NAMIC Wiki - User contributions [en]

Iowa-NA-MIC-2010-Kickoff

2010-10-19T07:06:12Z

Mruiz:

[[2010-09-Leadership-Brainstroming|Back to 2010 Brainstorming]]
=What=
Planning the 3-year course:
*Roadmap project
**What will the DBP engineer work on?
**Is the image data already in hand?

Yes. Over 2900 scan sessions collected. We will need to identify the meaningful subset of this data, get final approval from the Predict Steering Committee for that subset,and then re-deidentify it and post to XNAT for NA-MIC purposes.

*What modules for the NA-MIC Kit will result from this work?
#Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time.
#Create custom user interfaces that extend the diffusion tractography visualization modules in 3D Slicer to target reporting of longitudinal fiber tracking results to a clinical audience.
*Outreach
**Tutorial(s) on the wiki
**Presentation at a DBP conference for year 2. The PI suggested the AAN (American Academy of Neurology) meeting in April 21-28, 2012 New Orleans as a possible venue. See http://www.aan.com/go/am10/education/proposals; Proposals for 2012 meeting are due May 2011.
**Hands-on teaching event for the DBP scientific community for year 3

=Who=
*DBP: Hans Johnson, DBP engineer Mark Scully
*Algo: Martin Styner, DBP engineer Clement Vachet
*Eng: Dan Marcus, Jeff Grethe, Marco Ruiz

* Iowa Supporting Guests: Shuhua Wu, Joy Matsui, Ben Rogers

=When=
* Monday October 25th, 10:30am - 5:30pm
** 10:30-12:00 Overview of project, and background of PREDICT-HD
** 12:00- 1:00 Lunch
** 1:00- 5:30 Working meeting focused on informatics, computations and processing
** 6:30- 8:30 Dinnner @ One-Twenty-Six
* Tuesday October 26th, 8:00am - 3:30pm
** 8:00-12:00 Working meeting focused on algorithmic development
** 12:00- 1:00 Lunch
** 1:00- 3:30 Finalize timelines
** 3:30- 5:30 Discuss current limitions of XNAT, and determine how to overcome them
* Wednesday October 27th, 9:30am- 3:00pm
** GridWizard deployment

=Where=
The University of Iowa Campus, Meet in W240 Boyd Tower. The conference room is a short distance away from there in the Iowa Center for Translational Science.

Take elevator BW to the second floor, and take two immediate rights. The conference room shares a wall with the BW elevator shaft.

== Travel Information ==
The closest airport to Iowa City is the '''Cedar Rapids / Eastern Iowa Airport (CID)'''
which is about 20 minutes from the hotel.

===Airport Shuttle Services===
The easiest way to get from the airport to
Iowa City is via one of the shuttle services:
* [http://www.crshuttle.com/ Airport Shuttle Service] (Phone: 1-800-725-8460)
* [http://www.limosbyexpress.com/ Airport Express] (Phone: 319-626-5466)
Both are the same price and easiest to book before travel. The cost is roughly $60 round trip.

===Rental Cars===
Rental cars are also available from the Airport. The following companies have desks at the airport
* Avis
** [http://www.avis.com/ Website]
** Toll-Free Phone : 1-800-331-1212
** Local Phone : (319) 366-6418
* Hertz
** [http://www.hertz.com/ Website]
**Toll-Free Phone : 1-800-654-3131
**Local Phone : (319) 365-9184
* National and Alamo
** [http://www.nationalcar.com/ Website]
**Toll-Free Phone : 1-888-826-6890
**Local Phone : (319) 363-0249
*Enterprise
**[http://www.enterprise.com/car_rental/home.do Website]
**Local Phone : (319) 366-5522

If you have any questions regarding travel, feel free to contact Joe Ekdahl either via e-mail(joe-ekdahl@uiowa.edu) or phone (319-384-3026).

== Hotel Information ==
We reserved a block of hotel rooms at Hotel Vetro at a rate of $139. The group code to get this rate is ITK. These rooms will be held at this rate until October 22.
* [http://www.hotelvetro.com/ Hotel Vetro]
**Phone: 800-592-0355
**Address: 201 South Linn Street, Iowa City, Iowa 52240

Other hotels that are close to the conference site, University of Iowa, and downtown include:
*[http://www.Sheraton.com/IowaCity Sheraton hotel]
**Phone: 319-337-4058
**Address: 210 South Dubuque St, Iowa City, IA 52240
*[http://imu.uiowa.edu/iowahouse/ Iowa House Hotel]
**Phone: 319-335-3513
**Address: 125 North Madison St, Iowa City, IA 52242

== Meeting Room ==

TBD

Engineering:TCON 2010

2010-09-30T19:25:07Z

Mruiz:

Back to [[TCON:Main|TCON:Main]], [[Events]]

==2010-09-30==
Attendees: Ron, Will, Stephen, Steve, Wendy, Daniel, Casey, Nicole, JC, Dominic, Tina, Kurt, Marco

[http://www.facebook.com/album.php?aid=91423&id=1185661914&l=94b6b77893 photos of Barcelona]

NA-MIC renewal
* Barcelona - brief description of CTK DICOM/Slicer integration
*[[2010-09-Leadership-Brainstorming#Computer_Science|Short term activities]]
*[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues Slicer 3.6 debugging]
* migration of Slicer and Na-mic websites
** Currently on Solaris machine, moving to Linux machine
** Ron will be sending email when this happens
* 2010-Slicer-Factory [[2010-Slicer-Factory| factory.slicer.org]]
** [http://www.na-mic.org/Wiki/index.php/2010-09-Leadership-Brainstorming#Service Service Short Term Service Activity]
* Need to fix the slicer dashboards:
** split slicer4 to dedicated dashboard with superbuild and Qt
** fix remaining failing tests (EMSegmenter, SparseFieldLevelSet, other sporadic failures...)
** fix test machines with no X server (thurmite)

==2010-09-23==
Attendees: Steve, Wendy, Tina, Jim

*DBP meeting (Monday ~11am at AHM) will be sent out by Katie M. this week
* Slicer and OpenIGTLink featured in NDI booth at MICCAI 2010 ([http://www.slicer.org/slicerWiki/index.php/Slicer3:VisualBlog See slicer visual blog])

==2010-09-16==
Attendees: Jim, Tina, Wendy, Nicole, Dan, Dominik

*http://wiki.na-mic.org/Wiki/index.php/PeopleCycle2Staging

==2010-09-09==
Attendees: Jim, Stephen, Steve, Daniel, Nicole, Tina, Katie
*discussion about 3.6 versus 3.7 versus 4.0
**move to GIT will be deferred.
**discussion about svn for slicer 4
<pre>
Host TTL Numeric IP
www 7200 134.174.9.180
@ (None) 7200 134.174.9.180
* (All Others) 7200 134.174.9.180
ext.slicer.org 7200 75.101.141.190
i2b2.slicer.org 7200 184.73.243.106
mi2b2.slicer.org 7200 174.129.38.17
svn.slicer.org 7200 66.194.253.27
viewvc.slicer.org 7200 66.194.253.27
xnd.slicer.org 7200 75.101.141.190
</pre>
*Slicer 3.6 bug fixes. See: http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues
*[[QtAugust2010#Draft_Timeline_.26_To-Do_list|Slicer 4 roadmap]]

Plan for Slicer4 nightly builds:
* Funding will hopefully resume next week
* Zack will create a new Slicer4 svn repository
* The Slicer3 trunk will become Slicer 3.7
* Nightly binaries will be built from the Slicer3 trunk
* Nightly builds will eventually switch over to Slicer4
* A dashboard for both Slicer3 and Slicer4 builds will be set up

* [[2010-Slicer-Factory|factory.slicer.org]]

==2010-09-02==

Attendees: Jim, Steve, Nicole, Wendy, Tina, Vince, Ron, Jay

* Discuss additional slicer layout options (Wendy, Jim, Steve, Ron)
<gallery>
file:Conventional-rotated-layout-2010.png|Layouts that use widescreen displays better (request from Ron)
file:Layout-Endoscopy-2010.jpg|three-3D-viewer display (request from Jay for kidney navigation IGT)
</gallery>

==2010-08-26==

==2010-08-19==
* Discussion of slicer 3.6.1/2
http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues

==2010-08-13==
*No NA-MIC tcon this week (Event in progress: '''August 12-13:''' [[QtAugust2010| Review of Qt port]])

==2010-08-05==
Attendees: Xiaodong, Tina, Steve, Wendy, Nicole, Vince

Agenda:
*3.6.1 release update:
**http://wiki.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues
*Next week:
** '''August 11:''' [[2010-Slicer-UNCDuke|Slicer training event at UNC and Duke]]
** '''August 12-13:''' [[QtAugust2010| Review of Qt port]]

==2010-07-29==
Attendees: Steve, Jim, Nicole, Tina, Xiaodong, Wendy,

Agenda:
* discuss how to correctly remove display nodes if they become not needed after CLI invocation (this is just a hint for Nicole, we talked about this today, I will try to join around 3:45 --[[User:Fedorov|Fedorov]] 17:48, 29 July 2010 (UTC))
** usability level: what if there was something set on the output volume already? (Field of View)
** copy the input reference display node values inot the current output display node rather than creating a new one (if type is same)
** display node management is done when load volume back in
**if create new volume node (from a node selector), it doesn't create default display node automatically
**in command line module logic, store the information about what do you want to hook up (input volume display node id), and then in vtkSlicerApplication logic, when read things in set them up (around line 1570).
**if a display node should only be used by one thing (current implementation), in this rare case where change the type of the display node, remove the old display node node
**add method vtkMRMLScene to check if any displayable node references a given display node? Not necessary yet...
**every node has to be able to report everything it references (on vtkMRMLNode, see also UpdateReferenceID there)
**update the read data request with the reference display node and then put logic in the Slier application logic to deal with it, extend ReadDataRequest in vtkSlicerApplicationLogic.cxx

==2010-07-22==
Attendees: Xiaodong, Steve, Ron, Tina, Vince, Wendy, Katie

Agenda:
*http://wiki.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues

==2010-07-15==
Attendees: Jim, Xiaodong, Steve, Tina, Dominik, Vince, Wendy, Katie

*slicer 4 planning continues. next mtg+training session scheduled for aug 12-13 in chapel hill. details to appear on wiki soon.

==2010-07-08==
Attendees: Jim, Stephen, Nicole, Tina, Junichi, Xiaodong, Vince, Harini, Wendy

Agenda:
* Generalized plotting infrastructure in Slicer?
** Have DCE plotting infrastructure
** Also have [http://wiki.na-mic.org/Wiki/index.php/CTK_Transfer_function_widget CTK transfer function widget plotting]
** Need generalized base class for plots, upon which other specialized plotting can be based?
** 3D Slicer 4D Analysis Module has [http://www.slicer.org/slicerWiki/index.php/Slicer3:2DPlotting 2D plotting]
** Nicole's wish list, based on use of scatter plots in population studies (one brain surface geometry file will have multiple scalars defined at each vertex) (see pages 70 and up [http://www.na-mic.org/Wiki/images/4/4e/SlicerTraining6_vtkFreeSurferReaders.ppt here] where BLT was used):
*** highlight on mouse over a plotted point
*** toggle plotted point, or data set, visibility
*** legends: change text, colour, font, position for data set name, axis labels, chart title
*** print/save image to disk, export as table, postscript, pdf
*** set x/y axis variables (for example: input file has 10 values, allow selecting two to plot, and allow changing this at run time)
*** support plotting from multiple data sources
*** set plot symbol/colour/style to plot each data source
*** programmatic add/remove points from plot
*** on hover over a plotted point, pop up extra information about it (be able to associate extra info with a plotted point, for example if have a file that has an index, id, gender, age, val2, val1, when plot age versus val1, pop up id when hover over the point)
*** calculate average line through scatter plot
*** allow user to see values for all points

==2010-07-01==
Attendees: Xiadong, Nicole, Tina, Dominik

Agenda:
*[[2010_Summer_Project_Week|Project Week Summary]]
**(Katie is creating a Picasa album where we will use as a hopefully-persistent repository of photos)
*In Progress: [[2010-Slicer-StLouis|Slicer training event in St. Louis]]

==2010-06-23==

*[[2010_Summer_Project_Week|At Project Week]]

==2010-06-17==

Attendees: Katie, Jason White, Jim Barabas, Tamas, Xiaodong,Tina, Nicole, Steve, Vince, Luis, Sudhir Pathak (U Pittsburgh), Ron, Karl, Jim Miller, Marco, Hiro Yoshida

Agenda:
*Project Week Items
**Jason White project - transcranial ultrasound: [[2010_Summer_Project_Week_Intraoperative_Brain_Shift_Monitoring_Using_Shear_Mode_Transcranial_Ultrasound]]
**Sudhir project [[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data]]
**Karl Fracture [[2010_Summer_Project_Week_FractureClassification_Brainstorming]]

*'Record Set Explorer' version 0.6.2.alpha released
**Project site: http://www.gridwizardenterprise.org/rse/
**YouTube feature update video: http://www.youtube.com/watch?v=LWXannpfr6Y&hd=1

==2010-06-10==

Attendees: Jim, Tina, Dan, Tamas, Nicole, Wendy, Vince, Dominik, Jim Barabas, Katie, Luis, Hans

Agenda:
*project week review
*jim b's project
*Slicer 3.6 release
*http://www.slicer.org/
*Tutorial contest entries are due to Sonia Pujol on Monday

==2010-06-03==

Attendee: Jim, Tina, Wendy, Vince, Xioadong, Steve, Dan Marcus, Katie, Dominik, Sean Megason, Arnaud Gelas, Isaiah, Michel

Agenda:

*Project Week:
** In two weeks!
**75 registered attendees: [[2010_Summer_Project_Week#Attendee_List]]
**Review Projects/teams. Please note that deadline for completing project pages is BEFORE next week's TCON.
*Slicer Release http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:3.6_Final_Issues

Notes (discussing projects):
*community effort to make NA-MIC tools accessible to '''microscopy IA''' (Sean)
**[[Microscopy_Image_Analysis| Microscopy breakout session]]: standards, community needs.
**[[2010_Summer_Project_Week#Microscopy_Image_Analysis|Projects: detailed engineering efforts]]
**finding BWH investigators interested in microscopy: Liu, Yanling, SAIC-Frederick ; Lisle, Curtis, KnowledgeVis,
*[[Paraview_Support_for_Computational_Anatomy|Paraview]]: link via MRML or scene description file format w/o VTK dependencies. Which MRML node types should be supported.
*BrainLab-Aurora HybridNav (Isaiah Norton, A.Golby Lab): optical tracking system -> trying hybrid with AURORA, have both optical and EM tracking. Tool position history to track/document resection progress. -> add Dan Marcus (STEALTH -> openIGT) to project.
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise registration]]: (Ryan Eckbo); porting Matlab/C code into ITK -> Jim, Luiz
*removed ''Python'' & ''Execution models'' as project categories, fused into ''NA-MIC Kit Internals''
*Computer Aided Photodynamic Therapy: contacts?
*Slicer 3.6 release: last fixes: Editor, BRAINS, mutiple volume loading, DICOM series & XNAT, color LUT for generic use. New release scheduled June 10. If you know of critical issues please submit to http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:3.6_Final_Issues

==2010-05-27==
Atendees: Dan Marcus, Misha Milchenko, Tina, Nicole, Jim, Steve, Lorent, Greg, Wendy, Andre, Xiaodong, Leslie Holton, Tamas, Ron, Dominik

Agenda:
*OpenIGTLink discussion led by Junichi Tokuda. Agenda can be found in [[2010_Summer_Project_Week_Breakout_Session:OpenIGTLink| the OpenIGTLink breakout session page.]]
**Use case documentation/discussion can be found here: http://wiki.slicer.org/slicerWiki/index.php/Slicer3:BrainlabModule
*Problems with [http://en.wikipedia.org/wiki/Eclipse_(software) Eclipse] development

==2010-05-20==
Attendees: Jim, Tina, David Fuentes (MD Anderson), Dieter Hahn (Erlangen), Katie, Dominik, Xiaodong, Stephen, Andrej, Harini,Andrew Elliott (MD Anderson), Alex Z, Luis, Curt, Tamas (Queens), Nicole

Agenda:
*Discussion on adding Extensions to Slicer (led by Jim Miller). http://wiki.na-mic.org/Wiki/index.php/File:AHM2010-Plug-ins.ppt
** WebEx if needed https://emeetings.webex.com/emeetings/j.php?ED=135216267&UID=482060457&PW=NOGMwODUyMjM4

==2010-05-13==

Attendees: Sonia, Wendy, Ron, Tina, Katie, Haiying, Xiaodong, Nicole, Dominik, Vince, Marek, Andras, Tamas, Andrew Rauch, Ryan Eckbo (PNL), Mark Scully, Curt, Clement, Stephen, Harini, Isaiah, Luis Ibanez, Stuart

Agenda:
*Today's topic: Tutorial contest rules+discussion (http://www.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest)
*QA discussion
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer-3.6-QA QA Wiki]
**[http://www.na-mic.org/Wiki/index.php/Journal_of_Slicer_Tests Journal of Slicer Tests]
*Next two weeks:
**May 20th -- How to interface external software with Slicer (Jim)
**May 27th --OpenIGTLink discussion (Junichi)

==2010-05-06==
Attendees: Jim, Steve, Curt, Tina, Xiaodong, Nicole, Vince, Harini, Dominik, Ron

Agenda:
*http://wiki.na-mic.org/Wiki/index.php/2010_Summer_Project_Week
**registration via credit card available, make sure to book hotel before June 1
**updated project page Wiki template [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template], includes "Delivery Mechanism" section
**Tuesday: Slicer Handson workshop from 10-12
**Wednesday: QA training session
**new [[2010_Summer_Project_Week#Projects|Projects]]
***registration:promote unsolved registration problems as project: e.g. Stanford group & knee MRI
***connect Python tools with execution model (NiPYPE)
***Slicer 4
*** femur fracture classification (Karl from Prof. Schubert's group), project placeholder added (Analysis)
***category for meshing efforts
*prospective first-time AHM attendees are welcome to attend the TCon, feel free to invite
*NA-MIC renewal: Supplemental Information needed: latest software releases
**Slicer 3.6
**ITK 3.18 (fixing DICOM parsing)
**VTK 5.6 (integration of GPU ray casting)
**XNAT 1.4 (webservices API)

==2010-04-27==

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

Agenda:

*Please note that there will be two project-week specific tcons:
**May 13th - Sonia will lead the tutorial contest rules+discussion (http://www.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest)
**May 27th -- Junichi will lead OpenIGTLink discussion
*Discussion of help text of command line modules. [[image:Help-characters.png|thumb|100px|right|discussion topic]]
*Review of slicer3.6 release plans and bug tracker.

==2010-04-22==

Attendees: Wendy, Nicole, Steve, Sonia, Ron, Dan, Dominik, Adam, J2, Jean-Christophe.

Agenda:

*QT tutorials/discussion with Adam Weinrich, Nokia.
** Review of Slicer tutorial structure (Sonia)
** Adam works on strategic accounts (advanced development for new applications) and on university outreach to encourage creation of new developers
** Kitware is a key account for Nokia
** Review of current state of Qt with Slicer (Steve, Jc, Julien)
** Best to stick with first hands on session on Monday afternoon (Adam).
** Topics to cover:
*** Adam: Motivation (examples of other applications), Designer, available widgets, signals&slots, coding style, implicit representation
*** J2/Jc: how to make a simple module, working with the rest of the slicer application (Tuesday afternoon).
** Qt Q&A lunch on Tuesday. Adam will check with Boston-based Qt developer group about attending.
** TODO: get a lecture hall for Monday afternoon? Tina will check with Donna.
*Note: May 27th is the OpenIGTLink discussion, led by Junichi Tokuda.

==2010-04-15==
Attendees: Xiadong, Harini, Tina, Steve, Dan Marcus, Vince, Ron, Dominik, Luis, Dave P, Katie, Alex Z, Marco

Agenda:
*Project Week Kickoff Call for Engineering
**[[2010_Summer_Project_Week]]
**Start listing Engineering Projects
**Project Page Template: Add Delivery Mechanism (Extension-cmdline or loadable, Built-in)
**Ideas for handling Project Week Planning/calls

==2010-04-08==

Attendees: Jim, Dan, Nicole, Tina, Wendy, Ron, Stephen Aylward

Agenda:
*Slicer Training Course in Iowa city tomorrow.
*Added breakout sessions/talks for the project week

==2010-04-01==
Attendees: Curt, Nicole, Katie, Wendy, Tina, Dominik, Vince, Steve, Dan Marcus, Luis
*Slicer 3.6 Feature freeze
*Project Week breakout session: QT, ITK, git,...

==2010-03-25==
Attendees: wendy, nicole, dominik, vince, tina, jim, dave, luis, katie, steve, ron, xiaodong, stephen, jj, jc, j2
* MIDAS Feedback from John M./Tina
*[http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6Release Slicer 3.6]
**Documentation
**testing and code coverage
**VTK status
*[http://www.slicer.org/slicerWiki/index.php/Slicer4 Slicer 4.0]
**Community process (Stephen Aylward)
*** Superbuild status (Dave)
*** qt status (Julien)
*** Module acceptance process
**** From Nitrc
**** With Slicer
**Educating the community about the benefits of Qt (Steve Pieper)

''' Notes '''

* Slicer Extensions
** Reuse Statistics functionalities from MIDAS to report on downloads from
** http://ext.slicer.org/ext/trunk/
** Building Slicer extensions and submit them to the Slicer Dashboard
** Where are they located ? (it is described in the .s3ext files:)
*** http://ext.slicer.org/ext/trunk/12465-linux-x86_64/VmtkSlicerModule.s3ext
** Maybe build them only when their source code is actually modified ?
** Label extensions by a level of compliance with NAMIC practices ?
*** E.g. Gold, Silver, Bronze,... Coal.
**** '''Gold''': have > 80% coverage, 0 Valgrind errors, documentation and tutorial
**** '''Silver''': have > 70% coverage, < 10 Valgrind errors, and tutorial
**** '''Bronze''': have > 60% coverage, < 50 Valgrind errors, and tutorial
**** '''Coal''': have < 10% coverage, > 1000 Valgrind errors, no documentation, no tutorial
** Web of trust
*** Have gatekeepers who review the extension and label them accordingly.
*** Define a Testing procedure for Slicer 4.0. (Check lists)
** Community Support
*** Provide User Ratings (based on the Insight Journal / MIDAS functionality)
*** Use current MIDAS C++ API to Upload/Download data.
*** Create MIDAS Plugins to manage data / code for Slicer extensions
* Slicer Release 3.6
** VTK Release 5.6 : March 26th 2010
** Immediately after, switching Slicer to use VTK 5.6.
** Sorting out KWWidget issues on Windows 7 with VTK 5.6 (VTK CVS HEAD).
* Slicer Release 4.0
** Git: Conversion of CMake, VTK, Paraview
** Moving Slicer to Git ?
** ITK 4.0 will move to a clean Git repository (full reset of the history)
** Moving only Slicer modules that satisfy the '''Gold''' criteria.
** A2D2 Idea : port CLI modules to ITK 4.0
** Question about CLI modules in CTK for Slicer 4.0: Discovery process; making it cleaner by using Qt methods. But raise the concern of forcing a dependency on Qt (that not everybody may want).
*** Have specific mechanisms of discovery based on : Python, Qt, C++.
** MRML Refactoring ?
*** Jim suggests to add a dictionary-like organization to be able to query MRML nodes {by type,...}.
* Slicer Superbuild
** Dave reported on progress
*** Dealing with patches that getbuildtest.tcl applies to the third party libraries.
**** Difficulty of applying patches. Need for a multi-platform way of applying patches
**** Hosting git repositories with the patched versions of the third party libraries.
**** Use github ? create a "Slicer" user-account ?
**** CMake-ifying Python source tree ?
* Testing Modules and Extensions
** Hosting them in MIDAS
** Setting up Dashboard configuration to test modules as Slicer sub-projects
** Some CDash/CTest work is needed.
** Currently, sub-projects must be run from a common CTest script (the same of the host project).
** Needs to manage dependencies between extensions. (this can be done today with an XML file on CDash).
* Testing Submission Grouping
** Grouping {configure/build/test} submissions by Library and / or subdirectory
** Using CMake for generating labels that can be used later for grouping

==2010-03-18==
Attendees: Andriy (ran out of the room before he could take notes)
Nicole, Dominik Wendy, Steve, Stephen, Jim, Katie
* Andriy question about plots coming back from command line modules.
* Updated [[Downloads|Download page]]
** Images have been added.
** Lesion data still missing.
* Tracking downloads of extensions
** Use publication database? We can ask Julien next week.
** (See http://ext.slicer.org/ext/ for current layout - look in the trunk directory).
** Jim could use this functionality for renewal proposal
* DICOM Discussion
** http://www.slicer.org/slicerWiki/index.php/DICOM:Database
** Drag and Drop image files?
** DICOM sorter (osirix is useful for this)
* Slicer3.6 release planning
** Next release of ITK (3.18) should be in a couple of weeks
** http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6Release

==2010-03-11==
Attendees: Dan, Tina, Vince, Xiaodong, Wendy, Nicole, Katie, Kurt, Dominic, John

* Updated [[Downloads|Download page]]
** Do we want to add images?
***Yes, please. And also to format this into a table. Thanks.

* XNAT Workshop (June 28-30)
** Include a NAMIC presentation? TBD
** http://nrg.wikispaces.com/2010+XNAT+Workshop

* OpenIGT and Medtronic Navigation
** Consider a joint grant to fund the development

* Ron can kill 18 birds with one stone.

==2010-03-04==
Attendees: jim, ron, nicole, vince, dan, katie, wendy, dominic, tina

* GetNodesByName leaking the collection from Tcl ( set foo [$::slicer3::MRMLScene GetNodesByName bar] )
* VTK GPU Mapper - Mac driver issue. But otherwise is working well with compositing. Dual 3D issue tabled for now.
* Store the Collapse of the SliceController in the Layout node?
* Should the layout of the modules (left verses right) be stored in the scene? Not for now.
* DICOM databases. See discussion on mailing list.
** DICOM Schemas. Jim tried searching for Osirix's schema. What about the XNAT schema? What about ClearCanvas?
** Extend Schemas for MRML, Project views, NRRD, VTK files, etc.

==2010-02-25==

Attendees: john, marco, dominik jim, steve, wendy, tina, nicole, ron, vince, dan, katie

* MIDAS handles - fixed
* GWE's RSE ("Record Set Explorer") version 0.6.1.alpha released:
** [http://www.gridwizardenterprise.org/rse/ Project site]
** [http://www.youtube.com/watch?v=ebWqTHf5i5Y&hd=1 YouTube demo video]
*Slicer Release 3.6 Feature Freeze on April 1
*Japanese Slicer workshop in 2 weeks
*CTK workshop last week - went well

==2010-02-18==

Attendees: Jim, Steve, Wendy, Dan, Dominik, Katie, Nicole

* Discussion of whole body CT/MR data (Dan)
* Discussion of the [http://www.slicer.org/pages/Slicer_Community "Spit Kidney"]
* Dominik's registration case library data for download
* Discussion of download data for each module (like in ChangeTracker currently)
* Tutorials and Datasets
* Discussion of slicer 3.6 release schedule.

==2010-02-11==

Attendees: Jim, Katie, Curt, Casey, Tina, Xiaodong, Steve, Wendy, Dan, John, Dominik, Nicole

Agenda:
* NA-MIC data migration is complete and the Downloads page has been brought out to the Wiki sidebar (http://www.na-mic.org/Wiki/index.php/Downloads)
** Feedback is requested on the sidebar
** Feedback is requested on the Downloads page
** Feature request to track the downloads like it is done on the publication database. (Julien reports it is already available to administrators).
** Curt will work with John to add Meshing Module tutorial.
** Dominik will try putting some data in midas to see how much context can be added.
** John will check with Marek about Harvard data that had been on BIRN.
* Review of DBP2 webpages, which need updating
** Ron has contacted the parties directly
* Dan: XNAT workshop this summer (possibly June 28, 29, 30 in St. Louis)?
* Discussion of entry behavior on
* New Volume features from Xiaodong for viewing image sets in a directory (cool!)

==2010-02-04==

Attendees: Xiaodong, Tina, Casey, John, Dan, Vince, Stephen, Nicole

Agenda:
*http://www.na-mic.org/Wiki/index.php/Downloads
* [http://insight-journal.org/midas/community/view/21?path_navigation=19-15 Head MRI, MRA, DTI from 100 healthy volunteers]

DBP Tutorials should be listed at the top.
Software should point to Slicer and the NA-MIC Kit.
Data hosting is available on XNAT and Midas.

==2010-01-28==
Attendees: Xiaodong, Tina, John M, Katie, Nicole, Dominik, Vince, Casey

Agenda
* data update (john m): Discussion of Data & Tutorials on the following page. Discussion of where to put the data (XNAT or Midas).
**example downloadable resources page: http://www.ncigt.org/pages/Downloads

*Iowa Data
**Visible Human Datasets https://mri.radiology.uiowa.edu//visible_human_datasets.html

*Project Sikuli from CSAIL
**Scripted UI interaction -- GUI testing http://groups.csail.mit.edu/uid/sikuli/

==2010-01-21==
Attendees: Jim, Katie, Nicole, Wendy, Curt, Ron, Dominic, Steve, Dan

* Update wiki pages in preparation for the review of the NA-MIC renewal

==2010-01-14==

Attendees: Katie Ben Casey Yin Tina Vince Jim Satra Nicole Lauren Hiro Fernando Chris Brian Dominik Ron

* Discussion of [http://ipython.scipy.org/doc/rel-0.10/html/parallel/index.html parallel processing using ipython] for use with [[NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy|NA-MIC CT Colonography collaboration project]]. (confirmed).
** As a follow up people may be interested in the [http://www.enthought.com/training/webinars.php Enthought webinar on this topic 3pm eastern on Jan 22, 2010].
** Need real time processing speed. 10 fps for volume rendering. 5 minutes of image processing (down from 30 minutes)
** 512x512x1000 voxels
** GPU solutions or ipython solutions
** Python package for accessing to Slicer internals in a headless mode, i.e. run Slicer internals from Python instead of running Python from within Slicer
** iPython distinct from MPI (meet different needs)
** Microsoft interest in iPython
* Jim fell on the sword to take minutes
* Follow up information from Fernando about the new version of ipython in development:
** the docs for the in-testing ipython are at: http://ipython.scipy.org/doc/bzr.r1321/
** and downloads in various formats are at: http://ipython.scipy.org/dist/testing/
** ''Note:'' the files with .bzr.r1321 in the names are the relevant ones for today's call, NOT the 'nightly' ones.

2010 Summer Project Week Breakout Session:GWE

2010-06-24T06:20:31Z

Mruiz:

Back to [[2010 Summer Project Week#Agenda| Project Week Agenda]]

'''Session Leader: Marco Ruiz'''

==Objective==

Introduce researchers to [[Engineering:UCSD|open source systems]] created to aid them, with the tasks of building and executing parameter exploration experiments and reviewing the results of such experiments. These solutions are tailored to run equally in a local environment (personal computer or local/remote supercomputer) or in a cluster environment (Condor, SGE, PBS. LSP, Torque, etc).

[[image:Wcp-queue-1.png|thumb|left|300px|GWE: Queueing a parameter exploration experiment (order)]]

[[image:Rse-gwe-exp.gif|thumb|left|300px|RSE: Exploring the results of a GWE parameter exploration experiment]]

==Agenda==

* ''[http://www.gridwizardenterprise.org GWE System (Grid Wizard Enterprise)]''
** Installation and configuration.
** Creating and running a parameter exploration experiment.
** Reviewing results.
** Project information and other resources.

<pre>
export JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/1.5/Home/
export GWE_HOME=/demos/gwe/gwe-0.7.3.alpha
export PATH=$GWE_HOME/bin:$PATH
gwe-web.sh
</pre>

* ''[http://www.gridwizardenterprise.org/rse RSE System (Record Set Explorer)]''
** Installation and configuration.
** Creating a record set.
** Exploring a record set.
** View management.
** Project information and other resources.

<pre>
export JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/1.5/Home/
export RSE_HOME=/demos/gwe/rse-0.6.2.alpha
export PATH=$RSE_HOME/bin:$PATH
rse.sh
</pre>

* Q&A / Discussion

==Case Studies (parameter exploration experiments expressed as P2EL statements)==

* ''Slice all volumes found under a directory all of the axis, multiple planes''
<pre>
${SLICER_HOME}=/demos/gwe/Slicer3
${volumes_files_dir}=/demos/gwe/data
${volumes_name_regexp}=.*[.](nrrd|nhdr)
${volumes_filenames}=$dir(${volumes_files_dir},${volumes_name_regexp})
${axis}=$const(0,1,2)
${plane}=$range(40,140,4)
${slicingCmd}=$sliceGen(${SLICER_HOME},${volumes_filenames},${axis},${plane})

${slicingCmd}
</pre>

* ''Gradient anisotropic diffusion on a volume and take 3 representative slices of each run''
<pre>
${SLICER_HOME}=/demos/gwe/Slicer3
${conductance}=$range(0,3,1)
${timeStep}=$const(0,0.07,0.5)
${iterations}=$const(1,5)
${output}=$const(/demos/gradient-out/out-${SYSTEM_JOB_NUM}.nrrd)
${gradient}=$slicer(${SLICER_HOME},GradientAnisotropicDiffusion)

${SLICING_X_CMD}=$sliceGen(${SLICER_HOME},${output},0,100)
${SLICING_Y_CMD}=$sliceGen(${SLICER_HOME},${output},1,100)
${SLICING_Z_CMD}=$sliceGen(${SLICER_HOME},${output},2,100)

${gradient} --conductance ${conductance} --timeStep ${timeStep} --iterations ${iterations} /demos/gwe/data/brain.nrrd ${output}
&&
${SLICING_X_CMD} && ${SLICING_Y_CMD} && ${SLICING_Z_CMD}
</pre>

==References==

* [[Engineering:UCSD|Systems Wiki Page]]
* [http://www.gridwizardenterprise.org GWE Project Site]
* [http://www.gridwizardenterprise.org/rse RSE Project Site]

GWEReallyQuickStartGuide

2010-06-24T03:16:47Z

Mruiz:

== About ==

[http://gridwizardenterprise.org/ Grid Wizard Enterprise] provides powerful tools for harnessing the computing power and making tedious computations feasible. You can follow the instructions on the GWE web site, or the following steps to get running with GWE very quickly.

== Steps ==

These steps worked with GWE 0.7.3 on SPL '''linux''' machines

1. Download the installation package from [http://www.gridwizardenterprise.org/maven/org/gwe/client/0.7.3.alpha/gwe-0.7.3.alpha-client.zip here], and put it on your local machine where you are not restricted in disk space

2. Edit your .cshrc/.bashrc to set the environment variables that GWE requires, following by ''source ~/.chsrc''

<pre>
setenv GWE_HOME /path/to/gwe/directory
setenv PATH $GWE_HOME/bin:${PATH}
setenv JAVA_HOME /local/os-exact/bin/java
</pre>

3. edit ''$GWE_HOME/conf/gwe-auth.xml'' to include your login credentials for the resources you are planning to use:

<pre>


<keystore>
<accessControl>
<account user="fedorov" password="?"/>
<realms>
<realm schemes="ssh;sftp" domain="*.bwh.harvard.edu" testHost="george.bwh.harvard.edu"/>
</realms>
</accessControl>
</keystore>
</pre>

NOTE: setting password to "?" will force GWE to ask your password once to establish your credentials. This option must be preferred over saving your plain password in a configuration file.

and ''$GWE_HOME/conf/gwe-grid.xml'', to have the correct path to the Slicer installation you are planning to use:

<pre>


<grid>
<cluster name="LOCALHOST"
host="localhost"
installRootPath="/projects/birn/fedorov/software"
resourceManager="local"
queueSize="1"
maxWaitMins="0.5"
maxHijackMins="120"
maxIdleMins="1" >
<p2elVar name="SLICER_HOME" value="/projects/birn/fedorov/software/Slicer/Slicer3-3.4-2009-05-21-linux-x86_64" />
</cluster>
</grid>
</pre>

NOTE: If you are planning to use shared computing resources, it is advisable to configure all of the paths to have unique names to avoid clashes with other users. Do not use the default path settings!

4. launch gwe-web.sh

5. point your browser to [http://localhost:8080 http://localhost:8080]

6. you should see a web interface to GWE, and localhost in the "My Grid" tab. Click on "LOCALHOST", and in the bottom click on the button to install GWE daemon.

7. The daemon should be running, and you should be able to see in with the green "ok" triangle in the list "GWE Daemons"

8. Click on the "LOCALHOST" link to the daemon, and you should be able to submit the following P2EL script that describes a small parameter exploration study for GradientAnisotropicDiffucion filter:

<pre>
${CONDUCT}=$range(0.5,1.5,1)
${TIME}=$range(0.01,0.05,0.03)
${ITER}=$const(11)
${grad_EXPLORATION_ID}=${CONDUCT}-${TIME}-${ITER}

${output}=$out(sftp://localhost.bwh.harvard.edu/projects/birn/fedorov/data/Testing/${grad_EXPLORATION_ID}.nrrd)
${input}=$in(sftp://localhost.bwh.harvard.edu/projects/birn/fedorov/data/Testing/MRMeningioma1.nrrd) ${grad}=$const(${grad_SLICER} --conductance ${CONDUCT} --timeStep ${TIME} --iterations ${ITER}) ${grad_SLICER}=$const(${SLICER_HOME}/Slicer3 --launch ${SLICER_HOME}/lib/Slicer3/Plugins/GradientAnisotropicDiffusion)

${grad} ${input} ${output}
</pre>

At least, this should get you started. Good luck!

== Wish list ==
* improved error handling: exception stack trace like below is not helping in finding the source of the problem.

<pre>
at org.gwe.drivers.netAccess.ShellCommand.logResult(ShellCommand.java:186)
at org.gwe.drivers.netAccess.ShellCommand.runLocally(ShellCommand.java:162)
at org.gwe.persistence.model.order.OSCommandDaemonRequest.process(OSCommandDaemonRequest.java:68)
at org.gwe.app.agent.BaseAgent.processRequest(BaseAgent.java:85)
at org.gwe.app.agent.BaseAgent.call(BaseAgent.java:55)
at org.gwe.app.agent.AgentApp.main(AgentApp.java:44)
</pre>

Possible improvement: give the exact command line back to the user to try manual launch to debug the problem.

* Changes to variables in gwe-grid.xml are not propagated to the remote daemon, even if the daemon is manually restarted. The only means to propagate is to re-deploy. This is OK, but should be stated in the docs.

==Tricks==

* When you restart the demon on the local machine, kill the process
* If there is an error in the conf file, there is no error message, so if demon exists w/o error, check your conf files

==Examples==

<pre>
${DIM1}=$range(3,6,1)
${DIM2}=$range(3,6,1)
${DIM3}=$range(3,6,1)

${output}=/scratch/tmp/gwe-tmp/${SYSTEM_JOB_NUM}.nrrd

${m}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/BRAINSFitRegistration/t2ax-N4.nrrd
${f}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/t2ax-intraop-N4.nrrd

${mb}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/BRAINSFitRegistration/t2ax-TG.nrrd
${fb}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/t2ax-intraop-TG.nrrd

${SLICING_CMD}=$sliceGen(${SLICER_HOME},${output},2,17)

${SLICER_HOME}/Slicer3 --launch BRAINSFit --fixedVolume ${f} --movingVolume ${m} --outputVolume ${output} --transformType Rigid,ScaleVersor3D,Affine,BSpline --useCenterOfHeadAlign --splineGridSize ${DIM1},${DIM2},${DIM3} --maskProcessingMode ROI --fixedBinaryVolume ${fb} --movingBinaryVolume ${mb} --maskProcessingMode ROI && ${SLICING_CMD}
</pre>

Engineering:UCSD

2010-06-19T17:34:49Z

Mruiz:

Back to [[Engineering:Main|NA-MIC Engineering]]

= UCSD (PI: Jeffrey S. Grethe) =

[[Image:GWE-logo.jpg]]

= Overview =
A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter exploration experiments. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a "run-everywhere" philosophy for algorithm developers. By adopting a standard for algorithm "self-description" that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment.

A basic consideration of the GWE environment is that a researcher expert in a particular scientiﬁc discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:

* Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.
* Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).
* Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.
* Providing the researchers with the ability to easily review/manipulate the input and output data associated with the parameter exploration experiments executed.

= Projects =

For more information on these projects visit their respective project site; which contains all relevant information, including setup ready bundles, detailed user guides, demo videos, presentations, step by step tutorials, usage samples and complete source code.

== ''1. Grid Wizard Enterprise (GWE)'' ==

* ''[http://www.gridwizardenterprise.org/ Project Site]''

The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a system, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the ﬁelds of computational biology and medical image analysis.

[[image:Wcp-grid-1.png|thumb|left|300px|Configuration (clusters and keystores)]]

[[image:Wcp-cluster-1.png|thumb|left|300px|Cluster setup (just a single click after configured!)]]

[[image:Wcp-queue-1.png|thumb|left|300px|Queueing a parameter exploration experiment (order)]]

[[image:Wcp-order-1.png|thumb|left|300px|Reviewing description of a queued parameter exploration experiment]]

[[image:Wcp-order-3.png|thumb|left|300px|Reviewing execution status of a parameter exploration experiment]]

[[image:Wcp-job-2.png|thumb|left|300px|Reviewing execution status of a particular process of a parameter exploration experiment]]

== ''2. Record Set Explorer (GWE's RSE)'' ==

* ''[http://www.gridwizardenterprise.org/rse Project Site]''

Parameter exploration experiments consist of input parameter values and output result values (besides the abstract description of the experiment - algorithm/workflow). To review/manipulate these values (considering their typical large amount) a researcher is forced to deal with a great degree of manual work and error. These common tasks, performed before and after running the parameter exploration experiments (using automated systems such as GWE), can be eased by means of using an end user tool with the appropriate features. Here we present a software design and implementation of a system, Record Set Explorer (RSE; http://www.gridwizardenterprise.org/rse), aimed at providing a generic; but powerful and easy to use tool for users to interactively explore and manipulate record sets. RSE provides an easy to use tool that bridges the management of data to review/create/edit the input and output values of parameter exploration experiments. Its generality provides 3rd party adopters to easily extend the tool to include different source types for record sets such as CSV formatted files, XNAT databases (support already included in the core release of RSE), XML+XSL files, RSS feeds, Python data structures, JSON formatted files, etc.

[[image:Rse-xnat.gif|thumb|left|300px|Posting XNAT query and exploring its resulting records]]

[[image:Rse-oasis.gif|thumb|left|300px|Exploring OASIS Cross Sectional Database]]

[[image:Rse-gwe-exp.gif|thumb|left|300px|Exploring the results of a GWE parameter exploration experiment]]

= Progress (since July 2007) =

''July - September 2007''
* Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE) based on prior Grid Wizard prototype developed as part of NA-MIC.

''October 2007''
* Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])

''December 2007''
* Launch of GWE's:
** [http://www.gridwizardenterprise.org/ project site]
** [http://issues.nbirn.net/browse/GWE issue tracking system]
** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists].

''January 2008''
* Unit tests of GWE's first release candidate components.
* Internal pre-release of first version of GWE.
* Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].

''February 2008''
* First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.

''March 2008''
* GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).
* Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].

''April 2008''
* GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* Wrote paper "Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise" to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].

''May 2008''
* Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):
** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].
** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].

''June 2008''
* GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* NAMIC summer week presentations and projects:
** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]
** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]
** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]

''July 2008''
* Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.

''August 2008''
* GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.

''September 2008''
* Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf "Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise"] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.

''October 2008''
* Collected user requests at the BIRN AHM.

''November 2008''
* GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
** Major re-architecture to allow running GWE without clusters and with daemons per user.
** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database].
* Step by step tutorials:
** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]

''December 2008''
* GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).
** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|"GWE integration with catalog files" project]] (NAMIC Winter Project Week 2009)
** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.
* Step by step tutorials:
** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]

''January 2009''
* NAMIC Winter Project Week and AHM 2009.
* [[2009_Winter_Project_Week_GWE_Catalogs|"GWE integration with catalog files" project]] at the NAMIC Winter Project Week 2009.

''February 2009''
* GWE version 0.7.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* [[GWE_MiniRetreat|GWE Mini Retreat in Boston]].

''March 2009''
* GWE version 0.7.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* [http://www.gridwizardenterprise.org/media/gwe-intro-screencast.mov End-to-end Tutorial and Introductory Screencast].
* [http://www.youtube.com/watch?v=yXdRks5Wu5Q Featured Study Case (YouTube)]

''April-June 2009''
* Work towards GWE version 0.8.1.beta:
** Transparent multi cluster support (true grid support).
** Rearchitecture of transport layer to natively include sessions.
** P2EL redesign to include behavioral parameters and multi format (XML, CSV, etc).

''July-October 2009''
* NAMIC summer week presentations and projects:
** GWE end-to-end live demo.
** GWE-XNAT integration demo during XNAT presentation.
** [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_GWE_XNAT:GWE XNAT Integration Project]
** [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_GWE_Results_Browser:GWE Results Browser Improvements]
* Assistance for GWE's study case for COPD research effort: 30 thousands parameter exploration experiment.
* Work towards results browser improvements.

''November 2009-February 2010''
* Inception, analysis, architecture, design and implementation of new system: GWE's RSE (Record Set Explorer). It leverages on work done for GWE's results browser module.
* Unit tests of GWE's RSE first release candidate components.

''March 2010''
* GWE's RSE version 0.6.1.alpha release
** [http://www.youtube.com/watch?v=ebWqTHf5i5Y&hd=1 Feature Demo Video (YouTube)]

''April-June 2010''
* Work towards RSE version 0.6.2.alpha.
* GWE's RSE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/rse/changes-report.html release notes] for details.
** [http://www.youtube.com/watch?v=LWXannpfr6Y&hd=1 Feature Update Video (YouTube)]

= Miscellaneous =

* Weekly NAMIC engineering teleconferences.
* GWE testbed and user's support.

''' Dissemination Activities Prior to Monthly Progress Outlined Above '''
* Introductory meeting and demonstration with Tina Kapur & Birn-CC.
* Hosted NAMIC dissemination event (February 17-18).
* Taught Data Grid course at UCSD dissemination event.
* Attended NAMIC dissemination event.
* Attended SLC AHM.
* Instructions available for deploying a "tunneled" SRB server.

''' Infrastructure Prior to Monthly Progress Outlined Above '''
* Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.
* A server co-located at BWH will be discussed at the AHM.
* Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.
* Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms
* Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool

''' Data Sharing Prior to Monthly Progress Outlined Above '''
* Hosting NAMIC data on data grid accessible to all NAMIC participants.
* Providing data grid and Portal support to all NAMIC participants.
* Provided custom project space for NAMIC in BIRN Portal.
* Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.
* Working with Isomics to assist core 3 sites in their data uploads.
* Provided template data hierarchy constructs and integration of hierarchy in data grid.
* Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.

2010 Summer Project Week Breakout Session:GWE

2010-06-19T16:46:05Z

Mruiz:

Engineering:TCON 2010

2010-06-17T19:31:17Z

Mruiz:

Back to [[TCON:Main|TCON:Main]], [[Events]]

==2010-06-17==

Attendees: Katie, Jason White, Jim Barabas, Tamas, Xiaodong,Tina, Nicole, Steve, Vince, Luis, Sudhir Pathak (U Pittsburgh), Ron, Karl, Jim Miller, Marco

Agenda:
*Project Week Items
**Jason White project - transcranial ultrasound: [[2010_Summer_Project_Week_Intraoperative_Brain_Shift_Monitoring_Using_Shear_Mode_Transcranial_Ultrasound]]
**Sudhir project [[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data]]
**Karl Fracture [[2010_Summer_Project_Week_FractureClassification_Brainstorming]]

*'Record Set Explorer' version 0.6.2.alpha released
**Project site: http://www.gridwizardenterprise.org/rse/
**YouTube feature update video: http://www.youtube.com/watch?v=LWXannpfr6Y&hd=1

==2010-06-10==

Attendees: Jim, Tina, Dan, Tamas, Nicole, Wendy, Vince, Dominik, Jim Barabas, Katie, Luis, Hans

Agenda:
*project week review
*jim b's project
*Slicer 3.6 release
*http://www.slicer.org/
*Tutorial contest entries are due to Sonia Pujol on Monday

==2010-06-03==

Attendee: Jim, Tina, Wendy, Vince, Xioadong, Steve, Dan Marcus, Katie, Dominik, Sean Megason, Arnaud Gelas, Isaiah, Michel

Agenda:

*Project Week:
** In two weeks!
**75 registered attendees: [[2010_Summer_Project_Week#Attendee_List]]
**Review Projects/teams. Please note that deadline for completing project pages is BEFORE next week's TCON.
*Slicer Release http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:3.6_Final_Issues

Notes (discussing projects):
*community effort to make NA-MIC tools accessible to '''microscopy IA''' (Sean)
**[[Microscopy_Image_Analysis| Microscopy breakout session]]: standards, community needs.
**[[2010_Summer_Project_Week#Microscopy_Image_Analysis|Projects: detailed engineering efforts]]
**finding BWH investigators interested in microscopy: Liu, Yanling, SAIC-Frederick ; Lisle, Curtis, KnowledgeVis,
*[[Paraview_Support_for_Computational_Anatomy|Paraview]]: link via MRML or scene description file format w/o VTK dependencies. Which MRML node types should be supported.
*BrainLab-Aurora HybridNav (Isaiah Norton, A.Golby Lab): optical tracking system -> trying hybrid with AURORA, have both optical and EM tracking. Tool position history to track/document resection progress. -> add Dan Marcus (STEALTH -> openIGT) to project.
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise registration]]: (Ryan Eckbo); porting Matlab/C code into ITK -> Jim, Luiz
*removed ''Python'' & ''Execution models'' as project categories, fused into ''NA-MIC Kit Internals''
*Computer Aided Photodynamic Therapy: contacts?
*Slicer 3.6 release: last fixes: Editor, BRAINS, mutiple volume loading, DICOM series & XNAT, color LUT for generic use. New release scheduled June 10. If you know of critical issues please submit to http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:3.6_Final_Issues

==2010-05-27==
Atendees: Dan Marcus, Misha Milchenko, Tina, Nicole, Jim, Steve, Lorent, Greg, Wendy, Andre, Xiaodong, Leslie Holton, Tamas, Ron, Dominik

Agenda:
*OpenIGTLink discussion led by Junichi Tokuda. Agenda can be found in [[2010_Summer_Project_Week_Breakout_Session:OpenIGTLink| the OpenIGTLink breakout session page.]]
**Use case documentation/discussion can be found here: http://wiki.slicer.org/slicerWiki/index.php/Slicer3:BrainlabModule
*Problems with [http://en.wikipedia.org/wiki/Eclipse_(software) Eclipse] development

==2010-05-20==
Attendees: Jim, Tina, David Fuentes (MD Anderson), Dieter Hahn (Erlangen), Katie, Dominik, Xiaodong, Stephen, Andrej, Harini,Andrew Elliott (MD Anderson), Alex Z, Luis, Curt, Tamas (Queens), Nicole

Agenda:
*Discussion on adding Extensions to Slicer (led by Jim Miller). http://wiki.na-mic.org/Wiki/index.php/File:AHM2010-Plug-ins.ppt
** WebEx if needed https://emeetings.webex.com/emeetings/j.php?ED=135216267&UID=482060457&PW=NOGMwODUyMjM4

==2010-05-13==

Attendees: Sonia, Wendy, Ron, Tina, Katie, Haiying, Xiaodong, Nicole, Dominik, Vince, Marek, Andras, Tamas, Andrew Rauch, Ryan Eckbo (PNL), Mark Scully, Curt, Clement, Stephen, Harini, Isaiah, Luis Ibanez, Stuart

Agenda:
*Today's topic: Tutorial contest rules+discussion (http://www.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest)
*QA discussion
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer-3.6-QA QA Wiki]
**[http://www.na-mic.org/Wiki/index.php/Journal_of_Slicer_Tests Journal of Slicer Tests]
*Next two weeks:
**May 20th -- How to interface external software with Slicer (Jim)
**May 27th --OpenIGTLink discussion (Junichi)

==2010-05-06==
Attendees: Jim, Steve, Curt, Tina, Xiaodong, Nicole, Vince, Harini, Dominik, Ron

Agenda:
*http://wiki.na-mic.org/Wiki/index.php/2010_Summer_Project_Week
**registration via credit card available, make sure to book hotel before June 1
**updated project page Wiki template [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template], includes "Delivery Mechanism" section
**Tuesday: Slicer Handson workshop from 10-12
**Wednesday: QA training session
**new [[2010_Summer_Project_Week#Projects|Projects]]
***registration:promote unsolved registration problems as project: e.g. Stanford group & knee MRI
***connect Python tools with execution model (NiPYPE)
***Slicer 4
*** femur fracture classification (Karl from Prof. Schubert's group), project placeholder added (Analysis)
***category for meshing efforts
*prospective first-time AHM attendees are welcome to attend the TCon, feel free to invite
*NA-MIC renewal: Supplemental Information needed: latest software releases
**Slicer 3.6
**ITK 3.18 (fixing DICOM parsing)
**VTK 5.6 (integration of GPU ray casting)
**XNAT 1.4 (webservices API)

==2010-04-27==

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

Agenda:

*Please note that there will be two project-week specific tcons:
**May 13th - Sonia will lead the tutorial contest rules+discussion (http://www.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest)
**May 27th -- Junichi will lead OpenIGTLink discussion
*Discussion of help text of command line modules. [[image:Help-characters.png|thumb|100px|right|discussion topic]]
*Review of slicer3.6 release plans and bug tracker.

==2010-04-22==

Attendees: Wendy, Nicole, Steve, Sonia, Ron, Dan, Dominik, Adam, J2, Jean-Christophe.

Agenda:

*QT tutorials/discussion with Adam Weinrich, Nokia.
** Review of Slicer tutorial structure (Sonia)
** Adam works on strategic accounts (advanced development for new applications) and on university outreach to encourage creation of new developers
** Kitware is a key account for Nokia
** Review of current state of Qt with Slicer (Steve, Jc, Julien)
** Best to stick with first hands on session on Monday afternoon (Adam).
** Topics to cover:
*** Adam: Motivation (examples of other applications), Designer, available widgets, signals&slots, coding style, implicit representation
*** J2/Jc: how to make a simple module, working with the rest of the slicer application (Tuesday afternoon).
** Qt Q&A lunch on Tuesday. Adam will check with Boston-based Qt developer group about attending.
** TODO: get a lecture hall for Monday afternoon? Tina will check with Donna.
*Note: May 27th is the OpenIGTLink discussion, led by Junichi Tokuda.

==2010-04-15==
Attendees: Xiadong, Harini, Tina, Steve, Dan Marcus, Vince, Ron, Dominik, Luis, Dave P, Katie, Alex Z, Marco

Agenda:
*Project Week Kickoff Call for Engineering
**[[2010_Summer_Project_Week]]
**Start listing Engineering Projects
**Project Page Template: Add Delivery Mechanism (Extension-cmdline or loadable, Built-in)
**Ideas for handling Project Week Planning/calls

==2010-04-08==

Attendees: Jim, Dan, Nicole, Tina, Wendy, Ron, Stephen Aylward

Agenda:
*Slicer Training Course in Iowa city tomorrow.
*Added breakout sessions/talks for the project week

==2010-04-01==
Attendees: Curt, Nicole, Katie, Wendy, Tina, Dominik, Vince, Steve, Dan Marcus, Luis
*Slicer 3.6 Feature freeze
*Project Week breakout session: QT, ITK, git,...

==2010-03-25==
Attendees: wendy, nicole, dominik, vince, tina, jim, dave, luis, katie, steve, ron, xiaodong, stephen, jj, jc, j2
* MIDAS Feedback from John M./Tina
*[http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6Release Slicer 3.6]
**Documentation
**testing and code coverage
**VTK status
*[http://www.slicer.org/slicerWiki/index.php/Slicer4 Slicer 4.0]
**Community process (Stephen Aylward)
*** Superbuild status (Dave)
*** qt status (Julien)
*** Module acceptance process
**** From Nitrc
**** With Slicer
**Educating the community about the benefits of Qt (Steve Pieper)

''' Notes '''

* Slicer Extensions
** Reuse Statistics functionalities from MIDAS to report on downloads from
** http://ext.slicer.org/ext/trunk/
** Building Slicer extensions and submit them to the Slicer Dashboard
** Where are they located ? (it is described in the .s3ext files:)
*** http://ext.slicer.org/ext/trunk/12465-linux-x86_64/VmtkSlicerModule.s3ext
** Maybe build them only when their source code is actually modified ?
** Label extensions by a level of compliance with NAMIC practices ?
*** E.g. Gold, Silver, Bronze,... Coal.
**** '''Gold''': have > 80% coverage, 0 Valgrind errors, documentation and tutorial
**** '''Silver''': have > 70% coverage, < 10 Valgrind errors, and tutorial
**** '''Bronze''': have > 60% coverage, < 50 Valgrind errors, and tutorial
**** '''Coal''': have < 10% coverage, > 1000 Valgrind errors, no documentation, no tutorial
** Web of trust
*** Have gatekeepers who review the extension and label them accordingly.
*** Define a Testing procedure for Slicer 4.0. (Check lists)
** Community Support
*** Provide User Ratings (based on the Insight Journal / MIDAS functionality)
*** Use current MIDAS C++ API to Upload/Download data.
*** Create MIDAS Plugins to manage data / code for Slicer extensions
* Slicer Release 3.6
** VTK Release 5.6 : March 26th 2010
** Immediately after, switching Slicer to use VTK 5.6.
** Sorting out KWWidget issues on Windows 7 with VTK 5.6 (VTK CVS HEAD).
* Slicer Release 4.0
** Git: Conversion of CMake, VTK, Paraview
** Moving Slicer to Git ?
** ITK 4.0 will move to a clean Git repository (full reset of the history)
** Moving only Slicer modules that satisfy the '''Gold''' criteria.
** A2D2 Idea : port CLI modules to ITK 4.0
** Question about CLI modules in CTK for Slicer 4.0: Discovery process; making it cleaner by using Qt methods. But raise the concern of forcing a dependency on Qt (that not everybody may want).
*** Have specific mechanisms of discovery based on : Python, Qt, C++.
** MRML Refactoring ?
*** Jim suggests to add a dictionary-like organization to be able to query MRML nodes {by type,...}.
* Slicer Superbuild
** Dave reported on progress
*** Dealing with patches that getbuildtest.tcl applies to the third party libraries.
**** Difficulty of applying patches. Need for a multi-platform way of applying patches
**** Hosting git repositories with the patched versions of the third party libraries.
**** Use github ? create a "Slicer" user-account ?
**** CMake-ifying Python source tree ?
* Testing Modules and Extensions
** Hosting them in MIDAS
** Setting up Dashboard configuration to test modules as Slicer sub-projects
** Some CDash/CTest work is needed.
** Currently, sub-projects must be run from a common CTest script (the same of the host project).
** Needs to manage dependencies between extensions. (this can be done today with an XML file on CDash).
* Testing Submission Grouping
** Grouping {configure/build/test} submissions by Library and / or subdirectory
** Using CMake for generating labels that can be used later for grouping

==2010-03-18==
Attendees: Andriy (ran out of the room before he could take notes)
Nicole, Dominik Wendy, Steve, Stephen, Jim, Katie
* Andriy question about plots coming back from command line modules.
* Updated [[Downloads|Download page]]
** Images have been added.
** Lesion data still missing.
* Tracking downloads of extensions
** Use publication database? We can ask Julien next week.
** (See http://ext.slicer.org/ext/ for current layout - look in the trunk directory).
** Jim could use this functionality for renewal proposal
* DICOM Discussion
** http://www.slicer.org/slicerWiki/index.php/DICOM:Database
** Drag and Drop image files?
** DICOM sorter (osirix is useful for this)
* Slicer3.6 release planning
** Next release of ITK (3.18) should be in a couple of weeks
** http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6Release

==2010-03-11==
Attendees: Dan, Tina, Vince, Xiaodong, Wendy, Nicole, Katie, Kurt, Dominic, John

* Updated [[Downloads|Download page]]
** Do we want to add images?
***Yes, please. And also to format this into a table. Thanks.

* XNAT Workshop (June 28-30)
** Include a NAMIC presentation? TBD
** http://nrg.wikispaces.com/2010+XNAT+Workshop

* OpenIGT and Medtronic Navigation
** Consider a joint grant to fund the development

* Ron can kill 18 birds with one stone.

==2010-03-04==
Attendees: jim, ron, nicole, vince, dan, katie, wendy, dominic, tina

* GetNodesByName leaking the collection from Tcl ( set foo [$::slicer3::MRMLScene GetNodesByName bar] )
* VTK GPU Mapper - Mac driver issue. But otherwise is working well with compositing. Dual 3D issue tabled for now.
* Store the Collapse of the SliceController in the Layout node?
* Should the layout of the modules (left verses right) be stored in the scene? Not for now.
* DICOM databases. See discussion on mailing list.
** DICOM Schemas. Jim tried searching for Osirix's schema. What about the XNAT schema? What about ClearCanvas?
** Extend Schemas for MRML, Project views, NRRD, VTK files, etc.

==2010-02-25==

Attendees: john, marco, dominik jim, steve, wendy, tina, nicole, ron, vince, dan, katie

* MIDAS handles - fixed
* GWE's RSE ("Record Set Explorer") version 0.6.1.alpha released:
** [http://www.gridwizardenterprise.org/rse/ Project site]
** [http://www.youtube.com/watch?v=ebWqTHf5i5Y&hd=1 YouTube demo video]
*Slicer Release 3.6 Feature Freeze on April 1
*Japanese Slicer workshop in 2 weeks
*CTK workshop last week - went well

==2010-02-18==

Attendees: Jim, Steve, Wendy, Dan, Dominik, Katie, Nicole

* Discussion of whole body CT/MR data (Dan)
* Discussion of the [http://www.slicer.org/pages/Slicer_Community "Spit Kidney"]
* Dominik's registration case library data for download
* Discussion of download data for each module (like in ChangeTracker currently)
* Tutorials and Datasets
* Discussion of slicer 3.6 release schedule.

==2010-02-11==

Attendees: Jim, Katie, Curt, Casey, Tina, Xiaodong, Steve, Wendy, Dan, John, Dominik, Nicole

Agenda:
* NA-MIC data migration is complete and the Downloads page has been brought out to the Wiki sidebar (http://www.na-mic.org/Wiki/index.php/Downloads)
** Feedback is requested on the sidebar
** Feedback is requested on the Downloads page
** Feature request to track the downloads like it is done on the publication database. (Julien reports it is already available to administrators).
** Curt will work with John to add Meshing Module tutorial.
** Dominik will try putting some data in midas to see how much context can be added.
** John will check with Marek about Harvard data that had been on BIRN.
* Review of DBP2 webpages, which need updating
** Ron has contacted the parties directly
* Dan: XNAT workshop this summer (possibly June 28, 29, 30 in St. Louis)?
* Discussion of entry behavior on
* New Volume features from Xiaodong for viewing image sets in a directory (cool!)

==2010-02-04==

Attendees: Xiaodong, Tina, Casey, John, Dan, Vince, Stephen, Nicole

Agenda:
*http://www.na-mic.org/Wiki/index.php/Downloads
* [http://insight-journal.org/midas/community/view/21?path_navigation=19-15 Head MRI, MRA, DTI from 100 healthy volunteers]

DBP Tutorials should be listed at the top.
Software should point to Slicer and the NA-MIC Kit.
Data hosting is available on XNAT and Midas.

==2010-01-28==
Attendees: Xiaodong, Tina, John M, Katie, Nicole, Dominik, Vince, Casey

Agenda
* data update (john m): Discussion of Data & Tutorials on the following page. Discussion of where to put the data (XNAT or Midas).
**example downloadable resources page: http://www.ncigt.org/pages/Downloads

*Iowa Data
**Visible Human Datasets https://mri.radiology.uiowa.edu//visible_human_datasets.html

*Project Sikuli from CSAIL
**Scripted UI interaction -- GUI testing http://groups.csail.mit.edu/uid/sikuli/

==2010-01-21==
Attendees: Jim, Katie, Nicole, Wendy, Curt, Ron, Dominic, Steve, Dan

* Update wiki pages in preparation for the review of the NA-MIC renewal

==2010-01-14==

Attendees: Katie Ben Casey Yin Tina Vince Jim Satra Nicole Lauren Hiro Fernando Chris Brian Dominik Ron

* Discussion of [http://ipython.scipy.org/doc/rel-0.10/html/parallel/index.html parallel processing using ipython] for use with [[NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy|NA-MIC CT Colonography collaboration project]]. (confirmed).
** As a follow up people may be interested in the [http://www.enthought.com/training/webinars.php Enthought webinar on this topic 3pm eastern on Jan 22, 2010].
** Need real time processing speed. 10 fps for volume rendering. 5 minutes of image processing (down from 30 minutes)
** 512x512x1000 voxels
** GPU solutions or ipython solutions
** Python package for accessing to Slicer internals in a headless mode, i.e. run Slicer internals from Python instead of running Python from within Slicer
** iPython distinct from MPI (meet different needs)
** Microsoft interest in iPython
* Jim fell on the sword to take minutes
* Follow up information from Fernando about the new version of ipython in development:
** the docs for the in-testing ipython are at: http://ipython.scipy.org/doc/bzr.r1321/
** and downloads in various formats are at: http://ipython.scipy.org/dist/testing/
** ''Note:'' the files with .bzr.r1321 in the names are the relevant ones for today's call, NOT the 'nightly' ones.

Engineering:TCON 2010

2010-06-17T19:30:39Z

Mruiz:

Back to [[TCON:Main|TCON:Main]], [[Events]]

==2010-06-17==

Attendees: Katie, Jason White, Jim Barabas, Tamas, Xiaodong,Tina, Nicole, Steve, Vince, Luis, Sudhir Pathak (U Pittsburgh), Ron, Karl, Jim Miller.

Agenda:
*Project Week Items
**Jason White project - transcranial ultrasound: [[2010_Summer_Project_Week_Intraoperative_Brain_Shift_Monitoring_Using_Shear_Mode_Transcranial_Ultrasound]]
**Sudhir project [[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data]]
**Karl Fracture [[2010_Summer_Project_Week_FractureClassification_Brainstorming]]

*'Record Set Explorer' version 0.6.2.alpha released
**Project site: http://www.gridwizardenterprise.org/rse/
**YouTube feature update video: http://www.youtube.com/watch?v=LWXannpfr6Y&hd=1

==2010-06-10==

Attendees: Jim, Tina, Dan, Tamas, Nicole, Wendy, Vince, Dominik, Jim Barabas, Katie, Luis, Hans

Agenda:
*project week review
*jim b's project
*Slicer 3.6 release
*http://www.slicer.org/
*Tutorial contest entries are due to Sonia Pujol on Monday

==2010-06-03==

Attendee: Jim, Tina, Wendy, Vince, Xioadong, Steve, Dan Marcus, Katie, Dominik, Sean Megason, Arnaud Gelas, Isaiah, Michel

Agenda:

*Project Week:
** In two weeks!
**75 registered attendees: [[2010_Summer_Project_Week#Attendee_List]]
**Review Projects/teams. Please note that deadline for completing project pages is BEFORE next week's TCON.
*Slicer Release http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:3.6_Final_Issues

Notes (discussing projects):
*community effort to make NA-MIC tools accessible to '''microscopy IA''' (Sean)
**[[Microscopy_Image_Analysis| Microscopy breakout session]]: standards, community needs.
**[[2010_Summer_Project_Week#Microscopy_Image_Analysis|Projects: detailed engineering efforts]]
**finding BWH investigators interested in microscopy: Liu, Yanling, SAIC-Frederick ; Lisle, Curtis, KnowledgeVis,
*[[Paraview_Support_for_Computational_Anatomy|Paraview]]: link via MRML or scene description file format w/o VTK dependencies. Which MRML node types should be supported.
*BrainLab-Aurora HybridNav (Isaiah Norton, A.Golby Lab): optical tracking system -> trying hybrid with AURORA, have both optical and EM tracking. Tool position history to track/document resection progress. -> add Dan Marcus (STEALTH -> openIGT) to project.
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise registration]]: (Ryan Eckbo); porting Matlab/C code into ITK -> Jim, Luiz
*removed ''Python'' & ''Execution models'' as project categories, fused into ''NA-MIC Kit Internals''
*Computer Aided Photodynamic Therapy: contacts?
*Slicer 3.6 release: last fixes: Editor, BRAINS, mutiple volume loading, DICOM series & XNAT, color LUT for generic use. New release scheduled June 10. If you know of critical issues please submit to http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:3.6_Final_Issues

==2010-05-27==
Atendees: Dan Marcus, Misha Milchenko, Tina, Nicole, Jim, Steve, Lorent, Greg, Wendy, Andre, Xiaodong, Leslie Holton, Tamas, Ron, Dominik

Agenda:
*OpenIGTLink discussion led by Junichi Tokuda. Agenda can be found in [[2010_Summer_Project_Week_Breakout_Session:OpenIGTLink| the OpenIGTLink breakout session page.]]
**Use case documentation/discussion can be found here: http://wiki.slicer.org/slicerWiki/index.php/Slicer3:BrainlabModule
*Problems with [http://en.wikipedia.org/wiki/Eclipse_(software) Eclipse] development

==2010-05-20==
Attendees: Jim, Tina, David Fuentes (MD Anderson), Dieter Hahn (Erlangen), Katie, Dominik, Xiaodong, Stephen, Andrej, Harini,Andrew Elliott (MD Anderson), Alex Z, Luis, Curt, Tamas (Queens), Nicole

Agenda:
*Discussion on adding Extensions to Slicer (led by Jim Miller). http://wiki.na-mic.org/Wiki/index.php/File:AHM2010-Plug-ins.ppt
** WebEx if needed https://emeetings.webex.com/emeetings/j.php?ED=135216267&UID=482060457&PW=NOGMwODUyMjM4

==2010-05-13==

Attendees: Sonia, Wendy, Ron, Tina, Katie, Haiying, Xiaodong, Nicole, Dominik, Vince, Marek, Andras, Tamas, Andrew Rauch, Ryan Eckbo (PNL), Mark Scully, Curt, Clement, Stephen, Harini, Isaiah, Luis Ibanez, Stuart

Agenda:
*Today's topic: Tutorial contest rules+discussion (http://www.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest)
*QA discussion
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer-3.6-QA QA Wiki]
**[http://www.na-mic.org/Wiki/index.php/Journal_of_Slicer_Tests Journal of Slicer Tests]
*Next two weeks:
**May 20th -- How to interface external software with Slicer (Jim)
**May 27th --OpenIGTLink discussion (Junichi)

==2010-05-06==
Attendees: Jim, Steve, Curt, Tina, Xiaodong, Nicole, Vince, Harini, Dominik, Ron

Agenda:
*http://wiki.na-mic.org/Wiki/index.php/2010_Summer_Project_Week
**registration via credit card available, make sure to book hotel before June 1
**updated project page Wiki template [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template], includes "Delivery Mechanism" section
**Tuesday: Slicer Handson workshop from 10-12
**Wednesday: QA training session
**new [[2010_Summer_Project_Week#Projects|Projects]]
***registration:promote unsolved registration problems as project: e.g. Stanford group & knee MRI
***connect Python tools with execution model (NiPYPE)
***Slicer 4
*** femur fracture classification (Karl from Prof. Schubert's group), project placeholder added (Analysis)
***category for meshing efforts
*prospective first-time AHM attendees are welcome to attend the TCon, feel free to invite
*NA-MIC renewal: Supplemental Information needed: latest software releases
**Slicer 3.6
**ITK 3.18 (fixing DICOM parsing)
**VTK 5.6 (integration of GPU ray casting)
**XNAT 1.4 (webservices API)

==2010-04-27==

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

Agenda:

*Please note that there will be two project-week specific tcons:
**May 13th - Sonia will lead the tutorial contest rules+discussion (http://www.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest)
**May 27th -- Junichi will lead OpenIGTLink discussion
*Discussion of help text of command line modules. [[image:Help-characters.png|thumb|100px|right|discussion topic]]
*Review of slicer3.6 release plans and bug tracker.

==2010-04-22==

Attendees: Wendy, Nicole, Steve, Sonia, Ron, Dan, Dominik, Adam, J2, Jean-Christophe.

Agenda:

*QT tutorials/discussion with Adam Weinrich, Nokia.
** Review of Slicer tutorial structure (Sonia)
** Adam works on strategic accounts (advanced development for new applications) and on university outreach to encourage creation of new developers
** Kitware is a key account for Nokia
** Review of current state of Qt with Slicer (Steve, Jc, Julien)
** Best to stick with first hands on session on Monday afternoon (Adam).
** Topics to cover:
*** Adam: Motivation (examples of other applications), Designer, available widgets, signals&slots, coding style, implicit representation
*** J2/Jc: how to make a simple module, working with the rest of the slicer application (Tuesday afternoon).
** Qt Q&A lunch on Tuesday. Adam will check with Boston-based Qt developer group about attending.
** TODO: get a lecture hall for Monday afternoon? Tina will check with Donna.
*Note: May 27th is the OpenIGTLink discussion, led by Junichi Tokuda.

==2010-04-15==
Attendees: Xiadong, Harini, Tina, Steve, Dan Marcus, Vince, Ron, Dominik, Luis, Dave P, Katie, Alex Z, Marco

Agenda:
*Project Week Kickoff Call for Engineering
**[[2010_Summer_Project_Week]]
**Start listing Engineering Projects
**Project Page Template: Add Delivery Mechanism (Extension-cmdline or loadable, Built-in)
**Ideas for handling Project Week Planning/calls

==2010-04-08==

Attendees: Jim, Dan, Nicole, Tina, Wendy, Ron, Stephen Aylward

Agenda:
*Slicer Training Course in Iowa city tomorrow.
*Added breakout sessions/talks for the project week

==2010-04-01==
Attendees: Curt, Nicole, Katie, Wendy, Tina, Dominik, Vince, Steve, Dan Marcus, Luis
*Slicer 3.6 Feature freeze
*Project Week breakout session: QT, ITK, git,...

==2010-03-25==
Attendees: wendy, nicole, dominik, vince, tina, jim, dave, luis, katie, steve, ron, xiaodong, stephen, jj, jc, j2
* MIDAS Feedback from John M./Tina
*[http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6Release Slicer 3.6]
**Documentation
**testing and code coverage
**VTK status
*[http://www.slicer.org/slicerWiki/index.php/Slicer4 Slicer 4.0]
**Community process (Stephen Aylward)
*** Superbuild status (Dave)
*** qt status (Julien)
*** Module acceptance process
**** From Nitrc
**** With Slicer
**Educating the community about the benefits of Qt (Steve Pieper)

''' Notes '''

* Slicer Extensions
** Reuse Statistics functionalities from MIDAS to report on downloads from
** http://ext.slicer.org/ext/trunk/
** Building Slicer extensions and submit them to the Slicer Dashboard
** Where are they located ? (it is described in the .s3ext files:)
*** http://ext.slicer.org/ext/trunk/12465-linux-x86_64/VmtkSlicerModule.s3ext
** Maybe build them only when their source code is actually modified ?
** Label extensions by a level of compliance with NAMIC practices ?
*** E.g. Gold, Silver, Bronze,... Coal.
**** '''Gold''': have > 80% coverage, 0 Valgrind errors, documentation and tutorial
**** '''Silver''': have > 70% coverage, < 10 Valgrind errors, and tutorial
**** '''Bronze''': have > 60% coverage, < 50 Valgrind errors, and tutorial
**** '''Coal''': have < 10% coverage, > 1000 Valgrind errors, no documentation, no tutorial
** Web of trust
*** Have gatekeepers who review the extension and label them accordingly.
*** Define a Testing procedure for Slicer 4.0. (Check lists)
** Community Support
*** Provide User Ratings (based on the Insight Journal / MIDAS functionality)
*** Use current MIDAS C++ API to Upload/Download data.
*** Create MIDAS Plugins to manage data / code for Slicer extensions
* Slicer Release 3.6
** VTK Release 5.6 : March 26th 2010
** Immediately after, switching Slicer to use VTK 5.6.
** Sorting out KWWidget issues on Windows 7 with VTK 5.6 (VTK CVS HEAD).
* Slicer Release 4.0
** Git: Conversion of CMake, VTK, Paraview
** Moving Slicer to Git ?
** ITK 4.0 will move to a clean Git repository (full reset of the history)
** Moving only Slicer modules that satisfy the '''Gold''' criteria.
** A2D2 Idea : port CLI modules to ITK 4.0
** Question about CLI modules in CTK for Slicer 4.0: Discovery process; making it cleaner by using Qt methods. But raise the concern of forcing a dependency on Qt (that not everybody may want).
*** Have specific mechanisms of discovery based on : Python, Qt, C++.
** MRML Refactoring ?
*** Jim suggests to add a dictionary-like organization to be able to query MRML nodes {by type,...}.
* Slicer Superbuild
** Dave reported on progress
*** Dealing with patches that getbuildtest.tcl applies to the third party libraries.
**** Difficulty of applying patches. Need for a multi-platform way of applying patches
**** Hosting git repositories with the patched versions of the third party libraries.
**** Use github ? create a "Slicer" user-account ?
**** CMake-ifying Python source tree ?
* Testing Modules and Extensions
** Hosting them in MIDAS
** Setting up Dashboard configuration to test modules as Slicer sub-projects
** Some CDash/CTest work is needed.
** Currently, sub-projects must be run from a common CTest script (the same of the host project).
** Needs to manage dependencies between extensions. (this can be done today with an XML file on CDash).
* Testing Submission Grouping
** Grouping {configure/build/test} submissions by Library and / or subdirectory
** Using CMake for generating labels that can be used later for grouping

==2010-03-18==
Attendees: Andriy (ran out of the room before he could take notes)
Nicole, Dominik Wendy, Steve, Stephen, Jim, Katie
* Andriy question about plots coming back from command line modules.
* Updated [[Downloads|Download page]]
** Images have been added.
** Lesion data still missing.
* Tracking downloads of extensions
** Use publication database? We can ask Julien next week.
** (See http://ext.slicer.org/ext/ for current layout - look in the trunk directory).
** Jim could use this functionality for renewal proposal
* DICOM Discussion
** http://www.slicer.org/slicerWiki/index.php/DICOM:Database
** Drag and Drop image files?
** DICOM sorter (osirix is useful for this)
* Slicer3.6 release planning
** Next release of ITK (3.18) should be in a couple of weeks
** http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6Release

==2010-03-11==
Attendees: Dan, Tina, Vince, Xiaodong, Wendy, Nicole, Katie, Kurt, Dominic, John

* Updated [[Downloads|Download page]]
** Do we want to add images?
***Yes, please. And also to format this into a table. Thanks.

* XNAT Workshop (June 28-30)
** Include a NAMIC presentation? TBD
** http://nrg.wikispaces.com/2010+XNAT+Workshop

* OpenIGT and Medtronic Navigation
** Consider a joint grant to fund the development

* Ron can kill 18 birds with one stone.

==2010-03-04==
Attendees: jim, ron, nicole, vince, dan, katie, wendy, dominic, tina

* GetNodesByName leaking the collection from Tcl ( set foo [$::slicer3::MRMLScene GetNodesByName bar] )
* VTK GPU Mapper - Mac driver issue. But otherwise is working well with compositing. Dual 3D issue tabled for now.
* Store the Collapse of the SliceController in the Layout node?
* Should the layout of the modules (left verses right) be stored in the scene? Not for now.
* DICOM databases. See discussion on mailing list.
** DICOM Schemas. Jim tried searching for Osirix's schema. What about the XNAT schema? What about ClearCanvas?
** Extend Schemas for MRML, Project views, NRRD, VTK files, etc.

==2010-02-25==

Attendees: john, marco, dominik jim, steve, wendy, tina, nicole, ron, vince, dan, katie

* MIDAS handles - fixed
* GWE's RSE ("Record Set Explorer") version 0.6.1.alpha released:
** [http://www.gridwizardenterprise.org/rse/ Project site]
** [http://www.youtube.com/watch?v=ebWqTHf5i5Y&hd=1 YouTube demo video]
*Slicer Release 3.6 Feature Freeze on April 1
*Japanese Slicer workshop in 2 weeks
*CTK workshop last week - went well

==2010-02-18==

Attendees: Jim, Steve, Wendy, Dan, Dominik, Katie, Nicole

* Discussion of whole body CT/MR data (Dan)
* Discussion of the [http://www.slicer.org/pages/Slicer_Community "Spit Kidney"]
* Dominik's registration case library data for download
* Discussion of download data for each module (like in ChangeTracker currently)
* Tutorials and Datasets
* Discussion of slicer 3.6 release schedule.

==2010-02-11==

Attendees: Jim, Katie, Curt, Casey, Tina, Xiaodong, Steve, Wendy, Dan, John, Dominik, Nicole

Agenda:
* NA-MIC data migration is complete and the Downloads page has been brought out to the Wiki sidebar (http://www.na-mic.org/Wiki/index.php/Downloads)
** Feedback is requested on the sidebar
** Feedback is requested on the Downloads page
** Feature request to track the downloads like it is done on the publication database. (Julien reports it is already available to administrators).
** Curt will work with John to add Meshing Module tutorial.
** Dominik will try putting some data in midas to see how much context can be added.
** John will check with Marek about Harvard data that had been on BIRN.
* Review of DBP2 webpages, which need updating
** Ron has contacted the parties directly
* Dan: XNAT workshop this summer (possibly June 28, 29, 30 in St. Louis)?
* Discussion of entry behavior on
* New Volume features from Xiaodong for viewing image sets in a directory (cool!)

==2010-02-04==

Attendees: Xiaodong, Tina, Casey, John, Dan, Vince, Stephen, Nicole

Agenda:
*http://www.na-mic.org/Wiki/index.php/Downloads
* [http://insight-journal.org/midas/community/view/21?path_navigation=19-15 Head MRI, MRA, DTI from 100 healthy volunteers]

DBP Tutorials should be listed at the top.
Software should point to Slicer and the NA-MIC Kit.
Data hosting is available on XNAT and Midas.

==2010-01-28==
Attendees: Xiaodong, Tina, John M, Katie, Nicole, Dominik, Vince, Casey

Agenda
* data update (john m): Discussion of Data & Tutorials on the following page. Discussion of where to put the data (XNAT or Midas).
**example downloadable resources page: http://www.ncigt.org/pages/Downloads

*Iowa Data
**Visible Human Datasets https://mri.radiology.uiowa.edu//visible_human_datasets.html

*Project Sikuli from CSAIL
**Scripted UI interaction -- GUI testing http://groups.csail.mit.edu/uid/sikuli/

==2010-01-21==
Attendees: Jim, Katie, Nicole, Wendy, Curt, Ron, Dominic, Steve, Dan

* Update wiki pages in preparation for the review of the NA-MIC renewal

==2010-01-14==

Attendees: Katie Ben Casey Yin Tina Vince Jim Satra Nicole Lauren Hiro Fernando Chris Brian Dominik Ron

* Discussion of [http://ipython.scipy.org/doc/rel-0.10/html/parallel/index.html parallel processing using ipython] for use with [[NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy|NA-MIC CT Colonography collaboration project]]. (confirmed).
** As a follow up people may be interested in the [http://www.enthought.com/training/webinars.php Enthought webinar on this topic 3pm eastern on Jan 22, 2010].
** Need real time processing speed. 10 fps for volume rendering. 5 minutes of image processing (down from 30 minutes)
** 512x512x1000 voxels
** GPU solutions or ipython solutions
** Python package for accessing to Slicer internals in a headless mode, i.e. run Slicer internals from Python instead of running Python from within Slicer
** iPython distinct from MPI (meet different needs)
** Microsoft interest in iPython
* Jim fell on the sword to take minutes
* Follow up information from Fernando about the new version of ipython in development:
** the docs for the in-testing ipython are at: http://ipython.scipy.org/doc/bzr.r1321/
** and downloads in various formats are at: http://ipython.scipy.org/dist/testing/
** ''Note:'' the files with .bzr.r1321 in the names are the relevant ones for today's call, NOT the 'nightly' ones.

2010 Summer Project Week Breakout Session:GWE

2010-05-19T17:08:19Z

Mruiz:

Back to [[2010 Summer Project Week#Agenda| Project Week Agenda]]

'''Session Leader: Marco Ruiz'''

==Agenda==

=== GWE: Grid Wizard Enterprise ===

* Installation and configuration.
* Creating and running a parameter exploration experiment.
* Reviewing results.
* Project information and other resources.

=== RSE: Record Set Explorer ===

* Installation and configuration.
* Creating a record set.
* Exploring a record set.
* View management.
* Project information and other resources.

Engineering:TCON 2010

2010-04-15T20:02:10Z

Mruiz:

Back to [[TCON:Main|TCON:Main]], [[Events]]

==2010-04-15==
Attendees: Xiadong, Harini, Tina, Steve, Dan Marcus, Vince, Ron, Dominik, Luis, Dave P, Katie, Alex Z, Marco

Agenda:
*Project Week Kickoff Call for Engineering
**[[2010_Summer_Project_Week]]
**Start listing Engineering Projects
**Project Page Template: Add Delivery Mechanism (Extension-cmdline or loadable, Built-in)
**Ideas for handling Project Week Planning/calls

==2010-04-08==

Attendees: Jim, Dan, Nicole, Tina, Wendy, Ron, Stephen Aylward

Agenda:
*Slicer Training Course in Iowa city tomorrow.
*Added breakout sessions/talks for the project week

==2010-04-01==
Attendees: Curt, Nicole, Katie, Wendy, Tina, Dominik, Vince, Steve, Dan Marcus, Luis
*Slicer 3.6 Feature freeze
*Project Week breakout session: QT, ITK, git,...

==2010-03-25==
Attendees: wendy, nicole, dominik, vince, tina, jim, dave, luis, katie, steve, ron, xiaodong, stephen, jj, jc, j2
* MIDAS Feedback from John M./Tina
*[http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6Release Slicer 3.6]
**Documentation
**testing and code coverage
**VTK status
*[http://www.slicer.org/slicerWiki/index.php/Slicer4 Slicer 4.0]
**Community process (Stephen Aylward)
*** Superbuild status (Dave)
*** qt status (Julien)
*** Module acceptance process
**** From Nitrc
**** With Slicer
**Educating the community about the benefits of Qt (Steve Pieper)

''' Notes '''

* Slicer Extensions
** Reuse Statistics functionalities from MIDAS to report on downloads from
** http://ext.slicer.org/ext/trunk/
** Building Slicer extensions and submit them to the Slicer Dashboard
** Where are they located ? (it is described in the .s3ext files:)
*** http://ext.slicer.org/ext/trunk/12465-linux-x86_64/VmtkSlicerModule.s3ext
** Maybe build them only when their source code is actually modified ?
** Label extensions by a level of compliance with NAMIC practices ?
*** E.g. Gold, Silver, Bronze,... Coal.
**** '''Gold''': have > 80% coverage, 0 Valgrind errors, documentation and tutorial
**** '''Silver''': have > 70% coverage, < 10 Valgrind errors, and tutorial
**** '''Bronze''': have > 60% coverage, < 50 Valgrind errors, and tutorial
**** '''Coal''': have < 10% coverage, > 1000 Valgrind errors, no documentation, no tutorial
** Web of trust
*** Have gatekeepers who review the extension and label them accordingly.
*** Define a Testing procedure for Slicer 4.0. (Check lists)
** Community Support
*** Provide User Ratings (based on the Insight Journal / MIDAS functionality)
*** Use current MIDAS C++ API to Upload/Download data.
*** Create MIDAS Plugins to manage data / code for Slicer extensions
* Slicer Release 3.6
** VTK Release 5.6 : March 26th 2010
** Immediately after, switching Slicer to use VTK 5.6.
** Sorting out KWWidget issues on Windows 7 with VTK 5.6 (VTK CVS HEAD).
* Slicer Release 4.0
** Git: Conversion of CMake, VTK, Paraview
** Moving Slicer to Git ?
** ITK 4.0 will move to a clean Git repository (full reset of the history)
** Moving only Slicer modules that satisfy the '''Gold''' criteria.
** A2D2 Idea : port CLI modules to ITK 4.0
** Question about CLI modules in CTK for Slicer 4.0: Discovery process; making it cleaner by using Qt methods. But raise the concern of forcing a dependency on Qt (that not everybody may want).
*** Have specific mechanisms of discovery based on : Python, Qt, C++.
** MRML Refactoring ?
*** Jim suggests to add a dictionary-like organization to be able to query MRML nodes {by type,...}.
* Slicer Superbuild
** Dave reported on progress
*** Dealing with patches that getbuildtest.tcl applies to the third party libraries.
**** Difficulty of applying patches. Need for a multi-platform way of applying patches
**** Hosting git repositories with the patched versions of the third party libraries.
**** Use github ? create a "Slicer" user-account ?
**** CMake-ifying Python source tree ?
* Testing Modules and Extensions
** Hosting them in MIDAS
** Setting up Dashboard configuration to test modules as Slicer sub-projects
** Some CDash/CTest work is needed.
** Currently, sub-projects must be run from a common CTest script (the same of the host project).
** Needs to manage dependencies between extensions. (this can be done today with an XML file on CDash).
* Testing Submission Grouping
** Grouping {configure/build/test} submissions by Library and / or subdirectory
** Using CMake for generating labels that can be used later for grouping

==2010-03-18==
Attendees: Andriy (ran out of the room before he could take notes)
Nicole, Dominik Wendy, Steve, Stephen, Jim, Katie
* Andriy question about plots coming back from command line modules.
* Updated [[Downloads|Download page]]
** Images have been added.
** Lesion data still missing.
* Tracking downloads of extensions
** Use publication database? We can ask Julien next week.
** (See http://ext.slicer.org/ext/ for current layout - look in the trunk directory).
** Jim could use this functionality for renewal proposal
* DICOM Discussion
** http://www.slicer.org/slicerWiki/index.php/DICOM:Database
** Drag and Drop image files?
** DICOM sorter (osirix is useful for this)
* Slicer3.6 release planning
** Next release of ITK (3.18) should be in a couple of weeks
** http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6Release

==2010-03-11==
Attendees: Dan, Tina, Vince, Xiaodong, Wendy, Nicole, Katie, Kurt, Dominic, John

* Updated [[Downloads|Download page]]
** Do we want to add images?
***Yes, please. And also to format this into a table. Thanks.

* XNAT Workshop (June 28-30)
** Include a NAMIC presentation? TBD
** http://nrg.wikispaces.com/2010+XNAT+Workshop

* OpenIGT and Medtronic Navigation
** Consider a joint grant to fund the development

* Ron can kill 18 birds with one stone.

==2010-03-04==
Attendees: jim, ron, nicole, vince, dan, katie, wendy, dominic, tina

* GetNodesByName leaking the collection from Tcl ( set foo [$::slicer3::MRMLScene GetNodesByName bar] )
* VTK GPU Mapper - Mac driver issue. But otherwise is working well with compositing. Dual 3D issue tabled for now.
* Store the Collapse of the SliceController in the Layout node?
* Should the layout of the modules (left verses right) be stored in the scene? Not for now.
* DICOM databases. See discussion on mailing list.
** DICOM Schemas. Jim tried searching for Osirix's schema. What about the XNAT schema? What about ClearCanvas?
** Extend Schemas for MRML, Project views, NRRD, VTK files, etc.

==2010-02-25==

Attendees: john, marco, dominik jim, steve, wendy, tina, nicole, ron, vince, dan, katie

* MIDAS handles - fixed
* GWE's RSE ("Record Set Explorer") version 0.6.1.alpha released:
** [http://www.gridwizardenterprise.org/rse/ Project site]
** [http://www.youtube.com/watch?v=ebWqTHf5i5Y&hd=1 YouTube demo video]
*Slicer Release 3.6 Feature Freeze on April 1
*Japanese Slicer workshop in 2 weeks
*CTK workshop last week - went well

==2010-02-18==

Attendees: Jim, Steve, Wendy, Dan, Dominik, Katie, Nicole

* Discussion of whole body CT/MR data (Dan)
* Discussion of the [http://www.slicer.org/pages/Slicer_Community "Spit Kidney"]
* Dominik's registration case library data for download
* Discussion of download data for each module (like in ChangeTracker currently)
* Tutorials and Datasets
* Discussion of slicer 3.6 release schedule.

==2010-02-11==

Attendees: Jim, Katie, Curt, Casey, Tina, Xiaodong, Steve, Wendy, Dan, John, Dominik, Nicole

Agenda:
* NA-MIC data migration is complete and the Downloads page has been brought out to the Wiki sidebar (http://www.na-mic.org/Wiki/index.php/Downloads)
** Feedback is requested on the sidebar
** Feedback is requested on the Downloads page
** Feature request to track the downloads like it is done on the publication database. (Julien reports it is already available to administrators).
** Curt will work with John to add Meshing Module tutorial.
** Dominik will try putting some data in midas to see how much context can be added.
** John will check with Marek about Harvard data that had been on BIRN.
* Review of DBP2 webpages, which need updating
** Ron has contacted the parties directly
* Dan: XNAT workshop this summer (possibly June 28, 29, 30 in St. Louis)?
* Discussion of entry behavior on
* New Volume features from Xiaodong for viewing image sets in a directory (cool!)

==2010-02-04==

Attendees: Xiaodong, Tina, Casey, John, Dan, Vince, Stephen, Nicole

Agenda:
*http://www.na-mic.org/Wiki/index.php/Downloads
* [http://insight-journal.org/midas/community/view/21?path_navigation=19-15 Head MRI, MRA, DTI from 100 healthy volunteers]

DBP Tutorials should be listed at the top.
Software should point to Slicer and the NA-MIC Kit.
Data hosting is available on XNAT and Midas.

==2010-01-28==
Attendees: Xiaodong, Tina, John M, Katie, Nicole, Dominik, Vince, Casey

Agenda
* data update (john m): Discussion of Data & Tutorials on the following page. Discussion of where to put the data (XNAT or Midas).
**example downloadable resources page: http://www.ncigt.org/pages/Downloads

*Iowa Data
**Visible Human Datasets https://mri.radiology.uiowa.edu//visible_human_datasets.html

*Project Sikuli from CSAIL
**Scripted UI interaction -- GUI testing http://groups.csail.mit.edu/uid/sikuli/

==2010-01-21==
Attendees: Jim, Katie, Nicole, Wendy, Curt, Ron, Dominic, Steve, Dan

* Update wiki pages in preparation for the review of the NA-MIC renewal

==2010-01-14==

Attendees: Katie Ben Casey Yin Tina Vince Jim Satra Nicole Lauren Hiro Fernando Chris Brian Dominik Ron

* Discussion of [http://ipython.scipy.org/doc/rel-0.10/html/parallel/index.html parallel processing using ipython] for use with [[NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy|NA-MIC CT Colonography collaboration project]]. (confirmed).
** As a follow up people may be interested in the [http://www.enthought.com/training/webinars.php Enthought webinar on this topic 3pm eastern on Jan 22, 2010].
** Need real time processing speed. 10 fps for volume rendering. 5 minutes of image processing (down from 30 minutes)
** 512x512x1000 voxels
** GPU solutions or ipython solutions
** Python package for accessing to Slicer internals in a headless mode, i.e. run Slicer internals from Python instead of running Python from within Slicer
** iPython distinct from MPI (meet different needs)
** Microsoft interest in iPython
* Jim fell on the sword to take minutes
* Follow up information from Fernando about the new version of ipython in development:
** the docs for the in-testing ipython are at: http://ipython.scipy.org/doc/bzr.r1321/
** and downloads in various formats are at: http://ipython.scipy.org/dist/testing/
** ''Note:'' the files with .bzr.r1321 in the names are the relevant ones for today's call, NOT the 'nightly' ones.

Slicer3.2:Training

2010-03-06T03:40:52Z

Mruiz:

__NOTOC__
= Welcome to the 3D Slicer3.2 User Training 101=
*The information on this page applies to '''3D Slicer version 3.2'''.
**If you are looking for materials about Slicer version 3.4, please visit the [http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training#Software_tutorials Slicer3.4 training page]
**If you are looking for materials about Slicer version 2, please visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer2 101 page].
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2" align="left"|
* Slicer 3 has been designed as
** an easy-to-use application for 3D image analysis and visualization,
** an open-source environment for software development,
** a technology delivery platform for community breakthroughs.
*Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.
*This page contains training materials and data sets for self-guided training in the use of Slicer3

*'''For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu)'''.
| style="background: #ebeced" colspan="2" align="center"| <b>[http://www.slicer.org/slicerWiki/index.php/Slicer3:Slicer3Brand Slicer Logo]</b>
|-
| style="background: #ebeced"|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]]
|}

= Software Installation =
The [http://www.slicer.org/pages/Downloads '''Slicer download page'''] contains links for downloading the different versions of Slicer 3.

=Training Compendium=
{| border="1" cellpadding="5" width="1200px"
|- style="background:#BBE9E2; color:black" align="left"
| style="width:5%" | '''Category'''
| style="width:35%" | '''Tutorial'''
| style="width:30%" | '''Sample Data'''
| style="width:10%" | '''Image'''
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.1"></span> '''1.1'''
| style="background:#D1FFF9; color:black"| [[Media:3DVisualization_SoniaPujol_Munich2008_2.ppt| Data Loading and 3D Visualization in Slicer3 ]]
| style="background:#D1FFF9; color:black"| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz] <br> [http://www.na-mic.org/Wiki/index.php/media:SlicerSampleVisualization.zip SlicerSampleVisualization.zip‎ ]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:SceneRestore.png|200px|LoadingandVisualization]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.2"></span> '''1.2'''
| style="background:#D1FFF9; color:black"| [[Media:Manual Segmentation with 3DSlicer-mj.ppt‎| Manual segmentation with 3D Slicer]]
| style="background:#D1FFF9; color:black"|
| style="background:#C3D1C3; color:black" align="Center"| [[Image:OrbitSegmentationt.png|200px]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.3"></span> '''1.3'''
| style="background:#D1FFF9; color:black"| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]<br>
Background Materials:[[EMSegmenter| EMSegmenter History]]
| style="background:#D1FFF9; color:black"|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br>
[[Media:AutomaticSegmentation.zip | ‎AutomaticSegmentation.zip ]]

| style="background:#C3D1C3; color:black" align="Center"| [[Image:EMSegmentation2008.png|200px|EM Segmenter]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.4"></span> '''1.4'''
| style="background:#D1FFF9; color:black"|[[Media:Na-MIC-Slicer-Registration.ppt|Affine and Deformable Registration in Slicer 3]]
| style="background:#D1FFF9; color:black"| [[Media:SlicerSampleRegistration.tgz | SlicerSampleRegistration.tgz]]<br>
[[Media:SlicerSampleRegistration.zip |SlicerSampleRegistration.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Na-MIC-Slicer-Registration.png|200px|SlicerRegistration]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.5"></span> '''1.5'''
| style="background:#D1FFF9; color:black"| [[Media:slicer3diffusionTutorial7.pdf| Processing of Diffusion Weighted Imaging and Diffusion Tensor Imaging data in Slicer3]]<br>
Background Materials:[http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI DT-MRI module].
| style="background:#D1FFF9; color:black"|[[Media:Slicer3-diffusion-Tutorial material.zip| Slicer3DiffusionTutorialData.zip]] <br>
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Line-glyph-tracts.jpg|200px|Glyphs and tracts]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.6"></span> '''1.6'''
| style="background:#D1FFF9; color:black"| [[Media:Slicer3Training ChangeTracker.ppt| Detecting subtle change in pathology]] <br>
This tutorial consists of two MR scans of a patient with meningioma.
| style="background:#D1FFF9; color:black"|[[Media:ChangeTracker-Tutorial-Data.zip|ChangeTracker-Tutorial-Data.zip ]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:TumorGrowth-Tutorial-Image.png|200px|Meningioma Case]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.7"></span> '''1.7'''
| style="background:#D1FFF9; color:black"| [[media:Slicer3Training_WhiteMatterLesions_v2.3.pdf‎ |Detecting white matter lesions in lupus]] <br>
This tutorial teaches how to use an automated, multi-level method to segment white matter brain lesions in lupus.
| style="background:#D1FFF9; color:black"|Lupus Tutorial Data [[Media:LesionSegmentationTutorialData.tgz‎|(.tgz)]][[media:LesionSegmentationTutorialData.zip‎| (.zip)]]<br>
| style="background:#C3D1C3; color:black" align="Center"| [[Image:3dLupusLesionVolume.png|200px|Lesion Segmentation]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.8"></span> '''1.8'''
| style="background:#D1FFF9; color:black"| [[Media:FreeSurferCourse_SoniaPujol.ppt‎|FreeSurfer Course]] <br>
This tutorial teaches how to visualize FreeSurfer segmentations and parcellation maps of the brain.
| style="background:#D1FFF9; color:black"|[http://www.na-mic.org/Wiki/index.php/Image:FreeSurferData.tar.gz FreeSurfer Tutorial Data ] <br> [[media:FreeSurferTutorialData.zip|FreeSurferTutorialData.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:FreeSurferParcellation.PNG|200px|FreeSurfer segmentation]]
|-
| style="background:#8EDEB5; color:black" align="Center"| <span id="2.1"></span> '''2.1'''
| style="background:#D1FFF9; color:black"| [[media:ProgrammingIntoSlicer3_SoniaPujol.ppt‎ |Programming into Slicer3]]
This tutorial is intended for engineers and scientists who want to integrate stand-alone programs outside of the Slicer3 source tree.
| style="background:#D1FFF9; color:black"| [[Media:HelloWorld_Plugin.zip| HelloWorld_Plugin.zip ]]

| style="background:#C3D1C3; color:black" align="Center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]
|-
| style="background:#8EDEB5; color:black" align="Center"| <span id="2.2"></span> '''2.2'''
| style="background:#D1FFF9; color:black"| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]<br>
This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping.See pages 58 to 80 of this tutorial on using the '''"Simple region growing"''' segmentation module.
<br>Background Materials: [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning].
| style="background:#D1FFF9; color:black"|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|200px|Neurosurgical Planning Overview]]
|-
| style="background:#72b291; color:black" align="Center"| <span id="3.1"></span> '''3.1'''
| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]
This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.
| style="background:#D1FFF9; color:black"|
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Slicer IGTL NITRobot.jpg|200px|Slicer with robots]]
|-
| style="background:#72b291; color:black" align="Center"| <span id="3.2"></span> '''3.2'''
| style="background:#D1FFF9; color:black"| [[Media:Brain Atlas Tutorial08.ppt| SPL-PNL Brain Atlas Tutorial]]
This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial. <br>
Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas].
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Atlas.png|200px|Brain Atlas]]
|-
| style="background:#72b291; color:black" align="Center"| <span id="3.3"></span> '''3.3'''
| style="background:#D1FFF9; color:black"| [[Media:Abdominal_Atlas_Tutorial08.ppt| SPL Abdominal Atlas Tutorial]]
This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial.
<br> Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas].
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Abdominal-Atlas-3Dsnapshot.png|200px|Abdominal Atlas]]
|-
| style="background:#72b291; color:black" align="Center"| <span id="3.4"></span> '''3.4'''
| style="background:#D1FFF9; color:black"| [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:XND Using XNAT Desktop and Slicer3 for remote data handling ]
This tutorial is intended for researchers who wish to upload local datasets to a remote XNAT repository like [http://central.xnat.org '''XNAT Central'''] and retrieve catalog files that can be opened inside Slicer.
| style="background:#D1FFF9; color:black"|
| style="background:#C3D1C3; color:black" align="Center"| [[Image:XNDmanage2.png|200px|XNAT Desktop Manager]]
|-
| style="background:#72b291; color:black" align="Center"| <span id="3.5"></span> '''3.5'''
| style="background:#D1FFF9; color:black"| '''Harnessing Grid Computational Resources and integration with Slicer through the Grid Wizard Enterprise system'''
These tutorials are intended for researchers who wish to utilize distributed computational resources.
* [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
* [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]
* [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
* [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]
| style="background:#D1FFF9; color:black"| [http://www.gridwizardenterprise.org/ '''Grid Wizard Enterprise''']

* GWE Information
** [http://www.gridwizardenterprise.org/guides/install.html GWE Installation Guide]
** [http://www.gridwizardenterprise.org/guides/config.html GWE Configuration Guide]
** [http://www.gridwizardenterprise.org/guides/user.html End Users Guide]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:GWE-overview.jpg|200px|GWE Overview]][http://www.youtube.com/watch?v=yXdRks5Wu5Q Featured Study Case (YouTube)]
|-
| style="background:#72b291; color:black" align="Center"| <span id="3.6"></span> '''3.6'''
| style="background:#D1FFF9; color:black"| [http://www.youtube.com/watch?v=ebWqTHf5i5Y&hd=1 YouTube Video: Using "GWE's Record Set Explorer"]
This tutorial is intended for researchers who wish to interactively review local or remote datasets; such as input values of parameter exploration experiements, their output results, result sets of XNAT queries or any other type of dataset.
| style="background:#D1FFF9; color:black"|

* '''Sample data used in demo video:'''
* [http://www.oasis-brains.org/pdf/oasis_cross-sectional.csv OASIS Brain DB Cross Sectional Remote DataSet]
* [http://www.oasis-brains.org/pdf/oasis_longitudinal.csv OASIS Brain DB Longitudinal Remote DataSet]

* [http://www.gridwizardenterprise.org/rse '''RSE Project Site''']
(there you can find: binaries, installation guides, source code, other useful documentation and project related information)

| style="background:#C3D1C3; color:black" align="Center"| [[Image:Rse-gwe-exp.gif|200px|RSE browsing through the results of a parameter exploration experiment]]
|}

* Category 1 = Basic functionality
* Category 2 = Advanced functionality
* Category 3 = Specialized application packages

=Additional Materials=
For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].
<br /> Back to [[Training:Main|Training:Main]]

Engineering:UCSD

2010-02-28T20:39:52Z

Mruiz:

Back to [[Engineering:Main|NA-MIC Engineering]]

= UCSD (PI: Jeffrey S. Grethe) =

[[Image:GWE-logo.jpg]]

= Overview =
A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter exploration experiments. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a "run-everywhere" philosophy for algorithm developers. By adopting a standard for algorithm "self-description" that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment.

A basic requirement for the GWE environment is that a researcher expert in a particular scientiﬁc discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:

* Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.
* Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).
* Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.
* Providing the researchers with the ability to easily review/manipulate the input and output data associated with the parameter exploration experiments executed.

= Projects =

== Grid Wizard Enterprise (GWE) ==
The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a system, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the ﬁelds of computational biology and medical image analysis.

[[image:Wcp-grid-1.png|thumb|left|300px|Configuration (clusters and keystores)]]

[[image:Wcp-cluster-1.png|thumb|left|300px|Cluster setup (just a single click after configured!)]]

[[image:Wcp-queue-1.png|thumb|left|300px|Queueing a parameter exploration experiment (order)]]

[[image:Wcp-order-1.png|thumb|left|300px|Reviewing description of a queued parameter exploration experiment]]

[[image:Wcp-order-3.png|thumb|left|300px|Reviewing execution status of a parameter exploration experiment]]

[[image:Wcp-job-2.png|thumb|left|300px|Reviewing execution status of a particular process of a parameter exploration experiment]]

== Record Set Explorer (GWE's RSE) ==
Parameter exploration experiments consist of (besides the abstract description of the experiment - algorithm/workflow) input parameter values and output result values. To review/manipulate these values (considering their typical large amount) a researcher is forced to deal with a great degree of manual work and error. These common tasks, performed before and after running the parameter exploration experiments (using automated systems such as GWE) can be eased by means of using an end user tool with the appropriate features. Here we present a software design and implementation of a system, Record Set Explorer (RSE; http://www.gridwizardenterprise.org/rse), aimed at providing a generic; but powerful and easy to use tool for users to interactively explore and manipulate record sets. RSE provides an easy to use tool that bridges the management of data to review/create/edit the input and output values of parameter exploration experiments. Its generality provides 3rd party adopters to easily extend the tool to include different source types for record sets such as CSV formatted files, XNAT databases (support already included in the core release of RSE), XML+XSL files, Python data structures, JSON formatted files, etc.

[[image:Rse-xnat.gif|thumb|left|300px|Posting XNAT query and exploring its resulting records]]

[[image:Rse-oasis.gif|thumb|left|300px|Exploring OASIS Cross Sectional Database]]

[[image:Rse-gwe-exp.gif|thumb|left|300px|Exploring the results of a GWE parameter exploration experiment]]

= Information =

* YouTube Videos
** [http://www.youtube.com/watch?v=yXdRks5Wu5Q GWE Demo]
** [http://www.youtube.com/watch?v=ebWqTHf5i5Y RSE Demo]

* GWE
** [http://www.gridwizardenterprise.org/ project site]
** [http://issues.nbirn.net/browse/GWE issue tracking system]
** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]

* GWE Setup
** [http://www.gridwizardenterprise.org/guides/install.html GWE Installation Guide]
** [http://www.gridwizardenterprise.org/guides/config.html GWE Configuration Guide]
** [http://www.gridwizardenterprise.org/guides/user.html End Users Guide]
** [http://www.gridwizardenterprise.org/integration/slicer.html GSlicer3 Guide]

* Prior Presentations
** GWE Core - [[Media:GWE-Core.ppt|Overview Presentation]] / [[Media:GWECore-Demo.mov|Video Demo]]
** GSlicer - [[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]]

* Tutorials - Provided via the [[Slicer3.2:Training| Slicer Training Site]]. Links to the tutorials provided through this site are also provided below.
** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]
** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]

= Monthly Progress (since July 2007) =

''July - September 2007''
* Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE) based on prior Grid Wizard prototype developed as part of NA-MIC.

''October 2007''
* Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])

''December 2007''
* Launch of GWE's:
** [http://www.gridwizardenterprise.org/ project site]
** [http://issues.nbirn.net/browse/GWE issue tracking system]
** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists].

''January 2008''
* Unit tests of GWE's first release candidate components.
* Internal pre-release of first version of GWE.
* Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].

''February 2008''
* First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.

''March 2008''
* GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).
* Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].

''April 2008''
* GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* Wrote paper "Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise" to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].

''May 2008''
* Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):
** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].
** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].

''June 2008''
* GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* NAMIC summer week presentations and projects:
** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]
** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]
** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]

''July 2008''
* Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.

''August 2008''
* GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.

''September 2008''
* Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf "Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise"] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.

''October 2008''
* Collected user requests at the BIRN AHM.

''November 2008''
* GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
** Major re-architecture to allow running GWE without clusters and with daemons per user.
** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database].
* Step by step tutorials:
** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]

''December 2008''
* GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).
** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|"GWE integration with catalog files" project]] (NAMIC Winter Project Week 2009)
** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.
* Step by step tutorials:
** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]

''January 2009''
* NAMIC Winter Project Week and AHM 2009.
* [[2009_Winter_Project_Week_GWE_Catalogs|"GWE integration with catalog files" project]] at the NAMIC Winter Project Week 2009.

''February 2009''
* GWE version 0.7.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* [[GWE_MiniRetreat|GWE Mini Retreat in Boston]].

''March 2009''
* GWE version 0.7.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* [http://www.gridwizardenterprise.org/media/gwe-intro-screencast.mov End-to-end Tutorial and Introductory Screencast].
* [http://www.youtube.com/watch?v=yXdRks5Wu5Q Featured Study Case (YouTube)]

''April-June 2009''
* Work towards GWE version 0.8.1.beta:
** Transparent multi cluster support (true grid support).
** Rearchitecture of transport layer to natively include sessions.
** P2EL redesign to include behavioral parameters and multi format (XML, CSV, etc).

''July-October 2009''
* NAMIC summer week presentations and projects:
** GWE end-to-end live demo.
** GWE-XNAT integration demo during XNAT presentation.
** [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_GWE_XNAT:GWE XNAT Integration Project]
** [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_GWE_Results_Browser:GWE Results Browser Improvements]
* Assistance for GWE's study case for COPD research effort: 30 thousands parameter exploration experiment.
* Work towards results browser improvements.

''November 2009-February 2010''
* Inception, analysis, architecture, design and implementation of new system: GWE's RSE (Record Set Explorer). It leverages on work done for GWE's results browser module.
* Unit tests of GWE's RSE first release candidate components.

''March 2010''
* GWE's RSE version 0.6.1.alpha release

= Miscellaneous =

* Weekly NAMIC engineering teleconferences.
* GWE testbed and user's support.

''' Dissemination Activities Prior to Monthly Progress Outlined Above '''
* Introductory meeting and demonstration with Tina Kapur & Birn-CC.
* Hosted NAMIC dissemination event (February 17-18).
* Taught Data Grid course at UCSD dissemination event.
* Attended NAMIC dissemination event.
* Attended SLC AHM.
* Instructions available for deploying a "tunneled" SRB server.

''' Infrastructure Prior to Monthly Progress Outlined Above '''
* Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.
* A server co-located at BWH will be discussed at the AHM.
* Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.
* Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms
* Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool

''' Data Sharing Prior to Monthly Progress Outlined Above '''
* Hosting NAMIC data on data grid accessible to all NAMIC participants.
* Providing data grid and Portal support to all NAMIC participants.
* Provided custom project space for NAMIC in BIRN Portal.
* Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.
* Working with Isomics to assist core 3 sites in their data uploads.
* Provided template data hierarchy constructs and integration of hierarchy in data grid.
* Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.

File:Rse-xnat.gif

2010-02-28T20:32:22Z

Mruiz:

File:Rse-oasis.gif

2010-02-28T20:31:54Z

Mruiz:

File:Rse-gwe-exp.gif

2010-02-28T20:30:50Z

Mruiz: uploaded a new version of "File:Rse-gwe-exp.gif"

File:Rse-gwe-exp.gif

2010-02-28T19:26:05Z

Mruiz:

Slicer3.2:Training

2010-02-25T23:11:56Z

Mruiz:

__NOTOC__
= Welcome to the 3D Slicer3.2 User Training 101=
*The information on this page applies to '''3D Slicer version 3.2'''.
**If you are looking for materials about Slicer version 3.4, please visit the [http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training#Software_tutorials Slicer3.4 training page]
**If you are looking for materials about Slicer version 2, please visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer2 101 page].
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* Slicer 3 has been designed as
** an easy-to-use application for 3D image analysis and visualization,
** an open-source environment for software development,
** a technology delivery platform for community breakthroughs.
*Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.
*This page contains training materials and data sets for self-guided training in the use of Slicer3

*'''For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu)'''.
| style="background: #ebeced" colspan="2" align="center"| <b>[http://www.slicer.org/slicerWiki/index.php/Slicer3:Slicer3Brand Slicer Logo]</b>
|-
| style="background: #ebeced"|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]]
|}

= Software Installation =
The [http://www.slicer.org/pages/Downloads '''Slicer download page'''] contains links for downloading the different versions of Slicer 3.

=Training Compendium=
{| border="1" cellpadding="5" width="1200px"
|- style="background:#BBE9E2; color:black" align="left"
| style="width:5%" | '''Category'''
| style="width:35%" | '''Tutorial'''
| style="width:30%" | '''Sample Data'''
| style="width:10%" | '''Image'''
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.1"></span> '''1.1'''
| style="background:#D1FFF9; color:black"| [[Media:3DVisualization_SoniaPujol_Munich2008_2.ppt| Data Loading and 3D Visualization in Slicer3 ]]
| style="background:#D1FFF9; color:black"| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz] <br> [http://www.na-mic.org/Wiki/index.php/media:SlicerSampleVisualization.zip SlicerSampleVisualization.zip‎ ]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:SceneRestore.png|200px|LoadingandVisualization]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.2"></span> '''1.2'''
| style="background:#D1FFF9; color:black"| [[Media:Manual Segmentation with 3DSlicer-mj.ppt‎| Manual segmentation with 3D Slicer]]
| style="background:#D1FFF9; color:black"|
| style="background:#C3D1C3; color:black" align="Center"| [[Image:OrbitSegmentationt.png|200px]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.3"></span> '''1.3'''
| style="background:#D1FFF9; color:black"| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]<br>
Background Materials:[[EMSegmenter| EMSegmenter History]]
| style="background:#D1FFF9; color:black"|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br>
[[Media:AutomaticSegmentation.zip | ‎AutomaticSegmentation.zip ]]

| style="background:#C3D1C3; color:black" align="Center"| [[Image:EMSegmentation2008.png|200px|EM Segmenter]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.4"></span> '''1.4'''
| style="background:#D1FFF9; color:black"|[[Media:Na-MIC-Slicer-Registration.ppt|Affine and Deformable Registration in Slicer 3]]
| style="background:#D1FFF9; color:black"| [[Media:SlicerSampleRegistration.tgz | SlicerSampleRegistration.tgz]]<br>
[[Media:SlicerSampleRegistration.zip |SlicerSampleRegistration.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Na-MIC-Slicer-Registration.png|200px|SlicerRegistration]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.5"></span> '''1.5'''
| style="background:#D1FFF9; color:black"| [[Media:slicer3diffusionTutorial7.pdf| Processing of Diffusion Weighted Imaging and Diffusion Tensor Imaging data in Slicer3]]<br>
Background Materials:[http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI DT-MRI module].
| style="background:#D1FFF9; color:black"|[[Media:Slicer3-diffusion-Tutorial material.zip| Slicer3DiffusionTutorialData.zip]] <br>
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Line-glyph-tracts.jpg|200px|Glyphs and tracts]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.6"></span> '''1.6'''
| style="background:#D1FFF9; color:black"| [[Media:Slicer3Training ChangeTracker.ppt| Detecting subtle change in pathology]] <br>
This tutorial consists of two MR scans of a patient with meningioma.
| style="background:#D1FFF9; color:black"|[[Media:ChangeTracker-Tutorial-Data.zip|ChangeTracker-Tutorial-Data.zip ]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:TumorGrowth-Tutorial-Image.png|200px|Meningioma Case]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.7"></span> '''1.7'''
| style="background:#D1FFF9; color:black"| [[media:Slicer3Training_WhiteMatterLesions_v2.3.pdf‎ |Detecting white matter lesions in lupus]] <br>
This tutorial teaches how to use an automated, multi-level method to segment white matter brain lesions in lupus.
| style="background:#D1FFF9; color:black"|Lupus Tutorial Data [[Media:LesionSegmentationTutorialData.tgz‎|(.tgz)]][[media:LesionSegmentationTutorialData.zip‎| (.zip)]]<br>
| style="background:#C3D1C3; color:black" align="Center"| [[Image:3dLupusLesionVolume.png|200px|Lesion Segmentation]]
|-
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.8"></span> '''1.8'''
| style="background:#D1FFF9; color:black"| [[Media:FreeSurferCourse_SoniaPujol.ppt‎|FreeSurfer Course]] <br>
This tutorial teaches how to visualize FreeSurfer segmentations and parcellation maps of the brain.
| style="background:#D1FFF9; color:black"|[http://www.na-mic.org/Wiki/index.php/Image:FreeSurferData.tar.gz FreeSurfer Tutorial Data ] <br> [[media:FreeSurferTutorialData.zip|FreeSurferTutorialData.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:FreeSurferParcellation.PNG|200px|FreeSurfer segmentation]]
|-
| style="background:#8EDEB5; color:black" align="Center"| <span id="2.1"></span> '''2.1'''
| style="background:#D1FFF9; color:black"| [[media:ProgrammingIntoSlicer3_SoniaPujol.ppt‎ |Programming into Slicer3]]
This tutorial is intended for engineers and scientists who want to integrate stand-alone programs outside of the Slicer3 source tree.
| style="background:#D1FFF9; color:black"| [[Media:HelloWorld_Plugin.zip| HelloWorld_Plugin.zip ]]

| style="background:#C3D1C3; color:black" align="Center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]
|-
| style="background:#8EDEB5; color:black" align="Center"| <span id="2.2"></span> '''2.2'''
| style="background:#D1FFF9; color:black"| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]<br>
This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping.See pages 58 to 80 of this tutorial on using the '''"Simple region growing"''' segmentation module.
<br>Background Materials: [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning].
| style="background:#D1FFF9; color:black"|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|200px|Neurosurgical Planning Overview]]
|-
| style="background:#72b291; color:black" align="Center"| <span id="3.1"></span> '''3.1'''
| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]
This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.
| style="background:#D1FFF9; color:black"|
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Slicer IGTL NITRobot.jpg|200px|Slicer with robots]]
|-
| style="background:#72b291; color:black" align="Center"| <span id="3.2"></span> '''3.2'''
| style="background:#D1FFF9; color:black"| [[Media:Brain Atlas Tutorial08.ppt| SPL-PNL Brain Atlas Tutorial]]
This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial. <br>
Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas].
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Atlas.png|200px|Brain Atlas]]
|-
| style="background:#72b291; color:black" align="Center"| <span id="3.3"></span> '''3.3'''
| style="background:#D1FFF9; color:black"| [[Media:Abdominal_Atlas_Tutorial08.ppt| SPL Abdominal Atlas Tutorial]]
This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial.
<br> Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas].
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Abdominal-Atlas-3Dsnapshot.png|200px|Abdominal Atlas]]
|-
| style="background:#72b291; color:black" align="Center"| <span id="3.4"></span> '''3.4'''
| style="background:#D1FFF9; color:black"| [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:XND Using XNAT Desktop and Slicer3 for remote data handling ]
This tutorial is intended for researchers who wish to upload local datasets to a remote XNAT repository like [http://central.xnat.org '''XNAT Central'''] and retrieve catalog files that can be opened inside Slicer.
| style="background:#D1FFF9; color:black"|
| style="background:#C3D1C3; color:black" align="Center"| [[Image:XNDmanage2.png|200px|XNAT Desktop Manager]]
|-
| style="background:#72b291; color:black" align="Center"| <span id="3.5"></span> '''3.5'''
| style="background:#D1FFF9; color:black"| '''Harnessing Grid Computational Resources and integration with Slicer through the Grid Wizard Enterprise system'''
These tutorials are intended for researchers who wish to utilize distributed computational resources.
* [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
* [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]
* [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
* [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]
| style="background:#D1FFF9; color:black"| [http://www.gridwizardenterprise.org/ '''Grid Wizard Enterprise''']

* GWE Information
** [http://www.gridwizardenterprise.org/guides/install.html GWE Installation Guide]
** [http://www.gridwizardenterprise.org/guides/config.html GWE Configuration Guide]
** [http://www.gridwizardenterprise.org/guides/user.html End Users Guide]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:GWE-overview.jpg|200px|GWE Overview]][http://www.youtube.com/watch?v=yXdRks5Wu5Q Featured Study Case (YouTube)]
|-
| style="background:#72b291; color:black" align="Center"| <span id="3.6"></span> '''3.6'''
| style="background:#D1FFF9; color:black"| [http://www.youtube.com/watch?v=ebWqTHf5i5Y&hd=1 Using "GWE's Record Set Explorer"]
This tutorial is intended for researchers who wish to interactively review local or remote datasets such as input values of parameter exploration experiements, their output results, result sets of XNAT queries or any other type of dataset - currently only CSV format is supported.
| style="background:#D1FFF9; color:black"|

* '''Sample data used in demo video:'''
* [http://www.oasis-brains.org/pdf/oasis_cross-sectional.csv OASIS Brain DB Cross Sectional Remote DataSet]
* [http://www.oasis-brains.org/pdf/oasis_longitudinal.csv OASIS Brain DB Longitudinal Remote DataSet]

* [http://www.gridwizardenterprise.org/rse '''RSE Project Site''']
(there you can find: binaries, installation guides, source code, other useful documentation and project related information)

| style="background:#C3D1C3; color:black" align="Center"| [[Image:Rse-7-exploration-gwe-2.png|200px|RSE browsing through the results of a parameter exploration experiment]]
|}

* Category 1 = Basic functionality
* Category 2 = Advanced functionality
* Category 3 = Specialized application packages

=Additional Materials=
For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].
<br /> Back to [[Training:Main|Training:Main]]

Engineering:TCON 2010

2010-02-25T20:20:27Z

Mruiz:

Back to [[TCON:Main|TCON:Main]], [[Events]]

==2010-02-25==

Attendees: john, marco, dominik, jim, steve, wendy, tina, nicole, ron, vince, dan, katie

* MIDAS handles
* GWE's RSE ("Record Set Explorer") version 0.6.1.alpha released:
** [http://www.gridwizardenterprise.org/rse/ Project site]
** [http://www.youtube.com/watch?v=ebWqTHf5i5Y&hd=1 YouTube demo video]
*Slicer Release 3.6 Feature Freeze on April 1

==2010-02-18==

Attendees: Jim, Steve, Wendy, Dan, Dominik, Katie, Nicole

* Discussion of whole body CT/MR data (Dan)
* Discussion of the [http://www.slicer.org/pages/Slicer_Community "Spit Kidney"]
* Dominik's registration case library data for download
* Discussion of download data for each module (like in ChangeTracker currently)
* Tutorials and Datasets
* Discussion of slicer 3.6 release schedule.

==2010-02-11==

Attendees: Jim, Katie, Curt, Casey, Tina, Xiaodong, Steve, Wendy, Dan, John, Dominik, Nicole

Agenda:
* NA-MIC data migration is complete and the Downloads page has been brought out to the Wiki sidebar (http://www.na-mic.org/Wiki/index.php/Downloads)
** Feedback is requested on the sidebar
** Feedback is requested on the Downloads page
** Feature request to track the downloads like it is done on the publication database. (Julien reports it is already available to administrators).
** Curt will work with John to add Meshing Module tutorial.
** Dominik will try putting some data in midas to see how much context can be added.
** John will check with Marek about Harvard data that had been on BIRN.
* Review of DBP2 webpages, which need updating
** Ron has contacted the parties directly
* Dan: XNAT workshop this summer (possibly June 28, 29, 30 in St. Louis)?
* Discussion of entry behavior on
* New Volume features from Xiaodong for viewing image sets in a directory (cool!)

==2010-02-04==

Attendees: Xiaodong, Tina, Casey, John, Dan, Vince, Stephen, Nicole

Agenda:
*http://www.na-mic.org/Wiki/index.php/Downloads
* [http://insight-journal.org/midas/community/view/21?path_navigation=19-15 Head MRI, MRA, DTI from 100 healthy volunteers]

DBP Tutorials should be listed at the top.
Software should point to Slicer and the NA-MIC Kit.
Data hosting is available on XNAT and Midas.

==2010-01-28==
Attendees: Xiaodong, Tina, John M, Katie, Nicole, Dominik, Vince, Casey

Agenda
* data update (john m): Discussion of Data & Tutorials on the following page. Discussion of where to put the data (XNAT or Midas).
**example downloadable resources page: http://www.ncigt.org/pages/Downloads

*Iowa Data
**Visible Human Datasets https://mri.radiology.uiowa.edu//visible_human_datasets.html

*Project Sikuli from CSAIL
**Scripted UI interaction -- GUI testing http://groups.csail.mit.edu/uid/sikuli/

==2010-01-21==
Attendees: Jim, Katie, Nicole, Wendy, Curt, Ron, Dominic, Steve, Dan

* Update wiki pages in preparation for the review of the NA-MIC renewal

==2010-01-14==

Attendees: Katie Ben Casey Yin Tina Vince Jim Satra Nicole Lauren Hiro Fernando Chris Brian Dominik Ron

* Discussion of [http://ipython.scipy.org/doc/rel-0.10/html/parallel/index.html parallel processing using ipython] for use with [[NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy|NA-MIC CT Colonography collaboration project]]. (confirmed).
** As a follow up people may be interested in the [http://www.enthought.com/training/webinars.php Enthought webinar on this topic 3pm eastern on Jan 22, 2010].
** Need real time processing speed. 10 fps for volume rendering. 5 minutes of image processing (down from 30 minutes)
** 512x512x1000 voxels
** GPU solutions or ipython solutions
** Python package for accessing to Slicer internals in a headless mode, i.e. run Slicer internals from Python instead of running Python from within Slicer
** iPython distinct from MPI (meet different needs)
** Microsoft interest in iPython
* Jim fell on the sword to take minutes
* Follow up information from Fernando about the new version of ipython in development:
** the docs for the in-testing ipython are at: http://ipython.scipy.org/doc/bzr.r1321/
** and downloads in various formats are at: http://ipython.scipy.org/dist/testing/
** ''Note:'' the files with .bzr.r1321 in the names are the relevant ones for today's call, NOT the 'nightly' ones.

Engineering:TCON 2010

2010-02-25T20:18:19Z

Mruiz:

Back to [[TCON:Main|TCON:Main]], [[Events]]

==2010-02-25==

Attendees: john, marco, dominik, jim, steve, wendy, tina, nicole, ron, vince, dan, katie

* MIDAS handles
* Record Set Explorer version 0.6.1.alpha released:
** [http://www.gridwizardenterprise.org/rse/ Project site]
** [http://www.youtube.com/watch?v=ebWqTHf5i5Y&hd=1 YouTube demo video]

==2010-02-18==

Attendees: Jim, Steve, Wendy, Dan, Dominik, Katie, Nicole

* Discussion of whole body CT/MR data (Dan)
* Discussion of the [http://www.slicer.org/pages/Slicer_Community "Spit Kidney"]
* Dominik's registration case library data for download
* Discussion of download data for each module (like in ChangeTracker currently)
* Tutorials and Datasets
* Discussion of slicer 3.6 release schedule.

==2010-02-11==

Attendees: Jim, Katie, Curt, Casey, Tina, Xiaodong, Steve, Wendy, Dan, John, Dominik, Nicole

Agenda:
* NA-MIC data migration is complete and the Downloads page has been brought out to the Wiki sidebar (http://www.na-mic.org/Wiki/index.php/Downloads)
** Feedback is requested on the sidebar
** Feedback is requested on the Downloads page
** Feature request to track the downloads like it is done on the publication database. (Julien reports it is already available to administrators).
** Curt will work with John to add Meshing Module tutorial.
** Dominik will try putting some data in midas to see how much context can be added.
** John will check with Marek about Harvard data that had been on BIRN.
* Review of DBP2 webpages, which need updating
** Ron has contacted the parties directly
* Dan: XNAT workshop this summer (possibly June 28, 29, 30 in St. Louis)?
* Discussion of entry behavior on
* New Volume features from Xiaodong for viewing image sets in a directory (cool!)

==2010-02-04==

Attendees: Xiaodong, Tina, Casey, John, Dan, Vince, Stephen, Nicole

Agenda:
*http://www.na-mic.org/Wiki/index.php/Downloads
* [http://insight-journal.org/midas/community/view/21?path_navigation=19-15 Head MRI, MRA, DTI from 100 healthy volunteers]

DBP Tutorials should be listed at the top.
Software should point to Slicer and the NA-MIC Kit.
Data hosting is available on XNAT and Midas.

==2010-01-28==
Attendees: Xiaodong, Tina, John M, Katie, Nicole, Dominik, Vince, Casey

Agenda
* data update (john m): Discussion of Data & Tutorials on the following page. Discussion of where to put the data (XNAT or Midas).
**example downloadable resources page: http://www.ncigt.org/pages/Downloads

*Iowa Data
**Visible Human Datasets https://mri.radiology.uiowa.edu//visible_human_datasets.html

*Project Sikuli from CSAIL
**Scripted UI interaction -- GUI testing http://groups.csail.mit.edu/uid/sikuli/

==2010-01-21==
Attendees: Jim, Katie, Nicole, Wendy, Curt, Ron, Dominic, Steve, Dan

* Update wiki pages in preparation for the review of the NA-MIC renewal

==2010-01-14==

Attendees: Katie Ben Casey Yin Tina Vince Jim Satra Nicole Lauren Hiro Fernando Chris Brian Dominik Ron

* Discussion of [http://ipython.scipy.org/doc/rel-0.10/html/parallel/index.html parallel processing using ipython] for use with [[NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy|NA-MIC CT Colonography collaboration project]]. (confirmed).
** As a follow up people may be interested in the [http://www.enthought.com/training/webinars.php Enthought webinar on this topic 3pm eastern on Jan 22, 2010].
** Need real time processing speed. 10 fps for volume rendering. 5 minutes of image processing (down from 30 minutes)
** 512x512x1000 voxels
** GPU solutions or ipython solutions
** Python package for accessing to Slicer internals in a headless mode, i.e. run Slicer internals from Python instead of running Python from within Slicer
** iPython distinct from MPI (meet different needs)
** Microsoft interest in iPython
* Jim fell on the sword to take minutes
* Follow up information from Fernando about the new version of ipython in development:
** the docs for the in-testing ipython are at: http://ipython.scipy.org/doc/bzr.r1321/
** and downloads in various formats are at: http://ipython.scipy.org/dist/testing/
** ''Note:'' the files with .bzr.r1321 in the names are the relevant ones for today's call, NOT the 'nightly' ones.

Engineering:UCSD

2010-02-24T18:00:31Z

Mruiz:

Back to [[Engineering:Main|NA-MIC Engineering]]

= UCSD (PI: Jeffrey S. Grethe) =

[[Image:GWE-logo.jpg]]

= Overview =
A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter exploration experiments. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a "run-everywhere" philosophy for algorithm developers. By adopting a standard for algorithm "self-description" that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment.

A basic requirement for the GWE environment is that a researcher expert in a particular scientiﬁc discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:

* Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.
* Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).
* Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.
* Providing the researchers with the ability to easily review/manipulate the input and output data associated with the parameter exploration experiments executed.

= Projects =

== Grid Wizard Enterprise (GWE) ==
The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a system, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the ﬁelds of computational biology and medical image analysis.

[[image:Wcp-grid-1.png|thumb|left|300px|Configuration (clusters and keystores)]]

[[image:Wcp-cluster-1.png|thumb|left|300px|Cluster setup (just a single click after configured!)]]

[[image:Wcp-queue-1.png|thumb|left|300px|Queueing a parameter exploration experiment (order)]]

[[image:Wcp-order-1.png|thumb|left|300px|Reviewing description of a queued parameter exploration experiment]]

[[image:Wcp-order-3.png|thumb|left|300px|Reviewing execution status of a parameter exploration experiment]]

[[image:Wcp-job-2.png|thumb|left|300px|Reviewing execution status of a particular process of a parameter exploration experiment]]

== Record Set Explorer (GWE's RSE) ==
Parameter exploration experiments consist of (besides the abstract description of the experiment - algorithm/workflow) input parameter values and output result values. To review/manipulate these values (considering their typical large amount) a researcher is forced to deal with a great degree of manual work and error. These common tasks, performed before and after running the parameter exploration experiments (using automated systems such as GWE) can be eased by means of using an end user tool with the appropriate features. Here we present a software design and implementation of a system, Record Set Explorer (RSE; http://www.gridwizardenterprise.org/rse), aimed at providing a generic; but powerful and easy to use tool for users to interactively explore and manipulate record sets. RSE provides an easy to use tool that bridges the management of data to review/create/edit the input and output values of parameter exploration experiments. Its generality provides 3rd party adopters to easily extend the tool to include different source types for record sets such as CSV formatted files, XNAT databases (support already included in the core release of RSE), XML+XSL files, Python data structures, JSON formatted files, etc.

[[image:Rse-5-definition-gwe.png|thumb|left|300px|Record Set Definition (Results of executing a parameter exploration experiment using GWE)]]

[[image:Rse-7-exploration-gwe-2.png|thumb|left|300px|Exploration (Without filtering by volume image)]]

[[image:Rse-gwe-3.png|thumb|left|300px|Exploration (Filtering to navigate through records with volume image equal to 'brain')]]

= Information =

* YouTube Videos
** [http://www.youtube.com/watch?v=yXdRks5Wu5Q GWE Demo]
** [http://www.youtube.com/watch?v=ebWqTHf5i5Y RSE Demo]

* GWE
** [http://www.gridwizardenterprise.org/ project site]
** [http://issues.nbirn.net/browse/GWE issue tracking system]
** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]

* GWE Setup
** [http://www.gridwizardenterprise.org/guides/install.html GWE Installation Guide]
** [http://www.gridwizardenterprise.org/guides/config.html GWE Configuration Guide]
** [http://www.gridwizardenterprise.org/guides/user.html End Users Guide]
** [http://www.gridwizardenterprise.org/integration/slicer.html GSlicer3 Guide]

* Prior Presentations
** GWE Core - [[Media:GWE-Core.ppt|Overview Presentation]] / [[Media:GWECore-Demo.mov|Video Demo]]
** GSlicer - [[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]]

* Tutorials - Provided via the [[Slicer3.2:Training| Slicer Training Site]]. Links to the tutorials provided through this site are also provided below.
** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]
** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]

= Monthly Progress (since July 2007) =

''July - September 2007''
* Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE) based on prior Grid Wizard prototype developed as part of NA-MIC.

''October 2007''
* Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])

''December 2007''
* Launch of GWE's:
** [http://www.gridwizardenterprise.org/ project site]
** [http://issues.nbirn.net/browse/GWE issue tracking system]
** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists].

''January 2008''
* Unit tests of GWE's first release candidate components.
* Internal pre-release of first version of GWE.
* Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].

''February 2008''
* First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.

''March 2008''
* GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).
* Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].

''April 2008''
* GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* Wrote paper "Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise" to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].

''May 2008''
* Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):
** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].
** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].

''June 2008''
* GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* NAMIC summer week presentations and projects:
** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]
** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]
** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]

''July 2008''
* Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.

''August 2008''
* GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.

''September 2008''
* Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf "Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise"] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.

''October 2008''
* Collected user requests at the BIRN AHM.

''November 2008''
* GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
** Major re-architecture to allow running GWE without clusters and with daemons per user.
** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database].
* Step by step tutorials:
** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]

''December 2008''
* GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).
** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|"GWE integration with catalog files" project]] (NAMIC Winter Project Week 2009)
** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.
* Step by step tutorials:
** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]

''January 2009''
* NAMIC Winter Project Week and AHM 2009.
* [[2009_Winter_Project_Week_GWE_Catalogs|"GWE integration with catalog files" project]] at the NAMIC Winter Project Week 2009.

''February 2009''
* GWE version 0.7.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* [[GWE_MiniRetreat|GWE Mini Retreat in Boston]].

''March 2009''
* GWE version 0.7.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* [http://www.gridwizardenterprise.org/media/gwe-intro-screencast.mov End-to-end Tutorial and Introductory Screencast].
* [http://www.youtube.com/watch?v=yXdRks5Wu5Q Featured Study Case (YouTube)]

''April-June 2009''
* Work towards GWE version 0.8.1.beta:
** Transparent multi cluster support (true grid support).
** Rearchitecture of transport layer to natively include sessions.
** P2EL redesign to include behavioral parameters and multi format (XML, CSV, etc).

''July-October 2009''
* NAMIC summer week presentations and projects:
** GWE end-to-end live demo.
** GWE-XNAT integration demo during XNAT presentation.
** [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_GWE_XNAT:GWE XNAT Integration Project]
** [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_GWE_Results_Browser:GWE Results Browser Improvements]
* Assistance for GWE's study case for COPD research effort: 30 thousands parameter exploration experiment.
* Work towards results browser improvements.

''November 2009-February 2010''
* Inception, analysis, architecture, design and implementation of new system: GWE's RSE (Record Set Explorer). It leverages on work done for GWE's results browser module.
* Unit tests of GWE's RSE first release candidate components.

''March 2010''
* GWE's RSE version 0.6.1.alpha release

= Miscellaneous =

* Weekly NAMIC engineering teleconferences.
* GWE testbed and user's support.

''' Dissemination Activities Prior to Monthly Progress Outlined Above '''
* Introductory meeting and demonstration with Tina Kapur & Birn-CC.
* Hosted NAMIC dissemination event (February 17-18).
* Taught Data Grid course at UCSD dissemination event.
* Attended NAMIC dissemination event.
* Attended SLC AHM.
* Instructions available for deploying a "tunneled" SRB server.

''' Infrastructure Prior to Monthly Progress Outlined Above '''
* Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.
* A server co-located at BWH will be discussed at the AHM.
* Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.
* Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms
* Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool

''' Data Sharing Prior to Monthly Progress Outlined Above '''
* Hosting NAMIC data on data grid accessible to all NAMIC participants.
* Providing data grid and Portal support to all NAMIC participants.
* Provided custom project space for NAMIC in BIRN Portal.
* Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.
* Working with Isomics to assist core 3 sites in their data uploads.
* Provided template data hierarchy constructs and integration of hierarchy in data grid.
* Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.

File:Wcp-cluster-1.png

2010-02-24T17:56:05Z

Mruiz:

File:Wcp-order-1.png

2010-02-24T17:55:20Z

Mruiz:

File:Wcp-job-2.png

2010-02-24T17:54:16Z

Mruiz:

File:Wcp-grid-2.png

2010-02-24T17:50:56Z

Mruiz:

File:Wcp-grid-1.png

2010-02-24T17:49:12Z

Mruiz:

Engineering:UCSD

2010-02-09T22:02:16Z

Mruiz:

Back to [[Engineering:Main|NA-MIC Engineering]]

= UCSD (PI: Jeffrey S. Grethe) =

[[Image:GWE-logo.jpg]]

= Overview =
A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter exploration experiments. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a "run-everywhere" philosophy for algorithm developers. By adopting a standard for algorithm "self-description" that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment.

A basic requirement for the GWE environment is that a researcher expert in a particular scientiﬁc discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:

* Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.
* Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).
* Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.
* Providing the researchers with the ability to easily review/manipulate the input and output data associated with the parameter exploration experiments executed.

= Projects =

== Grid Wizard Enterprise (GWE) ==
The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a system, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the ﬁelds of computational biology and medical image analysis.

[[image:Wcp-queue-1.png|thumb|left|300px|Queueing Parameter Exploration Experiment]]

[[image:Wcp-order-3.png|thumb|left|300px|Reviewing Execution Status of Parameter Exploration Experiment]]

== Record Set Explorer (GWE's RSE) ==
Parameter exploration experiments consist of (besides the abstract description of the experiment - algorithm/workflow) input parameter values and output result values. To review/manipulate these values (considering their typical large amount) a researcher is forced to deal with a great degree of manual work and error. These common tasks, performed before and after running the parameter exploration experiments (using automated systems such as GWE) can be eased by means of using an end user tool with the appropriate features. Here we present a software design and implementation of a system, Record Set Explorer (RSE; http://www.gridwizardenterprise.org/rse), aimed at providing a generic; but powerful and easy to use tool for users to interactively explore and manipulate record sets. RSE provides an easy to use tool that bridges the management of data to review/create/edit the input and output values of parameter exploration experiments. Its generality provides 3rd party adopters to easily extend the tool to include different source types for record sets such as CSV formatted files, XNAT databases (support already included in the core release of RSE), XML+XSL files, Python data structures, JSON formatted files, etc.

[[image:Rse-5-definition-gwe.png|thumb|left|300px|Record Set Definition (Results of executing a parameter exploration experiment using GWE)]]

[[image:Rse-7-exploration-gwe-2.png|thumb|left|300px|Exploration (Without filtering by volume image)]]

[[image:Rse-gwe-3.png|thumb|left|300px|Exploration (Filtering to navigate through records with volume image equal to 'brain')]]

= Information =

* YouTube Videos
** [http://www.youtube.com/watch?v=yXdRks5Wu5Q GWE Demo]
** [http://www.youtube.com/watch?v=ebWqTHf5i5Y RSE Demo]

* GWE
** [http://www.gridwizardenterprise.org/ project site]
** [http://issues.nbirn.net/browse/GWE issue tracking system]
** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]

* GWE Setup
** [http://www.gridwizardenterprise.org/guides/install.html GWE Installation Guide]
** [http://www.gridwizardenterprise.org/guides/config.html GWE Configuration Guide]
** [http://www.gridwizardenterprise.org/guides/user.html End Users Guide]
** [http://www.gridwizardenterprise.org/integration/slicer.html GSlicer3 Guide]

* Prior Presentations
** GWE Core - [[Media:GWE-Core.ppt|Overview Presentation]] / [[Media:GWECore-Demo.mov|Video Demo]]
** GSlicer - [[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]]

* Tutorials - Provided via the [[Slicer3.2:Training| Slicer Training Site]]. Links to the tutorials provided through this site are also provided below.
** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]
** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]

= Monthly Progress (since July 2007) =

''July - September 2007''
* Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE) based on prior Grid Wizard prototype developed as part of NA-MIC.

''October 2007''
* Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])

''December 2007''
* Launch of GWE's:
** [http://www.gridwizardenterprise.org/ project site]
** [http://issues.nbirn.net/browse/GWE issue tracking system]
** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists].

''January 2008''
* Unit tests of GWE's first release candidate components.
* Internal pre-release of first version of GWE.
* Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].

''February 2008''
* First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.

''March 2008''
* GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).
* Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].

''April 2008''
* GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* Wrote paper "Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise" to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].

''May 2008''
* Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):
** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].
** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].

''June 2008''
* GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* NAMIC summer week presentations and projects:
** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]
** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]
** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]

''July 2008''
* Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.

''August 2008''
* GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.

''September 2008''
* Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf "Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise"] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.

''October 2008''
* Collected user requests at the BIRN AHM.

''November 2008''
* GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
** Major re-architecture to allow running GWE without clusters and with daemons per user.
** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database].
* Step by step tutorials:
** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]

''December 2008''
* GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).
** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|"GWE integration with catalog files" project]] (NAMIC Winter Project Week 2009)
** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.
* Step by step tutorials:
** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]

''January 2009''
* NAMIC Winter Project Week and AHM 2009.
* [[2009_Winter_Project_Week_GWE_Catalogs|"GWE integration with catalog files" project]] at the NAMIC Winter Project Week 2009.

''February 2009''
* GWE version 0.7.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* [[GWE_MiniRetreat|GWE Mini Retreat in Boston]].

''March 2009''
* GWE version 0.7.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* [http://www.gridwizardenterprise.org/media/gwe-intro-screencast.mov End-to-end Tutorial and Introductory Screencast].
* [http://www.youtube.com/watch?v=yXdRks5Wu5Q Featured Study Case (YouTube)]

''April-June 2009''
* Work towards GWE version 0.8.1.beta:
** Transparent multi cluster support (true grid support).
** Rearchitecture of transport layer to natively include sessions.
** P2EL redesign to include behavioral parameters and multi format (XML, CSV, etc).

''July-October 2009''
* NAMIC summer week presentations and projects:
** GWE end-to-end live demo.
** GWE-XNAT integration demo during XNAT presentation.
** [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_GWE_XNAT:GWE XNAT Integration Project]
** [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_GWE_Results_Browser:GWE Results Browser Improvements]
* Assistance for GWE's study case for COPD research effort: 30 thousands parameter exploration experiment.
* Work towards results browser improvements.

''November 2009-February 2010''
* Inception, analysis, architecture, design and implementation of new system: GWE's RSE (Record Set Explorer). It leverages on work done for GWE's results browser module.
* Unit tests of GWE's RSE first release candidate components.

''March 2010''
* GWE's RSE version 0.6.1.alpha release

= Miscellaneous =

* Weekly NAMIC engineering teleconferences.
* GWE testbed and user's support.

''' Dissemination Activities Prior to Monthly Progress Outlined Above '''
* Introductory meeting and demonstration with Tina Kapur & Birn-CC.
* Hosted NAMIC dissemination event (February 17-18).
* Taught Data Grid course at UCSD dissemination event.
* Attended NAMIC dissemination event.
* Attended SLC AHM.
* Instructions available for deploying a "tunneled" SRB server.

''' Infrastructure Prior to Monthly Progress Outlined Above '''
* Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.
* A server co-located at BWH will be discussed at the AHM.
* Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.
* Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms
* Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool

''' Data Sharing Prior to Monthly Progress Outlined Above '''
* Hosting NAMIC data on data grid accessible to all NAMIC participants.
* Providing data grid and Portal support to all NAMIC participants.
* Provided custom project space for NAMIC in BIRN Portal.
* Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.
* Working with Isomics to assist core 3 sites in their data uploads.
* Provided template data hierarchy constructs and integration of hierarchy in data grid.
* Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.

Engineering:UCSD

2010-02-08T23:29:41Z

Mruiz:

Back to [[Engineering:Main|NA-MIC Engineering]]

= UCSD (PI: Jeffrey S. Grethe) =

[[Image:GWE-logo.jpg]]

= Overview =
A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter exploration experiments. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a "run-everywhere" philosophy for algorithm developers. By adopting a standard for algorithm "self-description" that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment.

A basic requirement for the GWE environment is that a researcher expert in a particular scientiﬁc discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:

* Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.
* Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).
* Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.
* Providing the researchers with the ability to easily review/manipulate the input and output data associated with the parameter exploration experiments executed.

= Systems =

== Grid Wizard Enterprise (GWE) ==
The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a system, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the ﬁelds of computational biology and medical image analysis.

[[File:Wcp-queue-1.png]]

[[File:Wcp-order-3.png]]

== Record Set Explorer (GWE's RSE) ==
Parameter exploration experiments consist of (besides the abstract description of the experiment - algorithm/workflow) input parameter values and output result values. To review/manipulate these values (considering their typical large amount) a researcher is forced to deal with a great degree of manual work and error. These common tasks, performed before and after running the parameter exploration experiments (using automated systems such as GWE) can be eased by means of using an end user tool with the appropriate features. Here we present a software design and implementation of a system, Record Set Explorer (RSE; http://www.gridwizardenterprise.org/rse), aimed at providing a generic; but powerful and easy to use tool for users to interactively explore and manipulate record sets. RSE provides an easy to use tool that bridges the management of data to review/create/edit the input and output values of parameter exploration experiments. Its generality provides 3rd party adopters to easily extend the tool to include different source types for record sets such as CSV formatted files, XNAT databases (support already included in the core release of RSE), XML+XSL files, Python data structures, JSON formatted files, etc.

[[File:Rse-5-definition-gwe.png]]

[[File:Rse-7-exploration-gwe-2.png]]

[[File:Rse-gwe-3.png]]

= Information =

* GWE
** [http://www.gridwizardenterprise.org/ project site]
** [http://issues.nbirn.net/browse/GWE issue tracking system]
** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]

* GWE Setup
** [http://www.gridwizardenterprise.org/guides/install.html GWE Installation Guide]
** [http://www.gridwizardenterprise.org/guides/config.html GWE Configuration Guide]
** [http://www.gridwizardenterprise.org/guides/user.html End Users Guide]
** [http://www.gridwizardenterprise.org/integration/slicer.html GSlicer3 Guide]

* Prior Presentations
** GWE Core - [[Media:GWE-Core.ppt|Overview Presentation]] / [[Media:GWECore-Demo.mov|Video Demo]]
** GSlicer - [[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]]

* Tutorials
Tutorials are provided via the [[Slicer3.2:Training| Slicer Training Site]]. Links to the tutorials provided through this site are also provided below.
** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]
** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]

= Monthly Progress (since July 2007) =

''July - September 2007''
* Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE) based on prior Grid Wizard prototype developed as part of NA-MIC.

''October 2007''
* Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])

''December 2007''
* Launch of GWE's:
** [http://www.gridwizardenterprise.org/ project site]
** [http://issues.nbirn.net/browse/GWE issue tracking system]
** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists].

''January 2008''
* Unit tests of GWE's first release candidate components.
* Internal pre-release of first version of GWE.
* Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].

''February 2008''
* First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.

''March 2008''
* GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).
* Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].

''April 2008''
* GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* Wrote paper "Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise" to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].

''May 2008''
* Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):
** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].
** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].

''June 2008''
* GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* NAMIC summer week presentations and projects:
** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]
** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]
** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]

''July 2008''
* Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.

''August 2008''
* GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.

''September 2008''
* Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf "Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise"] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.

''October 2008''
* Collected user requests at the BIRN AHM.

''November 2008''
* GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
** Major re-architecture to allow running GWE without clusters and with daemons per user.
** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database].
* Step by step tutorials:
** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]

''December 2008''
* GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).
** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|"GWE integration with catalog files" project]] (NAMIC Winter Project Week 2009)
** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.
* Step by step tutorials:
** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]

''January 2009''
* NAMIC Winter Project Week and AHM 2009.
* [[2009_Winter_Project_Week_GWE_Catalogs|"GWE integration with catalog files" project]] at the NAMIC Winter Project Week 2009.

''February 2009''
* GWE version 0.7.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* [[GWE_MiniRetreat|GWE Mini Retreat in Boston]].

''March 2009''
* GWE version 0.7.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* [http://www.gridwizardenterprise.org/media/gwe-intro-screencast.mov End-to-end Tutorial and Introductory Screencast].
* [http://www.youtube.com/watch?v=yXdRks5Wu5Q Featured Study Case (YouTube)]

''April-June 2009''
* Work towards GWE version 0.8.1.beta:
** Transparent multi cluster support (true grid support).
** Rearchitecture of transport layer to natively include sessions.
** P2EL redesign to include behavioral parameters and multi format (XML, CSV, etc).

''July-October 2009''
* NAMIC summer week presentations and projects:
** GWE end-to-end live demo.
** GWE-XNAT integration demo during XNAT presentation.
** [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_GWE_XNAT:GWE XNAT Integration Project]
** [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_GWE_Results_Browser:GWE Results Browser Improvements]
* Assistance for GWE's study case for COPD research effort: 30 thousands parameter exploration experiment.
* Work towards results browser improvements.

''November 2009-February 2010''
* Inception, analysis, architecture, design and implementation of new system: GWE's RSE (Record Set Explorer). It leverages on work done for GWE's results browser module.
* Unit tests of GWE's RSE first release candidate components.

''March 2010''
* GWE's RSE version 0.6.1.alpha release

= Miscellaneous =

* Weekly NAMIC engineering teleconferences.
* GWE testbed and user's support.

''' Dissemination Activities Prior to Monthly Progress Outlined Above '''
* Introductory meeting and demonstration with Tina Kapur & Birn-CC.
* Hosted NAMIC dissemination event (February 17-18).
* Taught Data Grid course at UCSD dissemination event.
* Attended NAMIC dissemination event.
* Attended SLC AHM.
* Instructions available for deploying a "tunneled" SRB server.

''' Infrastructure Prior to Monthly Progress Outlined Above '''
* Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.
* A server co-located at BWH will be discussed at the AHM.
* Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.
* Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms
* Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool

''' Data Sharing Prior to Monthly Progress Outlined Above '''
* Hosting NAMIC data on data grid accessible to all NAMIC participants.
* Providing data grid and Portal support to all NAMIC participants.
* Provided custom project space for NAMIC in BIRN Portal.
* Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.
* Working with Isomics to assist core 3 sites in their data uploads.
* Provided template data hierarchy constructs and integration of hierarchy in data grid.
* Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.

File:Rse-7-exploration-gwe-2.png

2010-02-08T23:22:17Z

Mruiz: uploaded a new version of "File:Rse-7-exploration-gwe-2.png"

File:Rse-gwe-3.png

2010-02-08T23:22:00Z

Mruiz:

File:Rse-5-definition-gwe.png

2010-02-08T23:21:24Z

Mruiz: uploaded a new version of "File:Rse-5-definition-gwe.png"

File:Wcp-queue-1.png

2010-02-08T23:12:04Z

Mruiz:

File:Wcp-order-3.png

2010-02-08T23:11:06Z

Mruiz:

File:Rse-7-exploration-gwe-2.png

2010-02-08T23:09:03Z

Mruiz:

File:Rse-5-definition-gwe.png

2010-02-08T23:07:01Z

Mruiz:

Engineering:UCSD

2010-02-08T13:47:06Z

Mruiz: /* Monthly Progress (since July 2007) */

Back to [[Engineering:Main|NA-MIC Engineering]]

= UCSD (PI: Mark Ellisman) =

[[Image:GWE-logo.jpg]]

= Overview =
A core activity of UCSD is the development of infrastructure and support for the utilization of distributed computation resources (i.e. Grid Wizard Enterprise). This infrastructure allows, for example, Slicer3 to execute work in a distributed grid environment and enable NA-MIC algorithms to be tested in such a distributed environment. This will allow for much quicker validation of algorithms developed in Core 1 and also test effects of parameter settings, through large scale parameter searches. Work described in the previous progress report led to a prototype grid interface (aka Grid Wizard or gwiz). The overall purpose of this work in NA-MIC is to facilitate a "run-everywhere" philosophy for algorithm developers. By adopting a standard for algorithm "self-description" that is followed when command line executables are written, Slicer and distributed computational environments should be able to use the executables directly in their environment.

A basic requirement for the GWE environment is that a researcher expert in a particular scientiﬁc discipline should not need to also become an expert in grid computing in order to produce an application that uses grid technology. It is important to note that GWE is not meant to be another grid middleware package, rather, it is meant to be a large-scale job launching and management tool that bridges the gulf between these biomedical researchers and current grid middleware by:

* Providing the researcher with the ability to easily configure the heterogeneous clustered/grid resources that they have access to.
* Allowing a researcher to easily specify large parametric computational jobs using the same general syntax as is used in the command line invocation of the analysis algorithms (e.g. through the P2EL language) or through integration with community developed biomedical applications (e.g. Slicer3).
* Managing the most common house keeping tasks required to ensure end-to-end success of a computation thereby relieving the researcher of this burden.

= Grid Wizard Enterprise (GWE) Background =
The field of high performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete large scale analyses. These strategies range from the development of higher performance hardware to the assembly of large networks of commodity computers. However, for the non-computational scientist wishing to utilize these services, usable software remains elusive. Here we present a software design and implementation of a tool, Grid Wizard Enterprise (GWE; http://www.gridwizardenterprise.org/), aimed at providing a solution to the particular problem of the adoption of advanced grid technologies by biomedical researchers. GWE provides an intuitive environment and tools that bridge this gulf between the researcher and current grid technologies allowing them to run inter-independent computational processes faster by brokering their execution across a virtual grid of computational resources with a minimum of user intervention. The GWE architecture has been designed in close collaboration with NA-MIC researchers and supports the majority of every-day tasks performed by computational scientists in the ﬁelds of computational biology and medical image analysis.

= GWE Information =

* GWE
** [http://www.gridwizardenterprise.org/ project site]
** [http://issues.nbirn.net/browse/GWE issue tracking system]
** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists]

* GWE Setup
** [http://www.gridwizardenterprise.org/guides/install.html GWE Installation Guide]
** [http://www.gridwizardenterprise.org/guides/config.html GWE Configuration Guide]
** [http://www.gridwizardenterprise.org/guides/user.html End Users Guide]
** [http://www.gridwizardenterprise.org/integration/slicer.html GSlicer3 Guide]

* Prior Presentations
** GWE Core - [[Media:GWE-Core.ppt|Overview Presentation]] / [[Media:GWECore-Demo.mov|Video Demo]]
** GSlicer - [[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]]

* Tutorials
Tutorials are provided via the [[Slicer3.2:Training| Slicer Training Site]]. Links to the tutorials provided through this site are also provided below.
** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]
** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]

= Monthly Progress (since July 2007) =

''July - September 2007''
* Inception, analysis, architecture, design and implementation of Grid Wizard Enterprise (GWE) based on prior Grid Wizard prototype developed as part of NA-MIC.

''October 2007''
* Presentation and live demo of first GWE prototype at BIRN AHM. ([http://www.nbirn.net/about/archive/ahm_2007/gwe.ppt PowerPoint] / [http://www.nbirn.net/about/archive/ahm_2007/gwe.pdf PDF])

''December 2007''
* Launch of GWE's:
** [http://www.gridwizardenterprise.org/ project site]
** [http://issues.nbirn.net/browse/GWE issue tracking system]
** [http://www.gridwizardenterprise.org/mail-lists.html mailing lists].

''January 2008''
* Unit tests of GWE's first release candidate components.
* Internal pre-release of first version of GWE.
* Release of GWE guides, technical details and collaboration tools in the [http://www.gridwizardenterprise.org/ GWE project site].

''February 2008''
* First release of GWE (version 0.6.alpha). See its [http://www.gridwizardenterprise.org/features.html 'features'] page for details.

''March 2008''
* GWE version 0.6.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* GSlicer3 integration effort released. ([[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Documentation @ GWE Project Site] / [http://www.slicer.org/slicerWiki/index.php/Slicer3:GSlicer3 Documentation @ NAMIC Wiki Site]).
* Presentation of GWE and GSlicer3 at the [http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah 2008 Engineering review at Utah].

''April 2008''
* GWE version 0.6.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* Wrote paper "Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise" to be submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'].

''May 2008''
* Inception, design and implementation of the 'Chain Modules Engine' (a project different from GWE and which will be worked in parallel):
** [http://www.slicer.org/slicerWiki/index.php/Slicer3:Chain_CLMs Functional Specification].
** [http://www.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine Java implementation technical details].

''June 2008''
* GWE version 0.6.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* NAMIC summer week presentations and projects:
** [http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE GWE Special Topic Breakout]
** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing Grid Computing Project]
** [http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:ModuleChaining Module Chaining Project]

''July 2008''
* Two extra rounds of edition of the paper submitted to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop']. Paper was accepted and scheduled for a [http://www.i3s.unice.fr/~johan/MICCAI-Grid/program.html long presentation] in September.

''August 2008''
* GWE version 0.6.4.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.

''September 2008''
* Presented the paper [http://www.gridwizardenterprise.org/media/miccaig.pdf "Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise"] to the [http://www.i3s.unice.fr/~johan/MICCAI-Grid/index.html 'MICCAI Grid Workshop'] in New York.

''October 2008''
* Collected user requests at the BIRN AHM.

''November 2008''
* GWE version 0.7.0.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
** Major re-architecture to allow running GWE without clusters and with daemons per user.
** End to end study case to query and process images from remote [http://www.oasis-brains.org/ OASIS database].
* Step by step tutorials:
** [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
** [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
** [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]

''December 2008''
* GWE version 0.7.1.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
** New web client application ([http://www.gridwizardenterprise.org/guides/user-web.html GWE Web Control Panel]).
** Infrastructure to support integration of custom XML based catalogs to define experiments in preparation for the [[2009_Winter_Project_Week_GWE_Catalogs|"GWE integration with catalog files" project]] (NAMIC Winter Project Week 2009)
** Macro definitions to ease the description of medical imaging processes and Slicer3 usage.
* Step by step tutorials:
** [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]

''January 2009''
* NAMIC Winter Project Week and AHM 2009.
* [[2009_Winter_Project_Week_GWE_Catalogs|"GWE integration with catalog files" project]] at the NAMIC Winter Project Week 2009.

''February 2009''
* GWE version 0.7.2.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* [[GWE_MiniRetreat|GWE Mini Retreat in Boston]].

''March 2009''
* GWE version 0.7.3.alpha released. See its [http://www.gridwizardenterprise.org/changes-report.html release notes] for details.
* [http://www.gridwizardenterprise.org/media/gwe-intro-screencast.mov End-to-end Tutorial and Introductory Screencast].
* [http://www.youtube.com/watch?v=yXdRks5Wu5Q Featured Study Case (YouTube)]

''April-June 2009''
* Work towards GWE version 0.8.1.beta:
** Transparent multi cluster support (true grid support).
** Rearchitecture of transport layer to natively include sessions.
** P2EL redesign to include behavioral parameters and multi format (XML, CSV, etc).

''July-October 2009''
* NAMIC summer week presentations and projects:
** GWE end-to-end live demo.
** GWE-XNAT integration demo during XNAT presentation.
** [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_GWE_XNAT:GWE XNAT Integration Project]
** [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_GWE_Results_Browser:GWE Results Browser Improvements]
* Assistance for GWE's study case for COPD research effort: 30 thousands parameter exploration experiment.
* Work towards results browser improvements.

''November 2009-February 2010''
* Inception, analysis, architecture, design and implementation of new system: GWE's RSE (Record Set Explorer). It leverages on work done for GWE's results browser module.
* Unit tests of GWE's RSE first release candidate components.

''March 2010''
* GWE's RSE version 0.6.1.alpha release

= Miscellaneous =

* Weekly NAMIC engineering teleconferences.
* GWE testbed and user's support.

''' Dissemination Activities Prior to Monthly Progress Outlined Above '''
* Introductory meeting and demonstration with Tina Kapur & Birn-CC.
* Hosted NAMIC dissemination event (February 17-18).
* Taught Data Grid course at UCSD dissemination event.
* Attended NAMIC dissemination event.
* Attended SLC AHM.
* Instructions available for deploying a "tunneled" SRB server.

''' Infrastructure Prior to Monthly Progress Outlined Above '''
* Researched, tested and deployed a newly configured SRB server for NAMIC that allows for the tunneling of all SRB commands via SSH. This tunneling has been tested with the command line (SCommands), Java (JARGON) and Windows (InQ) clients. The current staging server is running at UCSD and is available for testing.
* A server co-located at BWH will be discussed at the AHM.
* Leveraged BWH BIRN Rack to provide gigabit connection for na-mic.org.
* Researching and developing a [[parallel system]] for backend parallel processing of Slicer3 algorithms
* Discussed the use of BatchMake for submitting grid-like jobs to a Condor pool

''' Data Sharing Prior to Monthly Progress Outlined Above '''
* Hosting NAMIC data on data grid accessible to all NAMIC participants.
* Providing data grid and Portal support to all NAMIC participants.
* Provided custom project space for NAMIC in BIRN Portal.
* Provided account generation for first batch of NAMIC users. New users can now utilize the new account request feature in the Portal.
* Working with Isomics to assist core 3 sites in their data uploads.
* Provided template data hierarchy constructs and integration of hierarchy in data grid.
* Provided statistics to Tina Kapur on account creation, number of uploaded data sets, and audit information.

AHM2010:NA-MIC Kit Update

2009-12-18T17:28:28Z

Mruiz:

==Goals==
Information about NA-MIC Kit component developments over the past year so that developers will have an idea of what new features are available for their use.

=== ITK ===

* Label image classes
* QuadEdgeMesh spherical registration
** Rigid
** Deformable (Diffeomorphic Demons)
* Region based Level Sets
* Pixel coordinates consistency

=== VTK ===

=== Teem ===

=== XNAT ===

=== GWE ===

* Interactive experiments' results browser.
* CSV and generated commands dumps and preview.
* Support for LSF and Lava cluster DRMs.
* Ability to override auto-discovered DRMs with configured ones.
* Ability to override default database installation location.
* Function to extract experiments' parameters from text files.
* Operations to delete, pause and resume experiments.
* Recommended to watch: [http://www.youtube.com/watch?v=yXdRks5Wu5Q 5 minutes demo video].

=== BatchMake ===

=== CMake/CPack/CTest/CDash ===

=== 3D Slicer ===
* List of new modules and features (TBD)
* 3.4/3.4.1 release information
* Extension Architecture and Extension Modules
* ARRA Supplement Projects
* Qt Port (lead in to Julien's 8:30 session)
* More info on the [http://www.slicer.org/slicerWiki/index.php/Main_Page#News Slicer wiki News Page]

=== Other Topics ===

* [http://Commontk.org Common Toolkit]

Engineering:TCON 2009

2009-12-11T21:02:02Z

Mruiz:

Back to [[TCON:Main|TCON:Main]], [[Events]]

==2009-12-10==
Attendees: Luis, nicole, katie, john melonakos, vince, tina, steve, jim, dominik, luke bloy, dan marcus, marco

Agenda:
*(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)
* Highlights:
**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. [http://www.gridwizardenterprise.org 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 [http://www.youtube.com/watch?v=yXdRks5Wu5Q 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.

==2009-12-03==
Agenda:
* [http://wiki.na-mic.org/Wiki/index.php/2010_Winter_Project_Week Link to AHM page] -- work through schedule.
* [http://wiki.na-mic.org/Wiki/index.php/2010_Winter_Project_Week Link to Project page] -- work through projects.

* Highlights
** 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

==2009-11-19==
Agenda:
*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.

==2009-11-12==
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

==2009-11-05==
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:
***http://ipython.scipy.org/doc/rel-0.10/html/parallel/index.html
***Satra's nipype project is described here:
***http://nipy.sourceforge.net/nipype/index.html
*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 [http://www.google.com/trends?q=java%2C+python%2C+c%2B%2B%2C+tcl&ctab=0&geo=all&date=all&sort=0 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

==2009-10-29==
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.
*

==2009-10-22==
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.

==2009-10-15==
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)
** John:

==2009-10-08==
Casey, Jim, Tina, Dominik, Curt, Wendy, Katie, Nicole,Stephen, Xiaodong, Ron, Steve

*Agenda:
*Resource page review - Dominik to add registration data to xnat central.
*[[Projects:ARRASuplements]]
*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

==2009-10-01==

Attendees: Xiaodong, Steve, Wendy, Nicole, Tina, Vince, Dominik, Katie

*CTK meeting update - DCMTK looks useful. QT development exchange.

==2009-09-24==

Attendees: Xiaodong, Nicole, Vince, Katie

* Waiting for people to come back from MICCAI.

==2009-09-17==

Attendees: Jim, Katie, Wendy, Steve, Nicole, Casey, Tina, Stephen

* Results of the QT brainstorming session this week are here: [http://www.na-mic.org/Wiki/index.php/Sept-2009-SlicerWidgetsBrainstorm#Attendance 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?

==2009-09-10==
* Attendees: Katie, Jim, Nicole, Steve, Sebastien, Casey, Xiaodong, Andriy, Tina, Ron, Dan, Stephen, JC, Dominik

* Discussion of [[Sept-2009-SlicerWidgetsBrainstorm | 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)

==2009-09-03==
* Attendees: Jim, Vince, Tina, Wendy, Nicole, Katie, Xiaodong
* Nicole bugged Jim about the test he said he would fix last week

==2009-08-27==
* Attendees: Jim, Steve, Wendy, Katie, Sebastian, Nicole, Dan, and somebody on mute
* fixing slicer's dashboard [http://www.cdash.org/CDash/index.php?project=Slicer3]
** 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?

==2009-08-20==
* Wendy, Casey, Stephen, Katie, Nicole, Steve
* Plans for [[Events:Registration_Summit_August_2009|registration meeting]]
* Update on Nokia/Qt meeting
* Update on MAF

==2009-08-13==

*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 [http://www.bioimagesuite.org/ 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 [http://www.slicer.org/slicerWiki/index.php/Slicer3:VisualBlog 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

==2009-08-06==

Attendees: Katie, Tina, Steve (Jim is off the grid this week. Good luck!),

* playing with Dropbox (http://getdropbox.com)

==2009-07-30==
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.
** from: http://lists.apple.com/archives/cocoa-dev/2005/Apr//msg01620.html
>
> 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.

==2009-07-23==
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?

==2009-07-16==

Attendees: Tina, Katie, Vince
*[[2009_Summer_Project_Week]] - check out google map of participant sites (thanks to marianna)

==2009-07-09==

Attendees: Jim, Steve, Tina, Ron, Stephen, Will
Agenda:

*http://www.washingtonpost.com/wp-dyn/content/article/2009/07/08/AR2009070802769.html
*update from Steve's WUSTL visit
*[[NA-MIC_External_Collaborations#Projects_funded_by_.22Collaborations_with_NCBC_PAR.22 |updated list of collaboration grants]]
** [[NA-MIC_External_Collaborations#Broader_Community_Involvement_of_NA-MIC_Investigators | placeholder for broader community grants]] - possibly for OpenMAF, IGSTK, SBIRs, etc...
* Steve's South America photos:
**Galapagos - http://www.facebook.com/album.php?aid=28255&id=1185661914&l=01b60d0091
**Amazon I - http://www.facebook.com/album.php?aid=28259&id=1185661914&l=c6cce28f96
**Amazon II - http://www.facebook.com/album.php?aid=28264&id=1185661914&l=c4a68b718b

==2009-07-02==

Attendees: Steve, Katie, Stephen, Tina, Luis, Andinet, Sebastien, Julien Finet, Will, Noby

* Report from Steve and Stephen about the recent [[Events:CTK-Workshop-June-2009|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).

==2009-06-18==
Attendees: Curt, Katie, Jim, Dan, Xiaodong, Tina

==2009-06-11==
Attendees (partial list): Randy Gollub, Steve Pieper, Nobi Hata, Snehashis Roy, Kenneth Hisley, Tina Kapur, Wendy, Nicole, Andras Lasso

Agenda:
*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.

==2009-06-04==
Agenda:
*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.

==2009-05-28==
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)

==2009-05-21==
Attendees: Will, Ron, Xiadong, Nicole, Vince
*A day of rest,

==2009-05-14==
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
*[http://tinyurl.com/cu9bzp remaining 3.4 release bugs]

==2009-05-07==
Xiadong, Tina, Katie, Nicole, Saikat, Harish, Wen, James, Steve, Vince, Dan M,

Agenda
*Stanford Simbios collaboration (Haikat, Saikat, need help on registration)
** http://slicer.spl.harvard.edu/slicerWiki/index.php/Stanford_Simbios_group

*NA-MIC engineering projects

==2009-04-30==

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
** 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?)

==2009-04-23==

Agenda

* [[2009_Summer_Project_Week]] - IGT projects
* projects for upcoming TCONS: MRSI, 2d-3d registration

==2009-04-16==
Agenda

* [[2009_Summer_Project_Week]]

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

==2009-04-09==
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)

==2009-04-02==

* 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

==03-26-2009==

* 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

Notes:
* 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)

==03-19-2009==
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.

==03-12-2009==

Agenda:
*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

Notes:
* 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
** http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:UIDesign:WorkingProblems:WelcomeModule:Draft
* 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

==03-05-2009==
Attendees: Ron, Jim, Tina, Xiaodong, Marco, Dan

Agenda:
*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).

==02-26-2009==

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.

==02-19-2009==
* 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

==02-12-2009==
*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 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

==02-05-2009==
Agenda:

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

*Topic #1 - Feature Freeze
*http://www.slicer.org/slicerWiki/index.php/Documentation-3.4#List_of_Modules_in_need_of_documentation

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
*http://wiki.na-mic.org/Wiki/index.php/NA-MIC:Site_PI_Other_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.

==01-29-2009==
Attendees: Jim, Steve, Tina, Dan, Nicole

* Discussion of [http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign:WorkingProblems:SlicerInformatics:Draft1 XNAT Integration Timeline]

==01-22-2009==
Attendees: Jim, Steve, Tina, Wendy, Xiadong, Nicole

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

==01-15-2009==

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

Agenda:
*LGPL QT - should we consider this going forward?
*Slicer code freeze on Feb 4th. [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Events Slicer3 Events] for requirements for modules to be included.

2009 Project Week Breakout Session: XNAT for Programmers

2009-06-26T13:01:32Z

Mruiz:

= Overview =

This breakout session will provide background and tutorials for programmers. The content will focus primarily on developing intereoperability between external applications (e.g. slicer, batchmake) and XNAT data repositories. We will also cover to a lesser degree contributing to the actual XNAT codebase.

= Who should attend =
Programmers who want their tools to talk to XNAT repositories. Programmers who want to contribute to the XNAT codebase. People who have Dan's keys and would please kindly return them.

= Topics =

* Interoperating with XNAT
** The XNAT Web Services API
** Examples: Slicer (Wendy [[media:ProjectWeek-06-25-09-Slicer3FetchMI.ppt| Slides]]), [http://www.gridwizardenterprise.org GWE] (Marco), XNAT File System (Dan Blezek [[media:Xnatfs_Overview.pdf‎|slides]] or [http://files.getdropbox.com/u/1363248/Summer%20Project%20Week%202009/xnatfs%20Overview.html online])

* Building on the XNAT platform
** XNAT Architecture
** Methods for extending XNAT
** Our wish list: protocol validation, UI improvements, search, etc.

2009 Summer Project Week GWE XNAT

2009-06-25T20:09:02Z

Mruiz:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:GweLogoSquare.png‎|[http://www.gridwizardenterprise.org GWE: Platform to run parameter exploration experiments]
</gallery>

==Key Investigators==
* UCSD: Marco Ruiz
* WU: Dan Marcus

<div style="margin: 20px;">
<div style="width: 22%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Collect specifications for P2EL macros/functions to upload data into XNAT systems.
* Review and refine production P2EL macros created to query XNAT systems (experiments, session, scans, images, etc.)
* Collect specifications for any other XNAT querying P2EL macros that may be useful to describe parameter exploration experiments.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Demo current state of XNAT querying support on GWE and share vision for how researchers can benefit and use it when running parameter exploration experiments.
* Discuss usability/feasibility of the vision to set a practical direction for this integration effort.
* Gather specs for the XNAT REST API to implement data upload and for the modications/additions of P2EL macros.
* Gather information about future modifications/gray areas on the XNAT REST API so can be considered in this integration effort.
</div>

<div style="width: 45%; float: left;">

<h3>Progress</h3>
* GWE 0.7.3.alpha (latest release) includes a [http://www.gridwizardenterprise.org/svn/gwe/gwe-core/trunk/src/main/config/base/gwe-macros/xnat.p2el P2EL macro library to support common querying operations].
* Presented XNAT querying capabilities curently supported by P2EL (GWE proprietary language) and demo it downloading images stored in XNAT and registering them in parallel using different set of parameters.
* Meet with Tim Olsen to discuss the XNAT upload REST API. Will need to extend the GWE HTTP driver for submitting PUT requests into XNAT and P2EL to accomodate the semantics for it.
</div>

<br style="clear: both;" />

</div>

===References===

*GWE Project Site: http://www.gridwizardenterprise.org
*P2EL Macros: http://www.gridwizardenterprise.org/guides/p2el-macros.html
*P2EL Macro Library for XNAT: http://www.gridwizardenterprise.org/svn/gwe/gwe-core/trunk/src/main/config/base/gwe-macros/xnat.p2el
*XNAT: http://www.xnat.org/
*XNAT REST API: http://nrg.wikispaces.com/XNAT+REST+API+Usage

2009 Summer Project Week GWE Results Browser

2009-06-25T19:50:11Z

Mruiz:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:GweLogoSquare.png‎|[http://www.gridwizardenterprise.org GWE: Platform to run parameter exploration experiments]
Image:Gwe_result_browser.png‎|GWE Experiment Results Browser
</gallery>

==Key Investigators==
* UCSD: Marco Ruiz
* Isomics: Steve Pieper
* BWH: Andriy Fedorov

<div style="margin: 20px;">
<div style="width: 22%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Determine the usability improvements and missing features for the GWE results browser prototype.
* Collect suggestions on desired interfaces to serve currently unresolved browsing scenarios, such as co-dependent variables.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Demo current state of the results browser.
* Describe currently resolved scenarios as well as unresolved ones such as co-dependent variables navigation.
* Describe limiting issues such as browsing media types located on remote clusters (size, network speed, etc) and rendering custom media types (pluggable rendering framework?)
* Open discussion and gather feedback.
</div>

<div style="width: 45%; float: left;">

<h3>Progress</h3>
* A prototype of the [http://wiki.na-mic.org/Wiki/index.php/File:Gwe_result_browser.png‎ experiment results browser] has been released in GWE 0.7.3.alpha (latest release) based on the ideas brainstormed a few months ago (during the [[GWE_MiniRetreat| GWE mini retreat]]).
* A [http://www.gridwizardenterprise.org YouTube video] has been created to show this prototype in action.

* A separate web server application to serve as a publisher of experiments results is of higher interest.
* For co-dependent variables the result browser will keep a tree of dependencies and re-render all the sliders accordingly every time than any of them changes.
</div>

<br style="clear: both;" />

</div>

===References===

*GWE Project Site: http://www.gridwizardenterprise.org
*YouTube Demo Video: http://www.youtube.com/user/GWEGuides
*[[GWE_MiniRetreat| GWE Mini Retreat Report]]

2009 Summer Project Week

2009-06-23T19:42:44Z

Mruiz:

Back to [[Project Events]], [[Events]]

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-G451 (in Stata)
**Tue, Wed, Thursday 9am to end
*32-D463 (Star conference room in Stata)
**Tuesday all day
**Wednesday 9-11:30, 1:30-end
*32-D451 (in Stata)
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 16th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
Breakout Rooms: 32-D451, 38-413

=== Monday===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
=== Tuesday ===
** 8:30am breakfast
** 8:30am-9:30am [[2009_Summer_Project_Week_4D_Imaging_discussion| 4D Imaging Meeting]]
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper) ([[media:2009 NA-MIC Project Week Slicer3.4.ppt|Slides]], [[2009_Summer_Project_Week_Extension_Manager|Project Page]])
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata [[Media:2009SummerProgrammingWeekHataIGT.ppt‎|Slides]], Scott Hoge [ [[Media:2009_NA-MIC_Project_Week_FastImagingLibrary.ppt|slides]] ])
** noon lunch
** 1pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W) (Star D463 Star Conference Room in Stata)
** 2:00pm-3.00pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis) (In Grier)
** 4:00pm: [[2009_Summer_Project_Week_GWE_Setup| GWE End-To-End Live Demo]] (Marco Ruiz)
** 4:30pm [http://www.cimit.org/forum-current.html CIMIT Forum (At BWH / Carl J. and Ruth Shapiro Cardiovascular Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc. ]
** 5:30pm adjourn for day

=== Wednesday ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (32-G451) (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (D463 Star conference room) (Alexandre Gouaillard)
** 5:30pm adjourn for day

=== Thursday===
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (32-G451) (Dan M.)
** 5:30pm adjourn for day

=== Friday===
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

==Projects==

=== Segmentation ===

#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation|Lupus Lesion Segmentation]] (Mark Scully MRN)
#[[2009_Summer_Project_Week_WML_SEgmentation|White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week_Skull_Stripping|Skull Stripping]] (Snehasish Roy JHU)
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation|FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)
#[[Summer2009:The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)
#[[2009 Summer Project Week Quantify VMTK seg error|Quantifying VMTK User Segmentation Error]] (Dave Welch UIowa)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Atrium_wall|Atrium Wall Segmentation]] (Behnood Gholami Georgia Tech)

=== Registration ===

#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration|Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
#[[BSpline Registration in Slicer3|BSpline Registration in Slicer3]] (Samuel Gerber Utah)
#[[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)
#[[2009_Summer_Project_Week_Slicer3_registration|Slicer 3 registration ]] (Andrew Rausch BWH PNL)
#[[EPI Correction in Slicer3|EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)
#[[2009_Summer_Project_Week_HAMMER_Registration|HAMMER Registration]] (Guorong Wu UNC)
#[[2009_Summer_Project_Week_MCMC_Cuda_Registration|Elastic Non-Rigid Registration using MCMC and CUDA]] (Petter Risholm BWH)
#[[2009_Summer_Project_Week_Cardiac_Blood_Pool_Registration|Cardiac Blood Pool Registration]] (Michal Depa MIT)

=== IGT ===

#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_Prostate_Robotics|Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)
#[[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
#[[Enhanced Neurosuregery navigation]] (Haytham Elhawary, Brigham and Women's Hospital)
#[[GPU accelerated FEM for simulation and segmentation]] (Megumi Nakao, Brigham and Women's Hospital)
#[[Liver EM segmentation]] (Padma Akella, Brigham and Women's Hlspital)
#[[MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement]] (Greg Fischer, WPI)

=== Radiotherapy ===

#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Adaptive_RT|Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov GATech)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](James Balter U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[2009_Summer_project_week_adaptive_radiation_planning_visualization]](Cal Hisley, Des Moines University/Mercy Des Moines Medical Center)

=== Analysis ===

#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Linking atlas data with ontologies of brain morphology and function]] (Michael Halle BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Imaging|4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer|Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox|multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)

=== Informatics ===

#[[2009_Summer_Project_Week_Slicer3_XNAT_UI|XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS|XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_GWE_XNAT|GWE-XNAT Integration]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_GWE_Results_Browser|GWE Results Browser Improvements]] (Marco Ruiz UCSD)
#[[Projects:ShapeCorrespondence_UNCOrthoApp|XNAT & Ortho App]] (Beatriz Paniagua UNC)

=== Diffusion ===

#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Sylvain Bouix BWH)
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep|DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom|DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_FMTractography|Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)

=== Python ===

#[[Summer2009:Using_ITK_in_python|Using ITK in python]] (Steve Pieper BWH)
#[[Summer2009:Using_cython|Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
#[[Summer2009:Implementing_parallelism_in_python|Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
#[[Summer2009:Using_client_server_paradigm_with_python_and_slicer|Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)

=== Slicer Internals ===

#[[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Colors_Module|Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)
#[[Slicer3 Informatics Workflow Design & XNAT updates|Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
#[[Slicer3_FlexibleLayouts | Slicer3 Flexible Layouts]] (Wendy Plesniak BWH)
#[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)
#[[MeshingSummer2009|IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)

=== Execution Model ===

#[[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
#[[Summer2009:Extension of the Command Line XML Syntax/Interface|Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Attendee List==

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''
{|
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{|class="wikitable"
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|
{| class="wikitable sortable"
!First
!Last
!Affiliation
|- style=&#34height:50px&#34
|John
|Melonakos
|AccelerEyes (Wed & Thu morning)
|- style=&#34height:50px&#34
|Jack
|Blevins
|Acoustic Med
|- style=&#34height:50px&#34
|Clif
|Burdette
|Acoustic Med (Mon-Wed)
|- style=&#34height:50px&#34
|Dana
|Peters
|Beth Israel Deaconess
|- style=&#34height:50px&#34
|Nicole
|Aucoin
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Giovanna
|Danagoulian
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haytham
|Elhawary
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Andriy
|Fedorov
|BWH (NAMIC Collaborator)
|- style=&#34height:50px&#34
|Daniel
|Haehn
|BWH (NAC)
|- style=&#34height:50px&#34
|Michael
|Halle
|BWH (NAC)
|- style=&#34height:50px&#34
|Nobuhiko
|Hata
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Katie
|Hayes
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Scott
|Hoge
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Tina
|Kapur
|BWH (NCIGT, NAMIC)
|- style=&#34height:50px&#34
|Ron
|Kikinis
|BWH (NAMIC, NAC, NCIGT)
|- style=&#34height:50px&#34
|Jayender
|Jagadeesan
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haying
|Liu
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Lauren
|O'Donnell
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Wendy
|Plesniak
|BWH (NAC)
|- style=&#34height:50px&#34
|Megumi
|Nakao
|BWH (NAIST)
|- style=&#34height:50px&#34
|Sonia
|Pujol
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Lei
|Qin
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Nicolas
|Rannou
|BWH (NAC)
|- style=&#34height:50px&#34
|Petter
|Risholm
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Florin
|Talos
|BWH (NAC)
|- style=&#34height:50px&#34
|Clare
|Tempany
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Junichi
|Tokuda
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Demian
|Wasserman
|BWH (INRIA)
|- style=&#34height:50px&#34
|Carl-Fredrik
|Westin
|BWH (NAC)
|- style=&#34height:50px&#34
|Sandy
|Wells
|BWH (NAC, NCIGT)
|- style=&#34height:50px&#34
|Lilla
|Zollei
|MGH (NAC)
|- style=&#34height:50px&#34
|Padma
|Akella
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Sylvain
|Bouix
|BWH (PNL)
|- style=&#34height:50px&#34
|Julien
|de Siebenthal
|BWH (PNL)
|- style=&#34height:50px&#34
|Marek
|Kubicki
|BWH (NAMIC DBP PNL)
|- style=&#34height:50px&#34
|Juhana
|Frosen
|BWH Tues only
|- style=&#34height:50px&#34
|Sun Woo
|Lee
|BWH (PNL)
|- style=&#34height:50px&#34
|Jimi
|Malcolm
|BWH (PNL)
|- style=&#34height:50px&#34
|Eric
|Melonakos
|BWH (PNL)
|- style=&#34height:50px&#34
|Yogesh
|Rathi
|BWH (PNL)
|- style=&#34height:50px&#34
|Peter
|Savadjiev
|BWH (PNL)
|- style=&#34height:50px&#34
|Doug
|Terry
|BWH (PNL)
|- style=&#34height:50px&#34
|Andrew
|Rausch
|BWH (Mon only)
|- style=&#34height:50px&#34
|Cal
|Hisley
|Des Moines Unive
|- style=&#34height:50px&#34
|Jim
|Miller
|GE
|- style=&#34height:50px&#34
|Xiaodong
|Tao
|GE
|- style=&#34height:50px&#34
|Vandana
|Mohan
|GA Tech
|- style=&#34height:50px&#34
|Yi
|Gao
|GA Tech
|- style=&#34height:50px&#34
|Ivan
|Kolosev
|GA Tech
|- style=&#34height:50px&#34
|Behnood
|Gholami
|GA Tech
|- style=&#34height:50px&#34
|Ziv
|Yaniv
|Georgetown
|- style=&#34height:50px&#34
|Alex
|Gouaillard
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Arnaud
|Gelas
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Sean
|Megason
|Harvard Systems Biology (Wed only)
|- style=&#34height:50px&#34
|Lydie
|Souhait
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Moti
|Freiman
|Hebrew University of Jerusalem
|- style=&#34height:50px&#34
|Amanda
|Peters
|Harvard SEAS
|- style=&#34height:50px&#34
|Maria Francesca
|Spadea
|Italy
|- style=&#34height:50px&#34
|Curtis
|Lisle
|KnowledgeVis
|- style=&#34height:50px&#34
|Steve
|Pieper
|Isomics
|- style=&#34height:50px&#34
|Alex
|Yarmarkovich
|Isomics
|- style=&#34height:50px&#34
|Nathan
|Cho
|JHU
|- style=&#34height:50px&#34
|Bennett
|Landman
|JHU
|- style=&#34height:50px&#34
|Snehashis
|Roy
|JHU
|- style=&#34height:50px&#34
|Sam
|Song
|JHU
|- style=&#34height:50px&#34
|Sebastien
|Barre
|Kitware
|- style=&#34height:50px&#34
|Luis
|Ibanez
|Kitware
|- style=&#34height:50px&#34
|Daniel
|Blezek
|Mayo
|- style=&#34height:50px&#34
|Yong
|Gao
|MGH
|- style=&#34height:50px&#34
|Randy
|Gollub
|MGH
|- style=&#34height:50px&#34
|Rui
|Li
|MGH
|- style=&#34height:50px&#34
|Greg
|Sharp
|MGH
|- style=&#34height:50px&#34
|Robert
|Yaffe
|MGH - Mon
|- style=&#34height:50px&#34
|Sylvain
|Jaume
|MIT
|- style=&#34height:50px&#34
|Bjoern
|Menze
|MIT
|- style=&#34height:50px&#34
|Jeremy
|Bockholt
|MRN (NAMIC Lupus DBP)
|- style=&#34height:50px&#34
|Mark
|Scully
|MRN (NAMIC Lupus DBP) Tue-Th
|- style=&#34height:50px&#34
|Joe
|Stam
|NVIDIA (Wed & Thurs)
|- style=&#34height:50px&#34
|Kimberly
|Powell
|NVIDIA (Wed)
|- style=&#34height:50px&#34
|Marta
|Peroni
|Politecnico di Milano
|- style=&#34height:50px&#34
|Andras
|Lasso
|Queen's (NAMIC DBP)
|- style=&#34height:50px&#34
|Yanling
|Liu
|SAIC/NCI-Frederick
|- style=&#34height:50px&#34
|Melanie
|Grebe
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Lining
|Yang
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Harish
|Doddi
|Stanford University
|- style=&#34height:50px&#34
|Marco
|Ruiz
|UCSD
|- style=&#34height:50px&#34
|Nathan
|Hageman
|UCLA (Mon-Thurs)
|- style=&#34height:50px&#34
|Hans
|Johnson
|U Iowa
|- style=&#34height:50px&#34
|Vincent
|Magnotta
|U Iowa
|- style=&#34height:50px&#34
|Jeffrey
|Yager
|U Iowa
|- style=&#34height:50px&#34
|Manasi
|Ramachandran
|U Iowa
|- style=&#34height:50px&#34
|Dave
|Welch
|U Iowa
|- style=&#34height:50px&#34
|Andrzej
|Przybyszewski
|UMass Med (Mon)
|- style=&#34height:50px&#34
|James
|Balter
|U Michigan
|- style=&#34height:50px&#34
|Dan
|McShan
|U Michigan
|- style=&#34height:50px&#34
|Zhou
|Shen
|U Michigan
|- style=&#34height:50px&#34
|Beatriz
|Paniagua
|UNC
|- style=&#34height:50px&#34
|Minjeong
|Kim
|UNC
|- style=&#34height:50px&#34
|Zhexing
|Liu
|UNC
|- style=&#34height:50px&#34
|Clement
|Vachet
|UNC (NAMIC DBP)
|- style=&#34height:50px&#34
|Guorong
|Wu
|UNC
|- style=&#34height:50px&#34
|Samuel
|Gerber
|SCI, Utah
|- style=&#34height:50px&#34
|Ran
|Tao
|SCI, Utah
|- style=&#34height:50px&#34
|Marcel
|Prastawa
|SCI, Utah
|- style=&#34height:50px&#34
|Ross
|Whitaker
|SCI, Utah
|- style=&#34height:50px&#34
|Curtis
|Rueden
|UW-Madison
|- style=&#34height:50px&#34
|Dan
|Marcus
|WUSTL
|- style=&#34height:50px&#34
|Misha
|Milchenko
|WUSTL
|- style=&#34height:50px&#34
|Kevin
|Archie
|WUSTL
|- style=&#34height:50px&#34
|Tim
|Olsen
|WUSTL
|- style=&#34height:50px&#34
|Mehdi
|Esteghamatian
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Diego
|Cantor
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Danielle
|Pace
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Vidya
|Rajagopalan
|VA Tech
|- style=&#34height:50px&#34
|Gregory
|Fischer
|WPI
|- style=&#34height:50px&#34
|Dominique
|Belhachemi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Alark
|Joshi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Xenios
|Papademetris
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Dustin
|Scheinost
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Michelle
|Borkin
|Harvard SEAS (Mon only)
|- style=&#34height:50px&#34
|Renxin
|Chu
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Ben
|Schwartz
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Marianna
|Jakab
|BWH (NCIGT, NAC) (Mon, Tue)
|- style=&#34height:50px&#34
|Viswanath
|Avasarala
|GE (Wed, Thurs)
|- style=&#34height:50px&#34
|Michal
|Depa
|MIT
|- style=&#34height:50px&#34
|}
|}

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''

The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php

2009 Summer Project Week

2009-06-23T19:29:21Z

Mruiz:

Back to [[Project Events]], [[Events]]

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-G451 (in Stata)
**Tue, Wed, Thursday 9am to end
*32-D463 (Star conference room in Stata)
**Tuesday all day
**Wednesday 9-11:30, 1:30-end
*32-D451 (in Stata)
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 16th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
Breakout Rooms: 32-D451, 38-413

=== Monday===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
=== Tuesday ===
** 8:30am breakfast
** 8:30am-9:30am [[2009_Summer_Project_Week_4D_Imaging_discussion| 4D Imaging Meeting]]
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper) ([[media:2009 NA-MIC Project Week Slicer3.4.ppt|Slides]], [[2009_Summer_Project_Week_Extension_Manager|Project Page]])
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata [[Media:2009SummerProgrammingWeekHataIGT.ppt‎|Slides]], Scott Hoge [ [[Media:2009_NA-MIC_Project_Week_FastImagingLibrary.ppt|slides]] ])
** noon lunch
** 1pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W) (Star D463 Star Conference Room in Stata)
** 2:00pm-3.00pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis) (In Grier)
** 3:30pm: [[2009_Summer_Project_Week_GWE_Setup| GWE End-To-End Live Demo]] (Marco Ruiz)
** 4:30pm [http://www.cimit.org/forum-current.html CIMIT Forum (At BWH / Carl J. and Ruth Shapiro Cardiovascular Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc. ]
** 5:30pm adjourn for day

=== Wednesday ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (32-G451) (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (D463 Star conference room) (Alexandre Gouaillard)
** 5:30pm adjourn for day

=== Thursday===
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (32-G451) (Dan M.)
** 5:30pm adjourn for day

=== Friday===
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

==Projects==

=== Segmentation ===

#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation|Lupus Lesion Segmentation]] (Mark Scully MRN)
#[[2009_Summer_Project_Week_WML_SEgmentation|White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week_Skull_Stripping|Skull Stripping]] (Snehasish Roy JHU)
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation|FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)
#[[Summer2009:The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)
#[[2009 Summer Project Week Quantify VMTK seg error|Quantifying VMTK User Segmentation Error]] (Dave Welch UIowa)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Atrium_wall|Atrium Wall Segmentation]] (Behnood Gholami Georgia Tech)

=== Registration ===

#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration|Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
#[[BSpline Registration in Slicer3|BSpline Registration in Slicer3]] (Samuel Gerber Utah)
#[[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)
#[[2009_Summer_Project_Week_Slicer3_registration|Slicer 3 registration ]] (Andrew Rausch BWH PNL)
#[[EPI Correction in Slicer3|EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)
#[[2009_Summer_Project_Week_HAMMER_Registration|HAMMER Registration]] (Guorong Wu UNC)
#[[2009_Summer_Project_Week_MCMC_Cuda_Registration|Elastic Non-Rigid Registration using MCMC and CUDA]] (Petter Risholm BWH)
#[[2009_Summer_Project_Week_Cardiac_Blood_Pool_Registration|Cardiac Blood Pool Registration]] (Michal Depa MIT)

=== IGT ===

#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_Prostate_Robotics|Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)
#[[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
#[[Enhanced Neurosuregery navigation]] (Haytham Elhawary, Brigham and Women's Hospital)
#[[GPU accelerated FEM for simulation and segmentation]] (Megumi Nakao, Brigham and Women's Hospital)
#[[Liver EM segmentation]] (Padma Akella, Brigham and Women's Hlspital)
#[[MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement]] (Greg Fischer, WPI)

=== Radiotherapy ===

#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Adaptive_RT|Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov GATech)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](James Balter U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[2009_Summer_project_week_adaptive_radiation_planning_visualization]](Cal Hisley, Des Moines University/Mercy Des Moines Medical Center)

=== Analysis ===

#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Linking atlas data with ontologies of brain morphology and function]] (Michael Halle BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Imaging|4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer|Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox|multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)

=== Informatics ===

#[[2009_Summer_Project_Week_Slicer3_XNAT_UI|XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS|XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_GWE_XNAT|GWE-XNAT Integration]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_GWE_Results_Browser|GWE Results Browser Improvements]] (Marco Ruiz UCSD)
#[[Projects:ShapeCorrespondence_UNCOrthoApp|XNAT & Ortho App]] (Beatriz Paniagua UNC)

=== Diffusion ===

#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Sylvain Bouix BWH)
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep|DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom|DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_FMTractography|Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)

=== Python ===

#[[Summer2009:Using_ITK_in_python|Using ITK in python]] (Steve Pieper BWH)
#[[Summer2009:Using_cython|Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
#[[Summer2009:Implementing_parallelism_in_python|Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
#[[Summer2009:Using_client_server_paradigm_with_python_and_slicer|Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)

=== Slicer Internals ===

#[[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Colors_Module|Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)
#[[Slicer3 Informatics Workflow Design & XNAT updates|Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
#[[Slicer3_FlexibleLayouts | Slicer3 Flexible Layouts]] (Wendy Plesniak BWH)
#[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)
#[[MeshingSummer2009|IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)

=== Execution Model ===

#[[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
#[[Summer2009:Extension of the Command Line XML Syntax/Interface|Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Attendee List==

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''
{|
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{|class="wikitable"
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|81
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|- style=&#34height:50px&#34
|84
|- style=&#34height:50px&#34
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|86
|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
|88
|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
|93
|- style=&#34height:50px&#34
|91
|- style=&#34height:50px&#34
|92
|- style=&#34height:50px&#34
|94
|- style=&#34height:50px&#34
|95
|- style=&#34height:50px&#34
|96
|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
|98
|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
|102
|- style=&#34height:50px&#34
|103
|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
|105
|- style=&#34height:50px&#34
|106
|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
|110
|- style=&#34height:50px&#34
|111
|- style=&#34height:50px&#34
|112
|- style=&#34height:50px&#34
|113
|- style=&#34height:50px&#34
|114
|- style=&#34height:50px&#34
|115
|- style=&#34height:50px&#34
|116
|- style=&#34height:50px&#34
|117
|- style=&#34height:50px&#34
|118
|- style=&#34height:50px&#34
|119
|- style=&#34height:50px&#34
|120
|- style=&#34height:50px&#34
|121
|- style=&#34height:50px&#34
|122
|- style=&#34height:50px&#34
|123
|- style=&#34height:50px&#34
|124
|- style=&#34height:50px&#34
|125
|- style=&#34height:50px&#34
|}
|
{| class="wikitable sortable"
!First
!Last
!Affiliation
|- style=&#34height:50px&#34
|John
|Melonakos
|AccelerEyes (Wed & Thu morning)
|- style=&#34height:50px&#34
|Jack
|Blevins
|Acoustic Med
|- style=&#34height:50px&#34
|Clif
|Burdette
|Acoustic Med (Mon-Wed)
|- style=&#34height:50px&#34
|Dana
|Peters
|Beth Israel Deaconess
|- style=&#34height:50px&#34
|Nicole
|Aucoin
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Giovanna
|Danagoulian
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haytham
|Elhawary
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Andriy
|Fedorov
|BWH (NAMIC Collaborator)
|- style=&#34height:50px&#34
|Daniel
|Haehn
|BWH (NAC)
|- style=&#34height:50px&#34
|Michael
|Halle
|BWH (NAC)
|- style=&#34height:50px&#34
|Nobuhiko
|Hata
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Katie
|Hayes
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Scott
|Hoge
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Tina
|Kapur
|BWH (NCIGT, NAMIC)
|- style=&#34height:50px&#34
|Ron
|Kikinis
|BWH (NAMIC, NAC, NCIGT)
|- style=&#34height:50px&#34
|Jayender
|Jagadeesan
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haying
|Liu
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Lauren
|O'Donnell
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Wendy
|Plesniak
|BWH (NAC)
|- style=&#34height:50px&#34
|Megumi
|Nakao
|BWH (NAIST)
|- style=&#34height:50px&#34
|Sonia
|Pujol
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Lei
|Qin
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Nicolas
|Rannou
|BWH (NAC)
|- style=&#34height:50px&#34
|Petter
|Risholm
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Florin
|Talos
|BWH (NAC)
|- style=&#34height:50px&#34
|Clare
|Tempany
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Junichi
|Tokuda
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Demian
|Wasserman
|BWH (INRIA)
|- style=&#34height:50px&#34
|Carl-Fredrik
|Westin
|BWH (NAC)
|- style=&#34height:50px&#34
|Sandy
|Wells
|BWH (NAC, NCIGT)
|- style=&#34height:50px&#34
|Lilla
|Zollei
|MGH (NAC)
|- style=&#34height:50px&#34
|Padma
|Akella
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Sylvain
|Bouix
|BWH (PNL)
|- style=&#34height:50px&#34
|Julien
|de Siebenthal
|BWH (PNL)
|- style=&#34height:50px&#34
|Marek
|Kubicki
|BWH (NAMIC DBP PNL)
|- style=&#34height:50px&#34
|Juhana
|Frosen
|BWH Tues only
|- style=&#34height:50px&#34
|Sun Woo
|Lee
|BWH (PNL)
|- style=&#34height:50px&#34
|Jimi
|Malcolm
|BWH (PNL)
|- style=&#34height:50px&#34
|Eric
|Melonakos
|BWH (PNL)
|- style=&#34height:50px&#34
|Yogesh
|Rathi
|BWH (PNL)
|- style=&#34height:50px&#34
|Peter
|Savadjiev
|BWH (PNL)
|- style=&#34height:50px&#34
|Doug
|Terry
|BWH (PNL)
|- style=&#34height:50px&#34
|Andrew
|Rausch
|BWH (Mon only)
|- style=&#34height:50px&#34
|Cal
|Hisley
|Des Moines Unive
|- style=&#34height:50px&#34
|Jim
|Miller
|GE
|- style=&#34height:50px&#34
|Xiaodong
|Tao
|GE
|- style=&#34height:50px&#34
|Vandana
|Mohan
|GA Tech
|- style=&#34height:50px&#34
|Yi
|Gao
|GA Tech
|- style=&#34height:50px&#34
|Ivan
|Kolosev
|GA Tech
|- style=&#34height:50px&#34
|Behnood
|Gholami
|GA Tech
|- style=&#34height:50px&#34
|Ziv
|Yaniv
|Georgetown
|- style=&#34height:50px&#34
|Alex
|Gouaillard
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Arnaud
|Gelas
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Sean
|Megason
|Harvard Systems Biology (Wed only)
|- style=&#34height:50px&#34
|Lydie
|Souhait
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Moti
|Freiman
|Hebrew University of Jerusalem
|- style=&#34height:50px&#34
|Amanda
|Peters
|Harvard SEAS
|- style=&#34height:50px&#34
|Maria Francesca
|Spadea
|Italy
|- style=&#34height:50px&#34
|Curtis
|Lisle
|KnowledgeVis
|- style=&#34height:50px&#34
|Steve
|Pieper
|Isomics
|- style=&#34height:50px&#34
|Alex
|Yarmarkovich
|Isomics
|- style=&#34height:50px&#34
|Nathan
|Cho
|JHU
|- style=&#34height:50px&#34
|Bennett
|Landman
|JHU
|- style=&#34height:50px&#34
|Snehashis
|Roy
|JHU
|- style=&#34height:50px&#34
|Sam
|Song
|JHU
|- style=&#34height:50px&#34
|Sebastien
|Barre
|Kitware
|- style=&#34height:50px&#34
|Luis
|Ibanez
|Kitware
|- style=&#34height:50px&#34
|Daniel
|Blezek
|Mayo
|- style=&#34height:50px&#34
|Yong
|Gao
|MGH
|- style=&#34height:50px&#34
|Randy
|Gollub
|MGH
|- style=&#34height:50px&#34
|Rui
|Li
|MGH
|- style=&#34height:50px&#34
|Greg
|Sharp
|MGH
|- style=&#34height:50px&#34
|Robert
|Yaffe
|MGH - Mon
|- style=&#34height:50px&#34
|Sylvain
|Jaume
|MIT
|- style=&#34height:50px&#34
|Bjoern
|Menze
|MIT
|- style=&#34height:50px&#34
|Jeremy
|Bockholt
|MRN (NAMIC Lupus DBP)
|- style=&#34height:50px&#34
|Mark
|Scully
|MRN (NAMIC Lupus DBP) Tue-Th
|- style=&#34height:50px&#34
|Joe
|Stam
|NVIDIA (Wed & Thurs)
|- style=&#34height:50px&#34
|Kimberly
|Powell
|NVIDIA (Wed)
|- style=&#34height:50px&#34
|Marta
|Peroni
|Politecnico di Milano
|- style=&#34height:50px&#34
|Andras
|Lasso
|Queen's (NAMIC DBP)
|- style=&#34height:50px&#34
|Yanling
|Liu
|SAIC/NCI-Frederick
|- style=&#34height:50px&#34
|Melanie
|Grebe
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Lining
|Yang
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Harish
|Doddi
|Stanford University
|- style=&#34height:50px&#34
|Marco
|Ruiz
|UCSD
|- style=&#34height:50px&#34
|Nathan
|Hageman
|UCLA (Mon-Thurs)
|- style=&#34height:50px&#34
|Hans
|Johnson
|U Iowa
|- style=&#34height:50px&#34
|Vincent
|Magnotta
|U Iowa
|- style=&#34height:50px&#34
|Jeffrey
|Yager
|U Iowa
|- style=&#34height:50px&#34
|Manasi
|Ramachandran
|U Iowa
|- style=&#34height:50px&#34
|Dave
|Welch
|U Iowa
|- style=&#34height:50px&#34
|Andrzej
|Przybyszewski
|UMass Med (Mon)
|- style=&#34height:50px&#34
|James
|Balter
|U Michigan
|- style=&#34height:50px&#34
|Dan
|McShan
|U Michigan
|- style=&#34height:50px&#34
|Zhou
|Shen
|U Michigan
|- style=&#34height:50px&#34
|Beatriz
|Paniagua
|UNC
|- style=&#34height:50px&#34
|Minjeong
|Kim
|UNC
|- style=&#34height:50px&#34
|Zhexing
|Liu
|UNC
|- style=&#34height:50px&#34
|Clement
|Vachet
|UNC (NAMIC DBP)
|- style=&#34height:50px&#34
|Guorong
|Wu
|UNC
|- style=&#34height:50px&#34
|Samuel
|Gerber
|SCI, Utah
|- style=&#34height:50px&#34
|Ran
|Tao
|SCI, Utah
|- style=&#34height:50px&#34
|Marcel
|Prastawa
|SCI, Utah
|- style=&#34height:50px&#34
|Ross
|Whitaker
|SCI, Utah
|- style=&#34height:50px&#34
|Curtis
|Rueden
|UW-Madison
|- style=&#34height:50px&#34
|Dan
|Marcus
|WUSTL
|- style=&#34height:50px&#34
|Misha
|Milchenko
|WUSTL
|- style=&#34height:50px&#34
|Kevin
|Archie
|WUSTL
|- style=&#34height:50px&#34
|Tim
|Olsen
|WUSTL
|- style=&#34height:50px&#34
|Mehdi
|Esteghamatian
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Diego
|Cantor
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Danielle
|Pace
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Vidya
|Rajagopalan
|VA Tech
|- style=&#34height:50px&#34
|Gregory
|Fischer
|WPI
|- style=&#34height:50px&#34
|Dominique
|Belhachemi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Alark
|Joshi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Xenios
|Papademetris
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Dustin
|Scheinost
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Michelle
|Borkin
|Harvard SEAS (Mon only)
|- style=&#34height:50px&#34
|Renxin
|Chu
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Ben
|Schwartz
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Marianna
|Jakab
|BWH (NCIGT, NAC) (Mon, Tue)
|- style=&#34height:50px&#34
|Viswanath
|Avasarala
|GE (Wed, Thurs)
|- style=&#34height:50px&#34
|Michal
|Depa
|MIT
|- style=&#34height:50px&#34
|}
|}

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''

The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php

2009 Summer Project Week

2009-06-23T17:00:42Z

Mruiz:

Back to [[Project Events]], [[Events]]

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-G451 (in Stata)
**Tue, Wed, Thursday 9am to end
*32-D463 (Star conference room in Stata)
**Tuesday all day
**Wednesday 9-11:30, 1:30-end
*32-D451 (in Stata)
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 16th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
Breakout Rooms: 32-D451, 38-413

=== Monday===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
=== Tuesday ===
** 8:30am breakfast
** 8:30am-9:30am [[2009_Summer_Project_Week_4D_Imaging_discussion| 4D Imaging Meeting]]
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper) ([[media:2009 NA-MIC Project Week Slicer3.4.ppt|Slides]], [[2009_Summer_Project_Week_Extension_Manager|Project Page]])
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata [[Media:2009SummerProgrammingWeekHataIGT.ppt‎|Slides]], Scott Hoge [ [[Media:2009_NA-MIC_Project_Week_FastImagingLibrary.ppt|slides]] ])
** noon lunch
** 1pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W) (Star D463 Star Conference Room in Stata)
** 2:00pm-3.00pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis) (In Grier)
** 3:30pm: [[2009_Summer_Project_Week_GWE_Setup| GWE Setup and Usage]] (Marco Ruiz)
** 4:30pm [http://www.cimit.org/forum-current.html CIMIT Forum (At BWH / Carl J. and Ruth Shapiro Cardiovascular Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc. ]
** 5:30pm adjourn for day

=== Wednesday ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (32-G451) (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (D463 Star conference room) (Alexandre Gouaillard)
** 5:30pm adjourn for day

=== Thursday===
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (32-G451) (Dan M.)
** 5:30pm adjourn for day

=== Friday===
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

==Projects==

=== Segmentation ===

#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation|Lupus Lesion Segmentation]] (Mark Scully MRN)
#[[2009_Summer_Project_Week_WML_SEgmentation|White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week_Skull_Stripping|Skull Stripping]] (Snehasish Roy JHU)
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation|FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)
#[[Summer2009:The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)
#[[2009 Summer Project Week Quantify VMTK seg error|Quantifying VMTK User Segmentation Error]] (Dave Welch UIowa)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Atrium_wall|Atrium Wall Segmentation]] (Behnood Gholami Georgia Tech)

=== Registration ===

#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration|Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
#[[BSpline Registration in Slicer3|BSpline Registration in Slicer3]] (Samuel Gerber Utah)
#[[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)
#[[2009_Summer_Project_Week_Slicer3_registration|Slicer 3 registration ]] (Andrew Rausch BWH PNL)
#[[EPI Correction in Slicer3|EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)
#[[2009_Summer_Project_Week_HAMMER_Registration|HAMMER Registration]] (Guorong Wu UNC)
#[[2009_Summer_Project_Week_MCMC_Cuda_Registration|Elastic Non-Rigid Registration using MCMC and CUDA]] (Petter Risholm BWH)
#[[2009_Summer_Project_Week_Cardiac_Blood_Pool_Registration|Cardiac Blood Pool Registration]] (Michal Depa MIT)

=== IGT ===

#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_Prostate_Robotics|Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)
#[[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
#[[Enhanced Neurosuregery navigation]] (Haytham Elhawary, Brigham and Women's Hospital)
#[[GPU accelerated FEM for simulation and segmentation]] (Megumi Nakao, Brigham and Women's Hospital)
#[[Liver EM segmentation]] (Padma Akella, Brigham and Women's Hlspital)
#[[MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement]] (Greg Fischer, WPI)

=== Radiotherapy ===

#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Adaptive_RT|Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov GATech)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](James Balter U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[2009_Summer_project_week_adaptive_radiation_planning_visualization]](Cal Hisley, Des Moines University/Mercy Des Moines Medical Center)

=== Analysis ===

#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Linking atlas data with ontologies of brain morphology and function]] (Michael Halle BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Imaging|4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer|Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox|multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)

=== Informatics ===

#[[2009_Summer_Project_Week_Slicer3_XNAT_UI|XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS|XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_GWE_XNAT|GWE-XNAT Integration]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_GWE_Results_Browser|GWE Results Browser Improvements]] (Marco Ruiz UCSD)
#[[Projects:ShapeCorrespondence_UNCOrthoApp|XNAT & Ortho App]] (Beatriz Paniagua UNC)

=== Diffusion ===

#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Sylvain Bouix BWH)
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep|DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom|DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_FMTractography|Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)

=== Python ===

#[[Summer2009:Using_ITK_in_python|Using ITK in python]] (Steve Pieper BWH)
#[[Summer2009:Using_cython|Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
#[[Summer2009:Implementing_parallelism_in_python|Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
#[[Summer2009:Using_client_server_paradigm_with_python_and_slicer|Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)

=== Slicer Internals ===

#[[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Colors_Module|Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)
#[[Slicer3 Informatics Workflow Design & XNAT updates|Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
#[[Slicer3_FlexibleLayouts | Slicer3 Flexible Layouts]] (Wendy Plesniak BWH)
#[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)
#[[MeshingSummer2009|IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)

=== Execution Model ===

#[[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
#[[Summer2009:Extension of the Command Line XML Syntax/Interface|Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Attendee List==

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''
{|
|-
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{|class="wikitable"
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|}
|
{| class="wikitable sortable"
!First
!Last
!Affiliation
|- style=&#34height:50px&#34
|John
|Melonakos
|AccelerEyes (Wed & Thu morning)
|- style=&#34height:50px&#34
|Jack
|Blevins
|Acoustic Med
|- style=&#34height:50px&#34
|Clif
|Burdette
|Acoustic Med (Mon-Wed)
|- style=&#34height:50px&#34
|Dana
|Peters
|Beth Israel Deaconess
|- style=&#34height:50px&#34
|Nicole
|Aucoin
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Giovanna
|Danagoulian
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haytham
|Elhawary
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Andriy
|Fedorov
|BWH (NAMIC Collaborator)
|- style=&#34height:50px&#34
|Daniel
|Haehn
|BWH (NAC)
|- style=&#34height:50px&#34
|Michael
|Halle
|BWH (NAC)
|- style=&#34height:50px&#34
|Nobuhiko
|Hata
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Katie
|Hayes
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Scott
|Hoge
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Tina
|Kapur
|BWH (NCIGT, NAMIC)
|- style=&#34height:50px&#34
|Ron
|Kikinis
|BWH (NAMIC, NAC, NCIGT)
|- style=&#34height:50px&#34
|Jayender
|Jagadeesan
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haying
|Liu
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Lauren
|O'Donnell
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Wendy
|Plesniak
|BWH (NAC)
|- style=&#34height:50px&#34
|Megumi
|Nakao
|BWH (NAIST)
|- style=&#34height:50px&#34
|Sonia
|Pujol
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Lei
|Qin
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Nicolas
|Rannou
|BWH (NAC)
|- style=&#34height:50px&#34
|Petter
|Risholm
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Florin
|Talos
|BWH (NAC)
|- style=&#34height:50px&#34
|Clare
|Tempany
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Junichi
|Tokuda
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Demian
|Wasserman
|BWH (INRIA)
|- style=&#34height:50px&#34
|Carl-Fredrik
|Westin
|BWH (NAC)
|- style=&#34height:50px&#34
|Sandy
|Wells
|BWH (NAC, NCIGT)
|- style=&#34height:50px&#34
|Lilla
|Zollei
|MGH (NAC)
|- style=&#34height:50px&#34
|Padma
|Akella
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Sylvain
|Bouix
|BWH (PNL)
|- style=&#34height:50px&#34
|Julien
|de Siebenthal
|BWH (PNL)
|- style=&#34height:50px&#34
|Marek
|Kubicki
|BWH (NAMIC DBP PNL)
|- style=&#34height:50px&#34
|Juhana
|Frosen
|BWH Tues only
|- style=&#34height:50px&#34
|Sun Woo
|Lee
|BWH (PNL)
|- style=&#34height:50px&#34
|Jimi
|Malcolm
|BWH (PNL)
|- style=&#34height:50px&#34
|Eric
|Melonakos
|BWH (PNL)
|- style=&#34height:50px&#34
|Yogesh
|Rathi
|BWH (PNL)
|- style=&#34height:50px&#34
|Peter
|Savadjiev
|BWH (PNL)
|- style=&#34height:50px&#34
|Doug
|Terry
|BWH (PNL)
|- style=&#34height:50px&#34
|Andrew
|Rausch
|BWH (Mon only)
|- style=&#34height:50px&#34
|Cal
|Hisley
|Des Moines Unive
|- style=&#34height:50px&#34
|Jim
|Miller
|GE
|- style=&#34height:50px&#34
|Xiaodong
|Tao
|GE
|- style=&#34height:50px&#34
|Vandana
|Mohan
|GA Tech
|- style=&#34height:50px&#34
|Yi
|Gao
|GA Tech
|- style=&#34height:50px&#34
|Ivan
|Kolosev
|GA Tech
|- style=&#34height:50px&#34
|Behnood
|Gholami
|GA Tech
|- style=&#34height:50px&#34
|Ziv
|Yaniv
|Georgetown
|- style=&#34height:50px&#34
|Alex
|Gouaillard
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Arnaud
|Gelas
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Sean
|Megason
|Harvard Systems Biology (Wed only)
|- style=&#34height:50px&#34
|Lydie
|Souhait
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Moti
|Freiman
|Hebrew University of Jerusalem
|- style=&#34height:50px&#34
|Amanda
|Peters
|Harvard SEAS
|- style=&#34height:50px&#34
|Maria Francesca
|Spadea
|Italy
|- style=&#34height:50px&#34
|Curtis
|Lisle
|KnowledgeVis
|- style=&#34height:50px&#34
|Steve
|Pieper
|Isomics
|- style=&#34height:50px&#34
|Alex
|Yarmarkovich
|Isomics
|- style=&#34height:50px&#34
|Nathan
|Cho
|JHU
|- style=&#34height:50px&#34
|Bennett
|Landman
|JHU
|- style=&#34height:50px&#34
|Snehashis
|Roy
|JHU
|- style=&#34height:50px&#34
|Sam
|Song
|JHU
|- style=&#34height:50px&#34
|Sebastien
|Barre
|Kitware
|- style=&#34height:50px&#34
|Luis
|Ibanez
|Kitware
|- style=&#34height:50px&#34
|Daniel
|Blezek
|Mayo
|- style=&#34height:50px&#34
|Yong
|Gao
|MGH
|- style=&#34height:50px&#34
|Randy
|Gollub
|MGH
|- style=&#34height:50px&#34
|Rui
|Li
|MGH
|- style=&#34height:50px&#34
|Greg
|Sharp
|MGH
|- style=&#34height:50px&#34
|Robert
|Yaffe
|MGH - Mon
|- style=&#34height:50px&#34
|Sylvain
|Jaume
|MIT
|- style=&#34height:50px&#34
|Bjoern
|Menze
|MIT
|- style=&#34height:50px&#34
|Jeremy
|Bockholt
|MRN (NAMIC Lupus DBP)
|- style=&#34height:50px&#34
|Mark
|Scully
|MRN (NAMIC Lupus DBP) Tue-Th
|- style=&#34height:50px&#34
|Joe
|Stam
|NVIDIA (Wed & Thurs)
|- style=&#34height:50px&#34
|Kimberly
|Powell
|NVIDIA (Wed)
|- style=&#34height:50px&#34
|Marta
|Peroni
|Politecnico di Milano
|- style=&#34height:50px&#34
|Andras
|Lasso
|Queen's (NAMIC DBP)
|- style=&#34height:50px&#34
|Yanling
|Liu
|SAIC/NCI-Frederick
|- style=&#34height:50px&#34
|Melanie
|Grebe
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Lining
|Yang
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Harish
|Doddi
|Stanford University
|- style=&#34height:50px&#34
|Marco
|Ruiz
|UCSD
|- style=&#34height:50px&#34
|Nathan
|Hageman
|UCLA (Mon-Thurs)
|- style=&#34height:50px&#34
|Hans
|Johnson
|U Iowa
|- style=&#34height:50px&#34
|Vincent
|Magnotta
|U Iowa
|- style=&#34height:50px&#34
|Jeffrey
|Yager
|U Iowa
|- style=&#34height:50px&#34
|Manasi
|Ramachandran
|U Iowa
|- style=&#34height:50px&#34
|Dave
|Welch
|U Iowa
|- style=&#34height:50px&#34
|Andrzej
|Przybyszewski
|UMass Med (Mon)
|- style=&#34height:50px&#34
|James
|Balter
|U Michigan
|- style=&#34height:50px&#34
|Dan
|McShan
|U Michigan
|- style=&#34height:50px&#34
|Zhou
|Shen
|U Michigan
|- style=&#34height:50px&#34
|Beatriz
|Paniagua
|UNC
|- style=&#34height:50px&#34
|Minjeong
|Kim
|UNC
|- style=&#34height:50px&#34
|Zhexing
|Liu
|UNC
|- style=&#34height:50px&#34
|Clement
|Vachet
|UNC (NAMIC DBP)
|- style=&#34height:50px&#34
|Guorong
|Wu
|UNC
|- style=&#34height:50px&#34
|Samuel
|Gerber
|SCI, Utah
|- style=&#34height:50px&#34
|Ran
|Tao
|SCI, Utah
|- style=&#34height:50px&#34
|Marcel
|Prastawa
|SCI, Utah
|- style=&#34height:50px&#34
|Ross
|Whitaker
|SCI, Utah
|- style=&#34height:50px&#34
|Curtis
|Rueden
|UW-Madison
|- style=&#34height:50px&#34
|Dan
|Marcus
|WUSTL
|- style=&#34height:50px&#34
|Misha
|Milchenko
|WUSTL
|- style=&#34height:50px&#34
|Kevin
|Archie
|WUSTL
|- style=&#34height:50px&#34
|Tim
|Olsen
|WUSTL
|- style=&#34height:50px&#34
|Mehdi
|Esteghamatian
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Diego
|Cantor
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Danielle
|Pace
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Vidya
|Rajagopalan
|VA Tech
|- style=&#34height:50px&#34
|Gregory
|Fischer
|WPI
|- style=&#34height:50px&#34
|Dominique
|Belhachemi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Alark
|Joshi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Xenios
|Papademetris
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Dustin
|Scheinost
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Michelle
|Borkin
|Harvard SEAS (Mon only)
|- style=&#34height:50px&#34
|Renxin
|Chu
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Ben
|Schwartz
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Marianna
|Jakab
|BWH (NCIGT, NAC) (Mon, Tue)
|- style=&#34height:50px&#34
|Viswanath
|Avasarala
|GE (Wed, Thurs)
|- style=&#34height:50px&#34
|Michal
|Depa
|MIT
|- style=&#34height:50px&#34
|}
|}

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''

The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php

2009 Summer Project Week GWE XNAT

2009-06-19T10:43:23Z

Mruiz:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:GweLogoSquare.png‎|[http://www.gridwizardenterprise.org GWE: Platform to run parameter exploration experiments]
</gallery>

==Key Investigators==
* UCSD: Marco Ruiz
* WU: Dan Marcus

<div style="margin: 20px;">
<div style="width: 22%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Collect specifications for P2EL macros/functions to upload data into XNAT systems.
* Review and refine production P2EL macros created to query XNAT systems (experiments, session, scans, images, etc.)
* Collect specifications for any other XNAT querying P2EL macros that may be useful to describe parameter exploration experiments.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Demo current state of XNAT querying support on GWE and share vision for how researchers can benefit and use it when running parameter exploration experiments.
* Discuss usability/feasibility of the vision to set a practical direction for this integration effort.
* Gather specs for the XNAT REST API to implement data upload and for the modications/additions of P2EL macros.
* Gather information about future modifications/gray areas on the XNAT REST API so can be considered in this integration effort.
</div>

<div style="width: 45%; float: left;">

<h3>Progress</h3>
* GWE 0.7.3.alpha (latest release) includes a [http://www.gridwizardenterprise.org/svn/gwe/gwe-core/trunk/src/main/config/base/gwe-macros/xnat.p2el P2EL macro library to support common querying operations].
* Some of these macros are currently misbehaving due to minor changes in the XNAT REST API. A "patch release" will be released before the project week to accomodate these changes.
</div>

<br style="clear: both;" />

</div>

===References===

*GWE Project Site: http://www.gridwizardenterprise.org
*P2EL Macros: http://www.gridwizardenterprise.org/guides/p2el-macros.html
*P2EL Macro Library for XNAT: http://www.gridwizardenterprise.org/svn/gwe/gwe-core/trunk/src/main/config/base/gwe-macros/xnat.p2el
*XNAT: http://www.xnat.org/
*XNAT REST API: http://nrg.wikispaces.com/XNAT+REST+API+Usage

2009 Summer Project Week GWE XNAT

2009-06-19T10:36:24Z

Mruiz:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:GweLogoSquare.png‎|[http://www.gridwizardenterprise.org GWE: Platform to run parameter exploration experiments]
</gallery>

==Key Investigators==
* UCSD: Marco Ruiz
* WU: Dan Marcus

<div style="margin: 20px;">
<div style="width: 22%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Collect specifications for P2EL macros/functions to upload data into XNAT systems.
* Review and refine production P2EL macros created to query XNAT systems (experiments, session, scans, images, etc.)
* Collect specifications for any other XNAT querying P2EL macros that may be useful to describe parameter exploration experiments.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Demo current state of XNAT querying support on GWE and share vision for how researchers can benefit and use it when running parameter exploration experiments.
* Discuss usability/feasibility of the vision to set a practical direction for this integration effort.
* Gather specs for the XNAT REST API to implement data upload and for the modications/additions of P2EL macros.
* Gather information about future modifications/gray areas on the XNAT REST API so can be considered in this integration effort.
</div>

<div style="width: 45%; float: left;">

<h3>Progress</h3>
* GWE 0.7.3.alpha (latest release) includes a [http://www.gridwizardenterprise.org/svn/gwe/gwe-core/trunk/src/main/config/base/gwe-macros/xnat.p2el P2EL macro library to support common querying operations].
* Some of these macros are currently misbehaving due to minor changes in the XNAT REST API. A "patch release" will be released before the project week to accomodate these changes.
</div>

<br style="clear: both;" />

</div>

===References===

*GWE Project Site: http://www.gridwizardenterprise.org
*P2EL Macros: http://www.gridwizardenterprise.org/guides/p2el-macros.html
*P2EL Macro Library for XNAT: http://www.gridwizardenterprise.org/svn/gwe/gwe-core/trunk/src/main/config/base/gwe-macros/xnat.p2el
*XNAT: http://www.xnat.org/
*XNAT REST API: http://nrg.wikispaces.com/XNAT+REST+API+Usage

2009 Summer Project Week GWE Results Browser

2009-06-19T10:35:47Z

Mruiz: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page Image:GweLogoSquare.png‎|[http://www.gridwizardenterprise.org GWE: Platform to run p...'

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:GweLogoSquare.png‎|[http://www.gridwizardenterprise.org GWE: Platform to run parameter exploration experiments]
Image:Gwe_result_browser.png‎|GWE Experiment Results Browser
</gallery>

==Key Investigators==
* UCSD: Marco Ruiz
* Isomics: Steve Pieper
* BWH: Andriy Fedorov

<div style="margin: 20px;">
<div style="width: 22%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Determine the usability improvements and missing features for the GWE results browser prototype.
* Collect suggestions on desired interfaces to serve currently unresolved browsing scenarios, such as co-dependent variables.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Demo current state of the results browser.
* Describe currently resolved scenarios as well as unresolved ones such as co-dependent variables navigation.
* Describe limiting issues such as browsing media types located on remote clusters (size, network speed, etc) and rendering custom media types (pluggable rendering framework?)
* Open discussion and gather feedback.
</div>

<div style="width: 45%; float: left;">

<h3>Progress</h3>
* A prototype of the [http://wiki.na-mic.org/Wiki/index.php/File:Gwe_result_browser.png‎ experiment results browser] has been released in GWE 0.7.3.alpha (latest release) based on the ideas brainstormed a few months ago (during the [[GWE_MiniRetreat| GWE mini retreat]]).
* A [http://www.gridwizardenterprise.org YouTube video] has been created to show this prototype in action.
</div>

<br style="clear: both;" />

</div>

===References===

*GWE Project Site: http://www.gridwizardenterprise.org
*YouTube Demo Video: http://www.youtube.com/user/GWEGuides
*[[GWE_MiniRetreat| GWE Mini Retreat Report]]

2009 Summer Project Week

2009-06-19T09:52:11Z

Mruiz:

Back to [[Project Events]], [[Events]]

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 16th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-4pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 4:30pm CIMIT Forum (at BWH Shapiro Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc. At BWH / Carl J. and Ruth Shapiro Cardiovascular Cente
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alexandre Gouaillard)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

== Projects ==
#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation |Lupus Lesion Segmentation]] (Jeremy Bockholt MRN)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Snehasish Roy JHU)
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos BWH)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu UNC)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber Utah)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)
#[[2009_Summer_Project_Week_Slicer3_registration| Slicer 3 registration ]] (Andrew Rausch BWH PNL)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)
#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Marek Kubicki BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)
#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Adaptive_RT| Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov,Vandana Mohan,Gregory Sharp, and Allen Tannenbaum)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins Acousticmed)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#acceleration of parallel real time processing of strain and elasticity images for monitoring of ablative therapy (Clif Burdette Acousticmed)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve Pieper BWH)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_cython| Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_GWE_XNAT | GWE-XNAT Integration]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_GWE_Results_Browser | GWE Results Browser Improvements]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]
==Attendee List==

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''
{|
|-
|
{|class="wikitable"
!Number
|- style=&#34height:50px&#34
|1
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|39
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|40
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|41
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|42
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|43
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|44
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|45
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|46
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|47
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|48
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|49
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|50
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|51
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|52
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|53
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|54
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|55
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|56
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|57
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|58
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|59
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|60
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|61
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|62
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|63
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|64
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|65
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|66
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|67
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|68
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|69
|- style=&#34height:50px&#34
|70
|- style=&#34height:50px&#34
|71
|- style=&#34height:50px&#34
|72
|- style=&#34height:50px&#34
|73
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|74
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|75
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|76
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|77
|- style=&#34height:50px&#34
|78
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|79
|- style=&#34height:50px&#34
|80
|- style=&#34height:50px&#34
|81
|- style=&#34height:50px&#34
|82
|- style=&#34height:50px&#34
|83
|- style=&#34height:50px&#34
|84
|- style=&#34height:50px&#34
|85
|- style=&#34height:50px&#34
|86
|- style=&#34height:50px&#34
|87
|- style=&#34height:50px&#34
|88
|- style=&#34height:50px&#34
|89
|- style=&#34height:50px&#34
|90
|- style=&#34height:50px&#34
|93
|- style=&#34height:50px&#34
|91
|- style=&#34height:50px&#34
|92
|- style=&#34height:50px&#34
|94
|- style=&#34height:50px&#34
|95
|- style=&#34height:50px&#34
|96
|- style=&#34height:50px&#34
|97
|- style=&#34height:50px&#34
|98
|- style=&#34height:50px&#34
|99
|- style=&#34height:50px&#34
|100
|- style=&#34height:50px&#34
|101
|- style=&#34height:50px&#34
|102
|- style=&#34height:50px&#34
|103
|- style=&#34height:50px&#34
|104
|- style=&#34height:50px&#34
|105
|- style=&#34height:50px&#34
|106
|- style=&#34height:50px&#34
|107
|- style=&#34height:50px&#34
|108
|- style=&#34height:50px&#34
|109
|- style=&#34height:50px&#34
|110
|- style=&#34height:50px&#34
|111
|- style=&#34height:50px&#34
|112
|- style=&#34height:50px&#34
|113
|- style=&#34height:50px&#34
|114
|- style=&#34height:50px&#34
|115
|- style=&#34height:50px&#34
|116
|- style=&#34height:50px&#34
|117
|- style=&#34height:50px&#34
|118
|- style=&#34height:50px&#34
|119
|- style=&#34height:50px&#34
|120
|- style=&#34height:50px&#34
|121
|- style=&#34height:50px&#34
|122
|- style=&#34height:50px&#34
|123
|- style=&#34height:50px&#34
|124
|- style=&#34height:50px&#34
|}
|
{| class="wikitable sortable"
!First
!Last
!Affiliation
|- style=&#34height:50px&#34
|John
|Melonakos
|AccelerEyes (Wed & Thu morning)
|- style=&#34height:50px&#34
|Jack
|Blevins
|Acoustic Med
|- style=&#34height:50px&#34
|Clif
|Burdette
|Acoustic Med (Mon-Wed)
|- style=&#34height:50px&#34
|Dana
|Peters
|Beth Israel Deaconess
|- style=&#34height:50px&#34
|Nicole
|Aucoin
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Giovanna
|Danagoulian
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haytham
|Elhawary
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Andriy
|Fedorov
|BWH (NAMIC Collaborator)
|- style=&#34height:50px&#34
|Daniel
|Haehn
|BWH (NAC)
|- style=&#34height:50px&#34
|Michael
|Halle
|BWH (NAC)
|- style=&#34height:50px&#34
|Nobuhiko
|Hata
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Katie
|Hayes
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Scott
|Hoge
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Tina
|Kapur
|BWH (NCIGT, NAMIC)
|- style=&#34height:50px&#34
|Ron
|Kikinis
|BWH (NAMIC, NAC, NCIGT)
|- style=&#34height:50px&#34
|Jayender
|Jagadeesan
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haying
|Liu
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Lauren
|O'Donnell
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Wendy
|Plesniak
|BWH (NAC)
|- style=&#34height:50px&#34
|Megumi
|Nakao
|BWH (NAIST)
|- style=&#34height:50px&#34
|Sonia
|Pujol
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Lei
|Qin
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Nicolas
|Rannou
|BWH (NAC)
|- style=&#34height:50px&#34
|Petter
|Risholm
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Florin
|Talos
|BWH (NAC)
|- style=&#34height:50px&#34
|Clare
|Tempany
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Junichi
|Tokuda
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Demian
|Wasserman
|BWH (INRIA)
|- style=&#34height:50px&#34
|Carl-Fredrik
|Westin
|BWH (NAC)
|- style=&#34height:50px&#34
|Sandy
|Wells
|BWH (NAC, NCIGT)
|- style=&#34height:50px&#34
|Lilla
|Zollei
|MGH (NAC)
|- style=&#34height:50px&#34
|Padma
|Akella
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Sylvain
|Bouix
|BWH (PNL)
|- style=&#34height:50px&#34
|Julien
|de Siebenthal
|BWH (PNL)
|- style=&#34height:50px&#34
|Marek
|Kubicki
|BWH (NAMIC DBP PNL)
|- style=&#34height:50px&#34
|Juhana
|Frosen
|BWH Tues only
|- style=&#34height:50px&#34
|Sun Woo
|Lee
|BWH (PNL)
|- style=&#34height:50px&#34
|Jimi
|Malcolm
|BWH (PNL)
|- style=&#34height:50px&#34
|Eric
|Melonakos
|BWH (PNL)
|- style=&#34height:50px&#34
|Yogesh
|Rathi
|BWH (PNL)
|- style=&#34height:50px&#34
|Peter
|Savadjiev
|BWH (PNL)
|- style=&#34height:50px&#34
|Doug
|Terry
|BWH (PNL)
|- style=&#34height:50px&#34
|Andrew
|Rausch
|BWH (Mon only)
|- style=&#34height:50px&#34
|Cal
|Hisley
|Des Moines Unive
|- style=&#34height:50px&#34
|Jim
|Miller
|GE
|- style=&#34height:50px&#34
|Xiaodong
|Tao
|GE
|- style=&#34height:50px&#34
|Vandana
|Mohan
|GA Tech
|- style=&#34height:50px&#34
|Yi
|Gao
|GA Tech
|- style=&#34height:50px&#34
|Ivan
|Kolosev
|GA Tech
|- style=&#34height:50px&#34
|Behnood
|Gholami
|GA Tech
|- style=&#34height:50px&#34
|Ziv
|Yaniv
|Georgetown
|- style=&#34height:50px&#34
|Alex
|Gouaillard
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Arnaud
|Gelas
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Sean
|Megason
|Harvard Systems Biology (Wed only)
|- style=&#34height:50px&#34
|Lydie
|Souhait
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Moti
|Freiman
|Hebrew University of Jerusalem
|- style=&#34height:50px&#34
|Amanda
|Peters
|Harvard SEAS
|- style=&#34height:50px&#34
|Maria Francesca
|Spadea
|Italy
|- style=&#34height:50px&#34
|Curtis
|Lisle
|KnowledgeVis
|- style=&#34height:50px&#34
|Steve
|Pieper
|Isomics
|- style=&#34height:50px&#34
|Alex
|Yarmarkovich
|Isomics
|- style=&#34height:50px&#34
|Nathan
|Cho
|JHU
|- style=&#34height:50px&#34
|Bennett
|Landman
|JHU
|- style=&#34height:50px&#34
|Snehashis
|Roy
|JHU
|- style=&#34height:50px&#34
|Sam
|Song
|JHU
|- style=&#34height:50px&#34
|Sebastien
|Barre
|Kitware
|- style=&#34height:50px&#34
|Luis
|Ibanez
|Kitware
|- style=&#34height:50px&#34
|Daniel
|Blezek
|Mayo
|- style=&#34height:50px&#34
|Yong
|Gao
|MGH
|- style=&#34height:50px&#34
|Randy
|Gollub
|MGH
|- style=&#34height:50px&#34
|Rui
|Li
|MGH
|- style=&#34height:50px&#34
|Greg
|Sharp
|MGH
|- style=&#34height:50px&#34
|Robert
|Yaffe
|MGH - Mon
|- style=&#34height:50px&#34
|Sylvain
|Jaume
|MIT
|- style=&#34height:50px&#34
|Bjoern
|Menze
|MIT
|- style=&#34height:50px&#34
|Jeremy
|Bockholt
|MRN (NAMIC Lupus DBP)
|- style=&#34height:50px&#34
|Mark
|Scully
|MRN (NAMIC Lupus DBP) Tue-Th
|- style=&#34height:50px&#34
|Joe
|Stam
|NVIDIA (Wed & Thurs)
|- style=&#34height:50px&#34
|Kimberly
|Powell
|NVIDIA (Wed)
|- style=&#34height:50px&#34
|Marta
|Peroni
|Politecnico di Milano
|- style=&#34height:50px&#34
|Andras
|Lasso
|Queen's (NAMIC DBP)
|- style=&#34height:50px&#34
|Yanling
|Liu
|SAIC/NCI-Frederick
|- style=&#34height:50px&#34
|Melanie
|Grebe
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Lining
|Yang
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Harish
|Doddi
|Stanford University
|- style=&#34height:50px&#34
|Marco
|Ruiz
|UCSD
|- style=&#34height:50px&#34
|Nathan
|Hageman
|UCLA (Mon-Thurs)
|- style=&#34height:50px&#34
|Hans
|Johnson
|U Iowa
|- style=&#34height:50px&#34
|Vincent
|Magnotta
|U Iowa
|- style=&#34height:50px&#34
|Jeffrey
|Yager
|U Iowa
|- style=&#34height:50px&#34
|Manasi
|Ramachandran
|U Iowa
|- style=&#34height:50px&#34
|Dave
|Welch
|U Iowa
|- style=&#34height:50px&#34
|Andrzej
|Przybyszewski
|UMass Med (Mon)
|- style=&#34height:50px&#34
|James
|Balter
|U Michigan
|- style=&#34height:50px&#34
|Dan
|McShan
|U Michigan
|- style=&#34height:50px&#34
|Zhou
|Shen
|U Michigan
|- style=&#34height:50px&#34
|Beatriz
|Paniagua
|UNC
|- style=&#34height:50px&#34
|Minjeong
|Kim
|UNC
|- style=&#34height:50px&#34
|Zhexing
|Liu
|UNC
|- style=&#34height:50px&#34
|Clement
|Vachet
|UNC (NAMIC DBP)
|- style=&#34height:50px&#34
|Guorong
|Wu
|UNC
|- style=&#34height:50px&#34
|Samuel
|Gerber
|SCI, Utah
|- style=&#34height:50px&#34
|Ran
|Tao
|SCI, Utah
|- style=&#34height:50px&#34
|Marcel
|Prastawa
|SCI, Utah
|- style=&#34height:50px&#34
|Ross
|Whitaker
|SCI, Utah
|- style=&#34height:50px&#34
|Curtis
|Rueden
|UW-Madison
|- style=&#34height:50px&#34
|Dan
|Marcus
|WUSTL
|- style=&#34height:50px&#34
|Misha
|Milchenko
|WUSTL
|- style=&#34height:50px&#34
|Kevin
|Archie
|WUSTL
|- style=&#34height:50px&#34
|Tim
|Olsen
|WUSTL
|- style=&#34height:50px&#34
|Mehdi
|Esteghamatian
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Diego
|Cantor
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Danielle
|Pace
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Vidya
|Rajagopalan
|VA Tech
|- style=&#34height:50px&#34
|Gregory
|Fischer
|WPI
|- style=&#34height:50px&#34
|Dominique
|Belhachemi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Alark
|Joshi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Xenios
|Papademetris
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Dustin
|Scheinost
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Michelle
|Borkin
|Harvard SEAS (Mon only)
|- style=&#34height:50px&#34
|Renxin
|Chu
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Ben
|Schwartz
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Marianna
|Jakab
|BWH (NCIGT, NAC) (Mon, Tue)
|- style=&#34height:50px&#34
|Viswanath
|Avasarala
|GE (Wed, Thurs)
|- style=&#34height:50px&#34
|}
|}

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''

The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php

2009 Summer Project Week GWE XNAT

2009-06-19T09:46:43Z

Mruiz:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:GweLogoSquare.png‎|[http://www.gridwizardenterprise.org GWE: Platform to run parameter exploration experiments]
Image:Gwe_result_browser.png‎|GWE Experiment Results Browser
</gallery>

==Key Investigators==
* UCSD: Marco Ruiz
* WU: Dan Marcus

<div style="margin: 20px;">
<div style="width: 22%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Collect specifications for P2EL macros/functions to upload data into XNAT systems.
* Review and refine production P2EL macros created to query XNAT systems (experiments, session, scans, images, etc.)
* Collect specifications for any other XNAT querying P2EL macros that may be useful to describe parameter exploration experiments.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Demo current state of XNAT querying support on GWE and share vision for how researchers can benefit and use it when running parameter exploration experiments.
* Discuss usability/feasibility of the vision to set a practical direction for this integration effort.
* Gather specs for the XNAT REST API to implement data upload and for the modications/additions of P2EL macros.
* Gather information about future modifications/gray areas on the XNAT REST API so can be considered in this integration effort.
</div>

<div style="width: 45%; float: left;">

<h3>Progress</h3>
* GWE 0.7.3.alpha (latest release) includes a [http://www.gridwizardenterprise.org/svn/gwe/gwe-core/trunk/src/main/config/base/gwe-macros/xnat.p2el P2EL macro library to support common querying operations].
* Some of these macros are currently misbehaving due to minor changes in the XNAT REST API. A "patch release" will be released before the project week to accomodate these changes.
</div>

<br style="clear: both;" />

</div>

===References===

*GWE Project Site: http://www.gridwizardenterprise.org
*P2EL Macros: http://www.gridwizardenterprise.org/guides/p2el-macros.html
*P2EL Macro Library for XNAT: http://www.gridwizardenterprise.org/svn/gwe/gwe-core/trunk/src/main/config/base/gwe-macros/xnat.p2el
*XNAT: http://www.xnat.org/
*XNAT REST API: http://nrg.wikispaces.com/XNAT+REST+API+Usage

File:Gwe result browser.png

2009-06-19T09:34:42Z

Mruiz: uploaded a new version of "File:Gwe result browser.png"

File:Gwe result browser.png

2009-06-19T09:33:42Z

Mruiz: uploaded a new version of "File:Gwe result browser.png"