Engineering:TCON 2008

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Slicer 3 Dartboard

Link to the Slicer 3 Dartboard here

2008-08-07

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

Agenda:

• 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 (www.airwayinspector.org) 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.)

2008-07-31

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

Agenda:

• 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
  • see XCEDE use cases
• 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.

2008-07-24

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

Agenda:

• URGENT: http://wiki.na-mic.org/Wiki/index.php/2008_Progress_Report_NIH_QnA
• FYI http://wiki.na-mic.org/Wiki/index.php/Events:TutorialContestJan2009
• Slicer 3.2 release
• XNAT visit in Boston

Notes:

• 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.

2008-07-17

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

Notes:

• 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 :)

2008-07-10

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

Notes:

• FYI Events:August_2008_NCBC_AHM
• FYI 2008_July_Slicer_IGT_VV_Link_Session_II
• Xenios from Yale at BWH on Wednesday, July 23rd to continue work on Slicer IGT+vvlink integration
• Dan Marcus to come to boston in late July to continue xnat integration

2008-07-03

• 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!

2008-06-19

• Agenda: svn repository switchover finalized for when? Wednesday morning?
  • Engr Business: Do we need any announcements for the
  • 3-3:30pm: Mesh Discussion for Core 1
  • 3:30-4pm: IGT Projects Discussion

2008-06-12

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

Highlights:

• 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.

2008-06-05

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.

Highlights:

• 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.

2008-05-29

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.,

Notes:

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.

• Info: Relative roles of Core 1, Core 2, Core 3

• 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.

• Ron's press 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)

2008-05-22

Dashboard

Agenda:

• A round of applause for Sebastian, Steve and all the code freezers
• http://www.slicer.org/slicerWiki/index.php/Announcements:Slicer3.2 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. http://www.csie.ntu.edu.tw/~cjlin/libsvm/

Highlights:

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

2008-05-15

Agenda:

• 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

Highlights:

• 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

2008-05-08

Agenda:

• 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?

2008-05-01

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.

2008-04-24

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

Agenda

• 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

2008-04-17

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

Topics:

• 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.

2008-04-03

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

Agenda

• discussion of xcede web services and mBIRN
• 2008_Engineering_review_at_Utah:FollowUp
• New! glyphs on slices movie!
  • made using wink from http://www.debugmode.com/wink/
  • add something like the following to your wiki page after uploading the .swf file to the wiki

<flash>file=dti_glyphs.swf|width=800|height=600|quality=best|loop=true|play=true</flash>

• 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

2008-03-27

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

Highlights:

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)

2008-03-20

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

2008-03-13

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

• Update on Loadable Modules project (Terry) and CMake updates for module builds (Sebastien)
• Engineering trip to Utah
• We are starting to use Categories to bin our pages. SuggestedCategories - suggestions?

2008-03-06

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

Highlights:

• Slicer page on wikipedia - http://en.wikipedia.org/wiki/3DSlicer. All engineering core members should visit this page and edit as needed. ASAP.
• dicom to nrrd converter in progress. Xiaodong working on it and expecting to complete in a few weeks.
• March 24-26 Meeting in Utah

2008-02-28

• 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.

2008-02-21

• 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.

2008-02-14

• 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]

2008-02-07

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

• Look at upcoming VTK 3D widgets
• Review of projects from SLC AHM 2008 http://wiki.na-mic.org/Wiki/index.php/2008_Winter_Project_Week

DBPs

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 www.slicer.org/Documentation 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.

2008-01-31

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
  • http://slicer.org
  • Uses wiki-to-web
  • Feel free to edit/improve
• 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
  • http://nitrc.org - 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
  • Working with UNC's BRIC (http://www.bric.unc.edu)
  • Sonja, Randy, Martin, Stephen
• User-level Slicer training - Feb 20 at BWH
  • 1249 Boyleston
  • Release version of Slicer3

2008-01-24

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

2008-01-17

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
• 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

2008-01-10

No tcon due to AHM

2008-01-03

• 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.