- 1 2009-12-31
- 2 2009-12-24
- 3 2009-12-17
- 4 2009-12-10
- 5 2009-12-03
- 6 2009-11-19
- 7 2009-11-12
- 8 2009-11-05
- 9 2009-10-29
- 10 2009-10-22
- 11 2009-10-15
- 12 2009-10-08
- 13 2009-10-01
- 14 2009-09-24
- 15 2009-09-17
- 16 2009-09-10
- 17 2009-09-03
- 18 2009-08-27
- 19 2009-08-20
- 20 2009-08-13
- 21 2009-08-06
- 22 2009-07-30
- 23 2009-07-23
- 24 2009-07-16
- 25 2009-07-09
- 26 2009-07-02
- 27 2009-06-18
- 28 2009-06-11
- 29 2009-06-04
- 30 2009-05-28
- 31 2009-05-21
- 32 2009-05-14
- 33 2009-05-07
- 34 2009-04-30
- 35 2009-04-23
- 36 2009-04-16
- 37 2009-04-09
- 38 2009-04-02
- 39 03-26-2009
- 40 03-19-2009
- 41 03-12-2009
- 42 03-05-2009
- 43 02-26-2009
- 44 02-19-2009
- 45 02-12-2009
- 46 02-05-2009
- 47 01-29-2009
- 48 01-22-2009
- 49 01-15-2009
No call. Happy New Year.
No call. Merry Christmas.
Attendees: Jim, Steve, Stephen, Nicole, Tina, Katie, Vince, Casey, Dominik, Dan, Marco, Jeff
- Discussion of Wizard and Annotation breakout sessions at project week
- ITK V4 - Stephen reports NLM has made new RFQ available. Still more details to come. Due January 20th.
- dicom options in java and c++
- neuroimaging python talk by Satra Ghosh at 2pm eastern on Friday 12/18. Contact Andriy Fedorov for webex contact info.
- project week prep
Attendees: Luis, nicole, katie, john melonakos, vince, tina, steve, jim, dominik, luke bloy, dan marcus, marco
- (early in the tcon - Luis has to go teach) Luis Ibanez: Promoting testing at during project week (5 min)
- Hiro Yoshida Collaboration: planning next few milestones, and Project week work (15-20 min)
- Luke Bloy: ensuring license compatibility for his slicer contributions(15-20 min)
- Luis: promoting testing for the gridwizard software, make the software usable for the NA-MIC community. Luis will set up the WIKI page for the tutorial polishing session (Tuesday 10.30am)
- Marco: gridwizard has been extensively tested on the BIRN cluster at UC San Diego, and it is already usable by the NA-MIC community - and in fact used, with already thousands of compute hours successfully completed on the SPL cluster. Anybody in the world is welcome to take advantage of it as well, since it is open source. If anybody has any issues with it, please don't hesiatate to contact me at "mruiz at ncmir.ucsd.edu" and I will promptly aid you with your particular needs. I built the system to be as robust, powerful and easy to use as possible. The project site has a great wealth of detailed information (step by step tutorials, extensive documentation, configuration and usage samples, publications, videos, etc) that should get you productive in your local machine within 15 minutes; and in a cluster environment within 30 minutes. I highly recommend (to anybody interested in using it) to start by viewing its 5 minutes introductory tutorial to get a feeling of the system. Finally, for those interested, the software development process (that I'm using to build gridwizard), has been detailed (a little outdated) in the following book's chapter (section 4): http://www.springerlink.com/content/j3l733vn48jp1911/
- Luke: looking for a non-copyrighted methods legendre polynomial method, patented in numerical recipes is the code, not the method. ITK contains a method. Also needed is numerically robust code for binomial coefficients w/o factorials; and finally looking for a method to determine equidistant points on sphere (suggested solutions: precomputed set of points or icosahedron subsampling)
- Ron: call/reminder for AHM breakout-session hosts to create their home/WIKI pages
- Steve, Jim, Stephen: AHM Tuesday morning session content: shorten the NAMIC kit update and lengthen the QT tutorial , 40 min QT general, 20 min QT slicer. Sync with afternoon session: plan to attend the morning session as primer and then return in afternoon with questions. Make afternoon session a panel discussion to incorporate ad hoc content? Paradigm for developers to port KW to QT by modifying sample QT code.
- Luis: promoting testing for the gridwizard software, make the software usable for the NA-MIC community. Luis will set up the WIKI page for the tutorial polishing session (Tuesday 10.30am)
- Working on scheduling breakout sessions: Qt breakout session will include a talk to bring all up to speed, and session on Tuesday afternoon (after tutorial) to handle remaining questions.
- Registration Module Redesign -- breakout session by Casey and Dominick: Overview, Description of work, and Collection of Use cases. scheduling it Tuesday at 1PM.
- Adding several informatics projects that include Dan, Wendy, Ron, Tim Olsen
- Nicole: 3D Widgets project and update to Colors Module project
- Katie Hayes: will participate in IGT projects
- Randy: will participate in Catalyst XNAT/Slicer integration (may bring new people as well);
- Randy, Stuart Wallace, Sonia: Tutorial "finishing/polishing" breakout session -- Tuesday, prior to Contest on Wednesday.
- Dan M: Tutorial for using XNAT, or testing the installation/performance of an instance.
- Kilian: 3D Widgets project, EMSegmenter project, Publishing Whole-body CT, Whole-body MR open access dataset in XNAT
- Adding various Slicer internals projects (Dave Partyka: CMake Build process; Dan M: XND packaging for Slicer)
- HARDI processing and tractography in DTI (Yundi Wendy Shi, Deepika Mali)
- DBP: Gabor? nothing yet -- Katie will follow up
- DBP: MIND? nothing yet.
Attendees: Tina, Jim Miller, Wendy, Dominick, Nicole, Katie Hayes, Casey, Ron, Dan Marcus, Randy Gollub, Stephen A.,Yundi Shi, Deepika Mali, Sebastien
- NCIGT Projects: Petter, Lauren, Junichi, Scott, Ben.
- HARDI Project: Luke Bloy
Attendees: Jim, Tina, Luke, Petter, Nicole, Junichi, Hans, Casey, Steve, Dominik, Hiro Yoshida, Vince, Dan, Andrej, Scott, Katie, Marco, Seb, Nathan
Highlights for project week work:
- Hans: will be working on namic dti tools (unc, dti prep tools for oblique tools). Team: Xiadong, Zhezing Liu, Vince, Martin, Steve,
- Petter: need data dependent mesh generation tools for brain tissue deformation modeling. Team: Vince, Dominik, Matt Jolley?, Chris Johnson - utah
- Junichi - ProstateNav module. Team: Andras Glasso, Queens.
- Luke: HARDI. have MRML nodes based on DTI nodes. Would like to add model (ODF, FOD modules) estimation. Who else is doing ODF modeling - lot of different harmonic basis sets - would be useful to have a community discussion on this. Team: Alex Y., Martin Styner?, xiaodong
- Scott Hoge: incorporate recon technology with EPI acquisition techniques by Dennis Parker HIFU for breast cancer project. Team: Dennis Parker, Nick Todd?
- Nathan Hageman: fluid mechanics module for tractography. brainlab. Team: Ron.
- Andrej: also have brainlab. want EP mapping functionality in Slicer, and then integrate with Brainlab.
Attendees: Wendy, Casey, Jim, Tina, Katie C-F, Steve, Alex Z., Dan, Vince, Sonia, John M., Xiaodong, Tom, Clement, Martin, Marco, Randy, Nicole, Dominik, Janet
- Janet Lainhart (recent collab R01 - autism) and Tom Fletcher to join this call from Utah. Clement and Martin from UNC DBP on autism.
- Tom: Abnormal connectivity in autism, structural and dti. Approx 200 subjects autism and control. Analysis pipeline needed for distortion correction, registration, analysis (morphometry, tractography, cortical thickness). Language areas are of interest. Ages range 3-30 years old (mostly 8-18). Longitudinal 1.5-3 year scan timing. Several analysis options are under consideration. New tools will be added to NA-MIC as they are developed.
- Martin: new analysis is on fiber tracking (based on Guido's atlas based method). No current plans for structural analysis jointly with dti.
- Clement: Cortical analysis pipeline in preparation.
- General discussion of dti related projects and how they interrelate with the new project.
- Janet - data can be available inside NA-MIC. Longer term will go to NDAR (National Database for Autism Research). Currently acess requires IRB.
- Discussion of data management - CTSC, XNAT, etc.
- DTI discussion: Martin, Randy, Guido possibly
Jim, Tina, Steve, Casey, Stephen, Alex Z, Nicole, Katie, Michele A, Dan M, Vince, Seb, Dominik, Ron, Marco, Michael Bowers (JHU)
- Workflow Engine Discussion (led by Alex Z)
- http://www.youtube.com/watch?v=yXdRks5Wu5Q - GWE example for Slicing 3D Volumes
- Steve Pieper: Per our conversation, here are some links about the python efforts.
- The ipython cluster tools are documented here:
- Satra's nipype project is described here:
- Batchmake discussion (Stephen)
- No firm decisions came out of the discussions, but there's general excitement about the functionality available in ipython.
- python seems to be developing into a defacto standard (gaining popularity compare to other languages as indicated by this google trends comparison)
- the numpy environment has proven valuable in developing slicer modules
- if good functionality exists external to NA-MIC we should look to adopt it rather than develop competing technologies
- JHU Miller collaboration grant
- stat methods at JHU to correlate shape to disease
- scene graph diagram in progress at kitware
Attendees: Jim, Casey, Stephen, Ginger, Xiaodong, Nicole, Andre, Dominic, Alex, Ron Agenda:
- FYI Janet Lainart (recent collab R01) to join on Nov 12
- Today's tcon is about Funded External Collaborations
- Stanford: MSK segmentation of MR. Apply atlas to new patient. Atlas is the form of the mesh. Could Georgia Tech new fast marching method help with the segmentation? Segmentation focus not a registration focus.Perhaps look at a registering bone by bone. Casey, Dominic, Yi may be references.
- Dominic: wants to talk to all researchers doing registration as part of their project to gather data and use cases
- Hopkins skull stipping: first loose implementation before project week. Goal to get tighter integration during the project week. Original implementation in java. First integration will be a CLI that runs the Java code.
- Ginger Li working with Andre. Segment deep brain structures. Using BrainsFit to construct atlas. Also looking at congealing. Registration and EM segmentation needs. Need better tools for manual segmentation (spline contour editing).
- Alex: Slicer + XNAT + GridWizard + Worflow engine. Workflow is based on Pipeline++. Combination of automated and interactive steps. Web services.
Participants: Tina, Vince, Alex, Stephen, Ron, Dominick, Cal, Casey, Nicole, Curt, Steve, Katie, Mike, Andres
- Project Week Discussion:
- Integration of XNAT and Slicer - Alex, Dan, Marco, Curt, Stephen
- Meshing module MRML integration - Curt, Vince, Nicole
- Radiation Treatment Planning - Cal, Randy, Jim, Visch,
- Computational neuroanatomy to develop a neuroanatomical model for neuroscience teaching
- Separation of registration point based methods - Nobe
- Slicer3 Shown to run on Windows 7 by Steve
- Technology by the maker community - embedded computers and prototype systems for OR. Interest at either of the Winter or summer AHM for a tutorial.
Steve, Vince, Tina, Kishore, Jim, Nicole, Casey, Dominik, Julien(2), Andriy, Yi, Andrvej, Min, Sylvain, Vandena, Dan, Xioadong, Peter, Andras, Ron, John Hazle, Ivan, Wendy
- Project Week Planning
- Tina reviews history and goals - this is NA-MIC, NAC and NCIGT joint effort.
- Schedule will be much like previous project weeks. Upcoming phone calls will go into more detail on projects.
- Reminder that it's good to be prepared for the project week by creating the wiki pages ahead of time and uploading papers, pictures, code, etc so others on their team can be prepared.
- Casey: Kitware, NA-MIC Registration Improvements
- Dominik: BWH, NA-MIC Registration uses cases
- Julien F: Working on Qt port of Slicer3 GUI
- Kishore, Arnaud: Presenting GoFigure microscopy app (ITK/VTK/Qt based) and plugin architecture; project on validation dashboard (Julien J?); python interpreter in GoFigure (Steve, Demian)
- Andras: IGT Prostate 1) dicom rt module (Greg), 2) prostate segmentation (Yi) 3) prostate nav (Junichi, Haiying) 4) Multiple Display (Seb, Wendy)
- Min: TBD
- Nicole: JHU skull stripping project
- Sylvain B: TBD, collaborations with Utah on DWI preprocessing; EM Segmentation; others
- Andrvej: Parkinson's surgery (electrodes in small thalamic nuclei) electrophysiology and MRI fusion (Noby, Junichi).
- Vince: finalize slicer3 integration with FEMesh. Research Qt options.
- Vandana: 1) high dimension tube structure surface segmentation dwi / cardiac (TBD) 2) population study of cingulum and other fibers (Marek)
- Yi: 1) fiber clustering (Yogesh); 2) Menangioma segmentation (Andriy) extension and interactive? 3) Prostate shape based/wavelets 4) atrium segmentation with Utah med school (Vhnood)
Casey, Jim, Tina, Dominik, Curt, Wendy, Katie, Nicole,Stephen, Xiaodong, Ron, Steve
- Resource page review - Dominik to add registration data to xnat central.
- challenge workshops (martin?) and DTI validation (sonia) sessions to be added to AHM agenda
- Regular QT phone calls with start soon. Anyone intersted should let Steve know.
- EMSegment clustering of DTI fibers is now an extension in Slicer
Attendees: Xiaodong, Steve, Wendy, Nicole, Tina, Vince, Dominik, Katie
- CTK meeting update - DCMTK looks useful. QT development exchange.
Attendees: Xiaodong, Nicole, Vince, Katie
- Waiting for people to come back from MICCAI.
Attendees: Jim, Katie, Wendy, Steve, Nicole, Casey, Tina, Stephen
- Results of the QT brainstorming session this week are here: Qt Brainstorming Results
- Downloading the latest QT gets you all related documentation
- First round of planning for AHM+Project Week
- Review Agenda: http://wiki.na-mic.org/Wiki/index.php/AHM_2010
- Which talks to add for Tuesday morning? Default is Slicer update, NA-MIC Kit update.
- Breakout session ideas: qSlicer (Will), TestFest (Stuart), Registration Use Cases (Casey and Dominik), EMSegment (Kilian), ITK (Luis), Meshes? (Vince), Cell? (Alex Gouillard), IGT topic (TBD), xnat
- Project Week kickoff tcon on October 15, with first 30 minutes of 7 subsequent tcons allocated to project week. Any objections?
- Attendees: Katie, Jim, Nicole, Steve, Sebastien, Casey, Xiaodong, Andriy, Tina, Ron, Dan, Stephen, JC, Dominik
- Discussion of Slicer Widget Brainstorming meeting
- Items need to be covered during the brainstorming session
- Priority for this project is to convert Slicer to QT
- QT back end with KWWidgets? - some widgets used by Slicer may not exist natively in QT
- Find out frequency of use of each KW Widget before the meeting (Steve?)
- CMake/CPack with QT
- Registration useability effort (Casey, Dominik)
- Multiple camera support in Slicer (Seb)
- Attendees: Jim, Vince, Tina, Wendy, Nicole, Katie, Xiaodong
- Nicole bugged Jim about the test he said he would fix last week
- Attendees: Jim, Steve, Wendy, Katie, Sebastian, Nicole, Dan, and somebody on mute
- fixing slicer's dashboard 
- Leaks (FourD)
- Failing Tests (Multiply)
- Needs to regression image since the method now enforces that we do not wrap around the dynamic range of the pixel type. Jim will look into that. Maybe with a new data.
- would be nice to have a few continuous builds
- can subprojects be used to test the Slicer extensions?
- Linked and compare view bug. Steve to dig into whether the slider/entry causes anything strange when a SliceNode is told to go to a particular RAS (not from the slider/entry)
- Defer population of color swatches?
- Collapsible frame collapse issue?
- Volume rendering colormaps: Lung, Lung + 1000
- FA values greater 1.0. Expose the option for negevalshift?
- Wendy, Casey, Stephen, Katie, Nicole, Steve
- Plans for registration meeting
- Update on Nokia/Qt meeting
- Update on MAF
- Review and add to : http://www.ncbcs.org/cal.html
- Discuss Attila's discovery of conflicting compiler settings for VTK and ITK for the Sun compiler http://massmail.spl.harvard.edu/pipermail/slicer-devel/2009/003393.html
- related discussion on tryng to compile VTK on Solaris: http://www.vtk.org/pipermail/vtkusers/2009-August/102171.html
- failing dashboard for VTK 5.4 with SunOS 5.8 and cc/CC: http://www.cdash.org/CDash/viewBuildError.php?buildid=401331. Andriy will (try to) set up that platform to send nightly builds with oth gcc and cc for ITK and VTK
- Update on Steve Pieper's trip to Yale to work with Xenios. Basically all of BioImageSuite's modules are available in slicer. We tested image filtering, model-to-model registration and they worked nicely. Outstanding to do items:
- Add biomimagesuite Logo (what is the format for the --logo flag exactly?) Partial success shown here
- Transfomations output format (where is document for ITK transform files?)
- Output format for filenames (nii) – hacked in code (need to use fileFormat attribute from XML)
- Point format as opposed to –seed –seed –seed (is this supported yet?)
- Xenios to test intensity based registration … for output of resliced image
- Discuss Qt progress http://my-trac.assembla.com/protoctk/wiki/WidgetPlans
- W&M Solaris platform for Slicer dashboard testing
Attendees: Katie, Tina, Steve (Jim is off the grid this week. Good luck!),
- playing with Dropbox (http://getdropbox.com)
Attendees: Jim, Xiaodong, Wendy, Steve, Nicole, Stephen, Dan
- Nokia/Qt update
- PythonQt is working nicely for Stephen - Qt wrapped slicer command line modules are auto-exported via signals and slots, making them callable from python
- Wendy debriefing about meeting with Curt about XNAT and FetchMI
- planned an extension for FetchMI that will work with XNE
- content type tags to identify data types (like multi-file volumes)
- possible use of Resources to handle multi-file volumes
- Dan says XNAT 1.4 is just "weeks away" (conservatively by end of August).
- XND discussion
- XND is not being released at the same time as XNE 1.4 (official XND is 0.8).
- XNE 1.4 API will eventually become the unified API for both XNE and XND
- XNAT DICOMGateway http://nrg.wustl.edu/xnd/download/gw/
- Dan says it works well, for example with scanners and osirix
- only handles dicom, not other research data types and metadata
- MICCAI Best Biomedical Image Visualization Contest - enter early and often!!! $750 first prize!
- After-tcon discussion of DYLD_LIBRARY_ISSUES on mac.
> > One idea I (probably stupid) idea is to set > > DYLD_LIBRARY_PATH at runtime. Is this possible? You cannot do this as the dynamic linker reads these variables at the time the application launches, and not each time a new framework is loaded.
Attendees: Katie, Wendy, Nicole, Xiaodong, Steve, Jim, Tina
- Jim built numpy for windows
- QT retreat to be planned in August
- opencv support to be considered?
Attendees: Tina, Katie, Vince
- 2009_Summer_Project_Week - check out google map of participant sites (thanks to marianna)
Attendees: Jim, Steve, Tina, Ron, Stephen, Will Agenda:
- update from Steve's WUSTL visit
- updated list of collaboration grants
- placeholder for broader community grants - possibly for OpenMAF, IGSTK, SBIRs, etc...
- Steve's South America photos:
Attendees: Steve, Katie, Stephen, Tina, Luis, Andinet, Sebastien, Julien Finet, Will, Noby
- Report from Steve and Stephen about the recent Common Toolkit Workshop
- QT has been used extensively by others presenting in the group. Great reinforcement that QT work planning for NA-MIC is heading in the right direction.
- Maverick discussion. (See link above for slides on it).
Attendees: Curt, Katie, Jim, Dan, Xiaodong, Tina
Attendees (partial list): Randy Gollub, Steve Pieper, Nobi Hata, Snehashis Roy, Kenneth Hisley, Tina Kapur, Wendy, Nicole, Andras Lasso
- DBP tutorials/tutorial contest: Events:TutorialContestJune2009. To be reviewed by Randy. Randy can be contacted any time by email and at the NAMIC week on Wednesday if there were any questions about how to create the tutorials. The tutorials will be presented on the NAMIC week on Thursday.
- Snehashis Roy (JHU) about Skull Stripping project: algorithm is based on deformable registration and segmentation; it is a Java software that will be ported into Slicer.
- Kenneth Hisley from Iowa (invited by Noby) was introduced to the concept of project week. He plans to do radiation treatment planning / longitudinal tracking with Slicer. Many interesting connection points with other projects, such as XNAT.
- CUDA intro by Joe Stam
- Snehashis Roy (Jerry Prince student) will join next week to discuss Skull stripping project at project week
Attendees (partial list): Joe Stam, Andrewy, danielle, Diego Cantor, Greg Sharp, Jack Blevins, James Balter, Jay, Jim Miller, Keith Gunderson, Kim Powell, Leiquin, Luis (+8 from kitware), Matthew lauer, Mike Halle, M. Hasak, Michel Audette, Nicole A, Petar S, Petter, Sandy, Seb, Shalini (NVIDIA), Sharon peled, Sylvain J, Torsten, Xenios (+10 from yale)
Highlights: 50+ people attended the webex presentation on CUDA. Projects for project week will be outlined in the next week.
Attendees: wendy, nicole, katie, jim, tina, dan
- next Thursday - CUDA intro
- vtk3d widgets project meeting is being organized by Nicole
- Katie will cmake project
- Jim will contact Ran and Sam G about project pages
- dan will complete project pages
- Only slicer3.4 bug fixes should go into the 3.4 branch (no new features)
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,
- Stanford Simbios collaboration (Haikat, Saikat, need help on registration)
- 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)
- Bjorn has MRSI code that is slicer-compatible for reconstruction and registration.
- Vince had MRSI phantom data (specially prepared phantom) so he can provide data.
- (See http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_MRSI)
- Project 2d-3d registration (3:30)
- Jim Balter, Sandy Wells, and probably Greg Sharp,
- GPGPU image registration
- 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?)
- 2009_Summer_Project_Week - IGT projects
- projects for upcoming TCONS: MRSI, 2d-3d registration
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
- http://www.slicer.org/pages/Special:SlicerDownloads - 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: http://tinyurl.com/cu9bzp
- 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? http://wiki.na-mic.org/Wiki/index.php/Slicer3:FourDAnalysis
- ITK by Luis
- Data Clinic (already on agenda)
- Tutorial Contest (already on agenda)
- Slicer-Python candidate tutorials/breakouts (Demian and maybe Luca and/or Daniel?)
- 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
- FYI http://wiki.na-mic.org/Wiki/index.php/2009_Summer_Project_Week#Preparation
- FYI http://wiki.na-mic.org/Wiki/index.php/Events:Slicer_Workshop_August_2009
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) http://www.na-mic.org/Bug/view.php?id=511 A few of the questions to discuss with the engineering core:
- rpaths in GenerateCLP/GenerateLM (should we be using the GenerateCLPLauncher instead)
- version numbers on all .so files
- Dominique's patches: http://svn.debian.org/wsvn/debian-science/packages/slicer/trunk/debian/patches/50_all_changes.dpatch?op=file&rev=0&sc=0
- Problems finding the tk.tcl file (build is looking in /usr/lib/tk8.5 but on debian it is in /usr/share/tcltk/tk8.5/tk.tcl
- 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.
- Registration in Slicer 3.4 (Ron)
- Which modules to list
- What guidance to give to potential end-users
- Check out http://www.ncbcs.org/cal.html
Attendees: Ron, Tina, Will, Nicole, Vince, Bill, +1
- 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
- Check out the NA-MIC Events Calendar (WIP) on google: http://www.google.com/calendar/embed?src=r8bddigidepgvog24cpfk1bjgs%40group.calendar.google.com&ctz=America/New_York
- Time to start thinking about the 2009_Annual_Scientific_Report, deadline May 15.
- NCI update
- Slicer release
- File format for sending/receiving displacement fields. Hans suggested MATLAB.
- Release notes for command line modules. Keep module name the same as the cxx/xml filename.
- 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
- 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 xnd.slicer.org, 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 central.xnat.org, 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 central.xnat.org
- 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
- Topic #1 - Feature Freeze
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.
- Topic #2 NA-MIC-related Research
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
- Discussion of XNAT Integration Timeline
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.