Engineering:TCON 2009

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Attendees: Will, Ron, Xiadong, Nicole, Vince

  • A day of rest,


Attendees: Will, Steve, Tina, Katie, Wendy, Seb, Jim, Xiaodong, Dan M, Ron

  • Progress Report - due tomorrow
  • When can we invite Utah student to discuss B-spline registration project? High priority for project week.
  • Review Project week list and pages
  • remaining 3.4 release bugs


Xiadong, Tina, Katie, Nicole, Saikat, Harish, Wen, James, Steve, Vince, Dan M,


  • NA-MIC engineering projects


Agenda Jim Balter, Vince, John M., Nicole A, Bjorn, Jim, Steve, Jim, Xiaodong, Alex G., Sandy, Eric, Katie, Will

  • Project: MRSI (3pm)
  • Project 2d-3d registration (3:30)
    • Jim Balter, Sandy Wells, and probably Greg Sharp,
    • GPGPU image registration
    • Targets:
      • Back projection
      • 2D/3D Registration
      • Jimmy and Yogesh have some GPGPU affine registration code
      • NVIDIA field engineer may attend
      • Look at CUDA Volume rendering to see if it can emulate radiographs
      • There is an nvidia ray casting framework that may be available soon
      • There will be cuda-enabled workstations available (Apple from SPL, Microway demo unit?)





Notes: discussion during this tcon was about projects, and these were added to the above link.


Attendees: Katie, Ron, Tina, Steve, Jim, Wendy, Kevin Archie, Nicole, Xiaodong, Randy

  • - can the OS and the last stable release be filled in automatically on this page?
    • forwarded request to Zack
  • Slicer 3.4 release
  • 3.4 bugs to be fixed:
    • Documentation still outstanding
  • 3.4 tutorials
  • Progress Report: please update project pages by April 15
  • Project Week Prep
    • next thursday, april 16th is kickoff tcon
    • april 23 - igt tcon?
    • Breakout/Tutorial candidate topics:
      • Slicer-Python candidate tutorials/breakouts (Demian and maybe Luca and/or Daniel?)
        • Introduction to Python/scipy developement
        • Exploratory image processing in Slicer through the python console
        • Slicer Modules in Python
      • 4D+t microscopy cell dataset segmentation (alex g.) What is the relation for FourDAnalysis?
      • ITK by Luis
      • Data Clinic (already on agenda)
      • Tutorial Contest (already on agenda)


  • Discussion of dicom handling (follow up on questions from Queen's DBP prostate MR) (Steve)
    • Issue with DICOM handling using gdcm with malformed DICOM
    • Read image data with wrong geometric information
    • Deprecate older DICOM parsers in ITK
    • Unregister older DICOM1 and DICOM2 versions of DICOM reading in ITK
  • Luca's question about how to avoid accidental program execution during module discovery (Steve)
    • Have CMake generate a manifest when building?
    • Possibly have subdirectories for support files

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


  • Making build/install compatible with LSB (Linux Standard Base) and FHS (File Hierarchy Standard) to support effort to put slicer into the debian repository. (Steve) A few of the questions to discuss with the engineering core:
  • Tutorials at/before Project Week?
  • FYI: starting this year, the project week is a joint activity between NA-MIC, NAC, and NCIGT. April 16th is the kickoff TCON.

Attendees: Steve, Jim, Will, Bill H., Nicole, Katie


  • Tina will Ron Steve talking about tutorials, will we hold them during the project week? proposed and nixed the idea of holding anything the week before project week. Hold it online (shared desktop)? Get them out of PW and into own spot, out of week before PW.
    • during PW they don't get the attention they deserve?
    • will concerned about travel time/costs
    • Tina not expanding the span of project week beyond the week, suggests keeping some tutorials in there, but not make them 5 hours long
    • ask potential attendees if they have specific things they want to learn about
    • try not to shuffle the tutorials as people plan to attend them on specific days
    • make electronic versions available ahead of time
  • PW is a join project week now with NAC and NCIGT, Apr 16th is kickoff TCON, Tina thinks 10-20 people more might attend
  • debian style Slicer compilation
    • GenerateCLP/GenerateLM, not using the launchers in general. Will fwd this to Sebastien and bill hoffman
    • GenerateCLP/LM lib and bin in different dirs, generated during compile time, not found
    • Bill H: not familiar with LSB and FHS
    • Jim: we could change how GenerateCLP is built so change how the rpaths are set?
    • Bill H: cmake can be set up with rpaths when building when install clear them out? skip rpaths, check with Brad King, check version of cmake
    • Steve: rpaths are off everywhere but 64 bit linux. May not be necessary any more. They don't want them at all in debian.
    • shared library version number, symlinks. Work on windows? in dll header, ignored. Is there a cmake command? set target properties, it'll set the name and set up the sym link.
    • #3 in bug tracker, use Slicer3-real in /usr/bin? two assumptions in launcher, in build or install dirs, if it's in /usr/bin that's different again. current cpack slicer3, top level has Slicer3 and then sub dirs bin and lib, launcher should be in the bin dir? makes sense for install, but not for a zipped up dev build where have to look in bin for what to run. If bypass the launcher and run the core exec, it should be able to find all the shared libs in a properly installed debian. Module libs don't' make sense in /usr/lib as they don't stand on their own. Jim: build two launchers? one in bin dir and one outside, and in debian package the outside one doesn't. Reliance on SLICER_HOME - is it where started, installed, where Slicer3-real is? Bill: depend on the launcher to get paths right, as opposed to ld paths. Worry about installing the vtk libs in places where others can find them. We treat them as our own private versions. Debian: system vtk, etc, and the package manager deals with the library versions.
    • #5 Bill: reason stick libraries in bin is due to Windows
    • #6, 7: fine to fix if it doesn't break modules/libs that depend on each other
  • Jim: Manaz want to do picking, fibre clustering into Slicer way.
    • look at the Base/GUI/vtkSlicerViewerWidget.cxx for the CellPicker, it is called from an observer on the vtkSlicerViewerInteractorStyle when that reports a mouse mode event (see the vtkSlicerFiducialListWidget for example of how to set up the observer and respond to PickEvent)


Attendees: Katie, Tina, Nicole, Steve, Vince, Jim, Xiaodong, Ron, Will

  • During Project Week: full integration of the roadmap projects into the NA-MIC kit
    • Tools developed under DBPs to be integrated to NA-MIC kit. Need to check progress and understand where we are. 1. MIND, 2. Harvard, 3. Queens, and 4. UNC.
  • Core 2 Renewal meeting
    • Mid-May in Georgia, Will to coordinate.
  • Modules in slicer release
    • Steve and Alex identified a list of bugs in Slicer 3.4 pre-release.



Attendees: Ron, Tina, Will, Nicole, Vince, Bill, +1


  • Registration
    • bspline registration is a deliverable for the project week
    • leaving registration as it is, Ron will reorder them:
      • linear then affine then deformable then register images
    • Ron will draft a note and send it around for comments
    • documentation needs to be updated, Bill Lorensen can do bspline?
  • Bill fixed the command line module loader to use an html to go to the web pages, use the documentation-url tag in your CLI xml file (See the Checkerboard filter help), update the CLIs to put them in
  • there may be some supplement money from the stimulus package for our grant
  • no release dates yet
  • working on a welcome module Slicer3 UI design wiki page has some details
  • Bill signing off to shoot off a pvc pipe model rocket, also found an open source project, put your GPS location in and it shows you the annotated night sky, Stellarium.
  • Will: are cheques being received, Tina hasn't heard yet, they're out and people should be receiving them.
  • Tina: one of the NIH people working with Joy the dissemination person at Stanford (?), put together a calendar.
    • Steve, Jim and Will are going to Georgia Tech in May, should show up on the calendar.
    • when events page on the wiki gets updated, it will show up on the calendar


Attendees: Ron, Jim, Tina, Xiaodong, Marco, Dan


  • Documentation for Slicer 3.4
  • New GWE released and tutorial added: Slicer3.2:Training
  • Xnat central has been updated so it doesn't require login (default is to login as guest).


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


  • Attendees: Katie, Wendy, Nicole, Will, Jim, Xiaodong, Vince, plus lurkers
  • VTK cvs repository frozen in preparation of a 5.4 release. Perhaps mid-March.
  • Teem can now build with CMake though no one can use it yet can because it is not checked in.
  • EM Segment bug wrt to signed data (i.e. CT data in Hounsfield numbers).
  • Slicer release tentative for first week in March


  • Agenda:
    • Topic #1: NA-MIC data repository
    • Topic #2: Python wrapping of ITK in Slicer: adding vtk-itk glue pipeline connection filters to Slicer build, so Python scripts can use ITK filters.
  • Attendees: Jim Miller, Tina Kapur, Nicole Aucoin, Kurt Lisle, Ron Kikinis, Clement, Dan Marcus, Katie Hayes, Wendy Plesniak, Xiodong, Vincent Magnotta, Steve Pieper, Will Schroeder
  • NAMIC data rep:
  • there is namic data, test data and tutorial data floating around in various places (including in Slicer download, different data bases), Ron suggests that we think about how we should organise it into one place for nightly builds, tutorials etc.
  • Wendy: we have an instance of XND web services running on, we could use it
    • Steve: it's on an Amazon cloud, fine for testing, but not good for a high availability server. Should be where BWH sysadmins can monitor it. Shouldn't be hidden by a firewall. Need something hardened.
    • also using, Midas
    • Dan: says right long term place for it is XNAT central, but right now Slicer is programmed against the desk top API. He suggests putting everything in a desktop and then porting it to central. WJP: could put .xcat files on central, Slicer3 can read them automatically.
    • Ron: manual upload is okay for now, need reliable downloads
    • Steve: for some tutorial and sample data put links in the GUI, ie file menu, sample data. Dan: start with XNAT Central, then.
    • Ron: Two areas: tutorial data sets, compiled test data sets. For read, completely open.
    • Use cases: Slicer 101 training page, link to data could point directly into xnat central. Nightly build: been using SVN, but the data is being packaged up for distribution right now, would like to avoid depending on another server, make it clear as to if need to install testing data (assume for now stay in source tree, but do need to test installed version - dl data in that case).
    • Clean up: take out extra data files, .h files, if not needing to build extra stuff against an installed Slicer (has been abandoned due to different compilers?). Need guidelines for the developers as to what should be installed.
      • If someone wants to write a CLI or loadable module, they have to have a built version of Slicer to do that
    • Action items: Create a Slicer tutorial data project on xnat central and upload to it, make it open. Make xnat central so can access open projects w/o having to log in at all. Can it be done within 2 days? Dan says: Monday. He'll send an email when it's set up, make a wiki page on how to upload it.
    • For the test data sets, keep using SVN, but encourage developers to make the smallest possible test data set
      • Add an upper limit for test data size, over it it should go in
      • Add documentation for the test data sets somewhere. In directory as a ReadMe.txt file?
      • Make sure fill in doxygen style comments for auto generated documentation
    • There will be a new Slicer 3.4 tutorial page, everything will be on the central xnat repository
  • Topic 2 : Curt: wrap ITK in python.
    • To be able to move Slicers python console and ITK filters en mass for experimental prototyping.
    • Historic vtkITK project, hand wrappers for indiv filters want to us, and CLI mechanism so can put in ITK filters directly.
    • If we do auto wrapping, the wrapping is there, but there's no vtkITK pipeline connection available.
    • Steve: You can go into ITK build and turn on the wrapping, Vince says builds take really long on Windows, so hesitant to turn it on by default in Slicer build.
    • in python console can instantiate an ITK filter, but getting things into and out of it is a problem. Curt envisions loading a data set into Slicer and trying out different filters to see what you want to put in a CLI. Can try using the numpy? get a numpy array of slicer image data and manipulate it w/numpy or use as a vtk array? Something else needed? Checking Luca's old emails... the Slicer way of wrapping for python is different than the native VTK way of wrapping python. Luca would like some examples from Curt, use cases. There is a way to go from Slicer mrml to numpy array to ITK. Jim could embed this into a helper.
    • Jim: want to grab a mrml node and say get the ITK representation of the data in that node (have the orientations come across, and meta data in mrml node that ITK can represent, LPS/RAS conversion).
    • no action items just yet, Curt will explore and report what is needed to make wrappers
    • Luca: need to be clear when working with VTK wrapped things versus Slicer wrapped things, can't go from one to the other, but each one individually should be able to do .
    • Will: some email on the ParaView list about wrapping, he'll send stuff to Curt and Steve.
    • building python problems on Dash18: connection problems with the scipy svn server. Mirror?
  • Dave Cole has been working with Gordon, has teem building with CMake, working on a "proper" Mac release (new feature?)
  • Jim updating a couple of builds today, errors building from getbuildtest.tcl, source tree is checked out of someplace else (teem, igt link), need to remove the directory and rebuild.
  • Steve: latest windows build installer can bring up the python console. Katie reports seg faults on Darwin (unrelated?).
    • there are python versions 2.6 and 3.0, but consensus here has been to stick with 2.5 for numpy and other packages.
  • Been going through the bug tracker and clean up things for the release of Slicer 3.4
  • Was there a recent workshop that Randy Gollub was involved in Puerto Rico? mBIRN spring last year



  • Attendees: Jim, Wendy, Tina, Ron, Nicole, Steve, Curt, Vince

Feature freeze occurred on 2/4/09 - we should be only cleaning up, fixing bugs, and writing documentation for existing Slicer modules.

Target for code freeze will be at the end of February. Please get bug fixes in during February, if possible. We will start making release candidate builds on or around March 1st.

Everyone please check the module documentation pages and make sure to fill out the documentation. Ron has added candidate names for individuals responsible for the modules. Please use the template and go along with the naming scheme. Some reorganization of the list may occur. Email will go out for everyone to finish their module in the next week or so.

Compile a list of grants that have benefitted from NA-MIC. Both active and expired grants which have benefitted should be entered. Collaborations with other groups is good. Joint publications are preferred to demonstrate effective collaboration. We are also trying to show that NA-MIC people are involved in other productive activities, as well.

Core 2 NAC and BIRN activity should be listed.

Collaboration grants should be added to be listed. We are looking to list solid grants or efforts that should be listed. Send to Tina or add to this list.

  • New Tools

New tools for registration and atlas development have been recently released. UCLA NCBC effort or related grant may have assisted with this (James Gee). Jim Miller evaluating to decide if these could make useful Slicer plug-ins. They are currently command line tools which could be adapted for use with Slicer. Is this a benefit to show that this NCBC's tool products are compatible with Slicer.

  • Python building in Windows

Steve is experiencing some Python build problems under Windows related to GenerateCLP. Jim and Steve discussed how to resolve.

iPython is now available for use with Slicer. There is a small installation script to run after Slicer is built. WrapITK is the newest way to wrap ITK in Python. vtkITK is the older way. All of ITK can be wrapped automatically, but this option is turned off by default, since it slows down the build.


Attendees: Jim, Steve, Tina, Dan, Nicole


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

  • collaboration grants - doesn't look like anything is going in feb


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


  • LGPL QT - should we consider this going forward?
  • Slicer code freeze on Feb 4th. Slicer3 Events for requirements for modules to be included.