlights:

  • Project Half-Week Activities - Focus on Slicer3 Projects. And any others that need resolution of title/team. 4-blocks should appear asap. Each project lead will use these to introduce their project on Wednesday, Jan 10th.
  • There are pages in google cache that are not yet on the namic-wiki. What is the process for pulling those in? Should each person who finds a page just cut and paste the text as best as they can? How should we use the "wanted pages" list on the wiki?


  • Slicer3 Projects have been added to the wiki.
  • Wanted page list is being pared down as a high priority item,.
  • Jim and Bill will be on Daniel Goldberg's project half week project.

Attendees: Bill, Will, Ron, Steve, Jim, Stephen, Neil, Andy, Luis, Nicole, Katie, Wendy, Jags, Tina