Engineering:Programmers Week Summer 2005 - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:43:37Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Marianna at 15:53, 30 March 2017

2017-03-30T15:53:19Z

Marianna at 15:21, 30 March 2017

2017-03-30T15:21:15Z

Marianna at 14:51, 30 March 2017

2017-03-30T14:51:15Z

Marianna at 18:22, 9 December 2016

2016-12-09T18:22:17Z

Marianna at 15:46, 9 December 2016

2016-12-09T15:46:58Z

Pieper at 22:19, 18 December 2013

2013-12-18T22:19:17Z

Melonakos at 01:29, 6 November 2008

2008-11-06T01:29:13Z

Andy: Update from Wiki

2006-12-18T13:40:14Z

Update from Wiki

New page

=== Summary ===

This programming event was successfully concluded. Results are summarized [[Engineering:2005_Programming_Week_Results|here]].

=== Logistics ===

'''Dates and Schedule''' Monday, June 27 - Friday, July 1st, 2005.

* Starting on Monday at noon, and ending on Friday at 2pm.
* We expect to start at 9am each day and end around 5:30pm.

'''Location'''

* Mon-Tue in [[Meeting_Locations:MIT_CSAIL_Star|MIT's Stata Center: Star Conference Room 32-D463 and Patil/Kiva Seminar Room 32-G449]]
* Wed-Thurs-Fri at [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]]

'''Hotel''' [http://www.hotelatmit.com/home/home.html University Hotel at MIT]

[http://whereis.mit.edu/map-jpg?selection=L7;selectfield=Loc_ID;selectlayer=Landmarks;zoom=level4;centerx=708811;centery=495953 Interactive map of Hotel@MIT and MIT]

'''Registration Fee''' $75. (This includes breakfast every day and lunch most days.)

Please make checks out to "Massachusetts Institute of Technology" and mail to:

 Donna Kaufman MIT 77 Massachusetts Ave., 38-409b Cambridge, MA 02139

 by Monday, June 20, 2005

You may contact Donna at 617.253.4624 or [mailto:dkauf@mit.edu dkauf@mit.edu]

=== Goals ===

The main goal of this week is to move forward the software deliverables of NAMIC. All NAMIC programmers, whether they are faculty, researcher, student, administrator, engineer, or anything else in their day job, are welcome to join us. Some key points:

* You don't need to be in core 1 or 2 to attend, even though most of the attendees are likely to be from these cores.
* You '''do''' need to be actively programming on a NAMIC project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who have an algorithm that needs to be moved into the NAMIC Kit, and those who can help make it happen.
* This is not an introduction to ITK or Slicer or LONI pipeline. If you have not had any introductory exposure to at least one of these three yet, and want to attend, please make sure that you have done all the programming exercises that were introduced in the NAMIC dissemination workshops.
* The following types of projects are included in this week:
** core 1 projects that need support from core 2
** core 2 projects on the NAMIC Toolkit
** core 2 project on the kickoff of the next generation of Slicer infrastructure
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== How will this week work? ===

The agenda below gives an idea of how the week will be structured. In addition, please note that:

* Everyone should bring a laptop. We will have three or four projectors.
* It looks like about half the week will be programming and the other half discussions.
* There is an optional DTI workshop hosted by Core 1 on Monday morning.
* Wednesday afternoon is open touring Boston and boxed lunches will be provided. Conference rooms (and coffee) will be supplied for those who prefer to continue working.

=== Preparation for the workshop ===

This is being prepared right now, so please check it often for changes. [[User:Tkapur|Tkapur]] 00:26, 10 Jun 2005 (EDT)

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# Thursday, April 14 at 3pm EST: Programming week Kickoff TCON. Details sent to mailing list.
# By Thursday April 21: Create a Wiki page per project (the participants must do this, hopefully jointly)
# By Friday April 22: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
# By Friday April 29: 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)
# By Friday April 29: 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.)
# By Friday May 6th: 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. (Andy)
# Two TCONS: Thursday June 16th at 3pm EST, and Thursday June 23rd at 3pm EST... if you don't have the details for these, add yourself to the programming week mailing list.
# Until June 27th: program, email, call, program (maybe take breaks to think in between...)
# Please note that by the time we get to Boston, we shouldn't be talking about which method to use, and what is the purpose of the application. At that point we should be talking about "how much computation time it took to run method A in image #5", and "how that compares to the results of method B in image #7".

=== Agenda ===

<blockquote style="background: white; border: 1px solid black; padding: 1em">

{| border="1"
|- bgcolor="#ffbbbb"
|
| Monday (Star, Kiva)
| Tuesday (Star, Kiva)
| Wednesday (Grier A and B)
| Thursday (Grier A and B)
| Friday (Grier A and B)
|- bgcolor="#ddffff"
| Goal
| '''Set the stage, share each team's goals for the week, make sure programming environment is functional'''
| '''Goal: Write code in small teams, start discussion of slicer 3.0'''
| '''Work... [[Programmingweek:funinBoston_%22retreating_in_Boston%22|Tour Boston]]'''
| '''Mostly finish up programming goals for the week. Report One Highlight.'''
| '''Tie loose ends. Wrap-up week.'''
|- bgcolor="#ffff99"
| bgcolor="#dddddd" | 8:30-9am
| Breakfast in the R&D Dining Room
| Breakfast in the R&D Dining Room
| Breakfast in Grier
| Breakfast in Grier
| Breakfast in Grier
|-
| bgcolor="#dddddd" | 9-10:30am
| bgcolor="#ffdddd" |
[[Diffusion_Workshop|Mathematics of Diffusion Workshop in Star(optional)]]
| bgcolor="#ddddff" | Meet in Kiva for 15 minutes, and then continue work in teams.
| bgcolor="#ddffdd" |
Meet for 15 minutes, and then [[Engineering:Project:Slicer3.0#Agenda|Slicer 3.0]] continue in Grier A, and other teams continue in Grier B.
| bgcolor="#ddddff" | One "mid-week" highlight by each project team
| bgcolor="#ddddff" | TBD based on feedback on Thursday evening
|- bgcolor="#ffff99"
| bgcolor="#dddddd" | 10:30-11am
| Coffee in the R&D Dining Room
| Coffee in the R&D Dining Room
| Coffee in Grier
| Coffee in Grier
| Coffee in Grier
|-
| bgcolor="#dddddd" | 11am-12pm
| bgcolor="#ffdddd" |
[[Diffusion_Workshop|Mathematics of Diffusion Workshop in Star(optional)]]
| bgcolor="#ddddff" | Continue...
| bgcolor="#ddffdd" | Continue...
| bgcolor="#ddddff" | Continue to work in teams.
| bgcolor="#ddddff" | Continue...
|- bgcolor="#ffff99"
| bgcolor="#dddddd" | 12-1pm
|
Welcome/Lunch in R&D Dining Room (Grimson, [[Media:Programmers-Week-Intro-2005-06-28.ppt|Kikinis]])
| Lunch in R&D Dining Room
| bgcolor="#ffddff" | Lunch Boxes in Grier
| Go out for lunch
| bgcolor="#ff6666" | Wrap-up week (Lorensen, Kapur)
|-
| bgcolor="#dddddd" | 1-2:15pm
| bgcolor="#ddddff" |
Programming Week Kickoff in Kiva(Lorensen, Kapur, Pieper, Schroeder). 1:50pm: [[Media:Namic-reqs-pilot-001.ppt| On requirements gathering]] (Tuch). 2:05pm: Sample Training Document(Pujol)

[[Media:SPujol_ProgrammingWeek_TrainingPresentation.ppt|Training Presentation]]

[[Media:DocumentationTemplate_ProgrammingWeek.ppt| Documentation Template ]]
| bgcolor="#ddffdd" |
[[Engineering:Project:Slicer3.0#Agenda|Slicer 3.0]] in Kiva for the afternoon. Other Project Teams continue in Star for the afternoon.
| bgcolor="#ffddff" | Take a break to tour Boston (optional)
| bgcolor="#ddddff" | Continue ...
|-
| bgcolor="#dddddd" | 2:15-3:30pm
| bgcolor="#ddddff" | Core 1 Projects Overview by Team Leads (10 min each)
| bgcolor="#ddffdd" | Continue...
| bgcolor="#ffddff" | Continue ...
| bgcolor="#ddddff" | Continue ...
|- bgcolor="#ffff99"
| bgcolor="#dddddd" | 3:30-4pm
| Coffee in the R&D Dining Room
| Coffee in the R&D Dining Room
| bgcolor="#ffddff" | Coffee in Grier
| Coffee in Grier
|-
| bgcolor="#dddddd" | 4-5:30pm
| bgcolor="#ddddff" | Computer/Env Setup
| bgcolor="#ddffdd" | Continue ...
| bgcolor="#ffddff" | Continue ...
| bgcolor="#ddddff" | Continue ...
|- bgcolor="#ff6666"
| bgcolor="#dddddd" | 5:30-6pm
| Wrap-up for Day in Kiva (Lorensen, Kapur)
| Wrap-up for Day in Kiva (Lorensen, Kapur)
| bgcolor="#ffddff" | Continue ...
| Wrap-up for Day in Grier and identify critical items for Friday morning (Lorensen, Kapur)
|-
| bgcolor="#dddddd" | 6:30pm
|
| bgcolor="#ff99ff" |
[[NAMIC_Wiki:Community_Licensing|Licensing]] Discussion over Dinner (Hosts:Ibanez, Kindlmann)
|}

</blockquote>

=== Participants ===

We are now beyond capacity (35) for this workshop. '''Please don't add any more names to this list.''' If you are still interested in attending, please identify the team that you will work with and send an email to tkapur at epiphanymedical com and hopefully we will be able to figure something out.

When you add a name to this list, please also make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list].

# John Melonakos (Georgia Tech, Core 1)
# Ramsey Al-Hakim (Georgia Tech, Core 1)
# Casey Goodlett (UNC, Core 1)
# Ipek Oguz (UNC, Core 1)
# Christine Xu (UNC, Core 1)
# Martin Styner (UNC, Core 1)
# Isabelle Corouge (UNC, Core 1)
# Tom Fletcher (Utah, Core 1)
# Josh Snyder (MGH, Core 1)
# Mahnaz Maddah (MIT, Core 1)
# Lauren O'Donnell (MIT, Core 1)
# Steve Pieper (BWH, Core 2)
# Jags (UCLA, Core 2)
# Luis Ibanez (Kitware, Core 2)
# Andy Cedilnik (Kitware, Core 2)
# Sebastien Barre (Kitware, Core 2)
# Andinet Enquobahrie (Kitware, Core 2)
# Berk Geveci (Kitware, Core 2 ParaView expert)
# Rick Avila (Kitware, Core 2)
# Alex Yarmarkovich (BWH, Core 2)
# Jim Miller (GE, Core 2)
# Xiaodong Tao (GE, Core 2)
# Bill Lorensen (GE, Core 2 PI)
# Jason Gerk(UCSD, Core 2)
# Jeff Grethe(UCSD, Core 2)
# Sylvain Bouix (Harvard, Core 3)
# Will Schroeder (Kitware, Core 4 PI)
# Randy Gollub (MGH, Core 5)
# Sonia Pujol (BWH, Core 5)
# Tina Kapur (Epiphany Medical, Core 6)
# Katie Hayes (BWH, Collaborator)
# Raul San Jose Estepar (BWH, Collaborator)
# Karl Krissian (BWH, Collaborator)
# Chand John (Stanford, Collaborator)
# Michael Halle (BWH, Collaborator)
# Nicole Aucoin (BWH, Collaborator)
# Besam Khidhir (BWH, Collaborator)
# Neculai Archip (BWH, Collaborator)
# Bryn Lloyd (BWH, Collaborator)
# Andriy Fedorov (College of William and Mary/BWH, Collaborator)
# Torsten Rohlfing (SRI, Collaborator [http://wiki.na-mic.org/Wiki/images/8/80/TorstenRohlfing_Intro_ProgWeek.pdf introduction to Torsten's fields of work])
# Neil Weisenfeld (BWH, Collaborator)
# Ron Kikinis (BWH, PI)
# Eric Grimson (MIT, Core 1 PI)

=== Projects ===

'''Applications'''

==== [[Engineering:Project:Non-rigid_EPI_registration|(Kiva) Non-rigid EPI registration using ITK (Snyder, Tuch, Ibanez)]] ====

==== [[Engineering:Project:ITK_Tract_Analysis|(Star) Prototype ITK system for Quantitative Fiber Tract Analysis (Casey - UNC, Xiaodong - GE), Isabelle - UNC]] ====

==== [[Engineering:Project:Shape_Analysis|(Star)Processing modules and visualization tools for shape analysis (Ipek Oguz, Christine Xu, Martin Styner - UNC, Jim Miller - GE Research)]] ====

==== [[Engineering:Project:Feature_Analysis_Framework|(Star)Object population desription and general feature analysis framework (Martin Styner - UNC, Tom Fletcher - Utah, Jim Miller - GE Research)]] ====

==== [[Engineering:Project:Bayesian_Segmentation|(Kiva)Addition of Bayesian Segmentation Module to ITK (John Melonakos, Ibanez)]] ====

==== [[Engineering:Project:Motion_Robust_Registration|(Kiva)Wrap motion robust matching code using ITK (Khidhir, Warfield, Archip, Lorensen)]] ====

==== [[Engineering:Project:DLPFC_Semi-Automatic_Segmentor|(Kiva)DLPFC Semi-Automatic Segmentor (Ramsey Al-Hakim, Alex Yarmakovich)]] ====

==== [[Flux_Diffusion_in_ITK_%28Karl_Krissian%29|(Star)Flux Diffusion in ITK (Karl Krissian)]] ====

==== [[ITKu%2C_minimalist_commandline_tools_using_ITK_%28Raul_San-Jose_Estepar%29|(Star) ITKu, minimalist commandline tools using ITK (Raul San Jose, Gordon Kindlmann) ]] ====

==== [[Nrrd_ITK_IO%2C_read_and_write_nrrd_tensor_data_with_ITK_%28Gordon_Kindlmann%29|(Star) nrrd ITK IO, read and write nrrd tensor data with ITK (Gordon Kindlmann)]] ====

==== [[Engineering:Project:DTMRI_Testing|(Kiva) Slicer DTMRI module nightly testing (Lauren O'Donnell, Raul San Jose Estepar, Andy Cedilnik)]] ====

==== [[Engineering:Project:Spectral_Clustering_in_ITK|(Kiva) Spectral Clustering in ITK (Lauren O'Donnell, Luis Ibanez)]] ====

==== [[Engineering:Project:Intensity_Normalization|(Kiva) ITK Wrap Intensity Correction and Normalization Methods (Weisenfeld, Warfield) ]] ====

==== [[Engineering:Project:UNC_Shape_AnalysisLONI_pipeline|(Star)LONI pipeline for UNC script based shape analysis pipeline (Martin Styner, Ipek Oguz - UNC, Jags Rajendiran - UCLA)]] ====

==== [[3D_Adaptive_Tetrahedral_Mesh_Generation_in_ITK_%28Fedorov%2C_Chrisochoides%2C_Warfield%2C_Schroeder%29|(Kiva)3D Adaptive Tetrahedral Mesh Generation in ITK (Fedorov, Chrisochoides, Warfield, Schroeder)]] ====

==== [[2D/3D_Point_landmark_detection_in_ITK_%28Lloyd%2C_Warfield%29|(Kiva)2D/3D Point landmark detection in ITK (Lloyd, Warfield)]] ====

==== [[Engineering:Project:Condor_Job_Submission|(Star)Large Scale Algorithm Job Submission via Condor(Jason, Jeff, Pieper)]] ====

==== [[Engineering:Project:Pipelining_ITK_Modules|(Star)Pipelining ITK modules(Jags, Pieper)]] ====

=== [[Engineering:Project:Slicer3.0|Slicer3.0 Architecture Kickoff]] ===

 

=== Computer Resources ===

* All participants should bring laptops with development software and sample data loaded.

* See, for example, the instructions for the [[Dissemination:Workshop_Feb17-18_2005|Feb 17-18, 2005 Dissemination Workshop at UCSD]] for background material.

* Some cluster computing resources are being prepared.
** More details to follow [[Engineering:Project:Condor_Job_Submission|here]].
** Example code and data for testing is [[Engineering:ITK_Grid_Pipeline|here]].

=== Social stuff ===

* Pictures from [[http://www.cs.unc.edu/~styner/pics/2005_namic_prog_week/2005_namic_prog_week.html Martin's Treo camera]]

← Older revision		Revision as of 17:43, 10 July 2017
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	==== [[Engineering:Project:Pipelining_ITK_Modules\|(Star)Pipelining ITK modules(Jags, Pieper)]] ====		==== [[Engineering:Project:Pipelining_ITK_Modules\|(Star)Pipelining ITK modules(Jags, Pieper)]] ====

−	=== [~~http~~://www.slicer.org/~~slicerWiki/index.php~~/Main_Page Slicer3.0 Architecture Kickoff] ===	+	=== [https://www.slicer.org/wiki/Main_Page Slicer3.0 Architecture Kickoff] ===

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 __NOTOC__
 Back to [[Events]]
-A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].
+=Welcome to the web page for the 1st Project Week!=
 === Summary ===
 The first NA-MIC Programming Week was successfully concluded on July 1, 2005 at MIT.  Results are summarized [[Engineering:2005_Programming_Week_Results|here]].

@@ Line 2: / Line 2: @@
 Back to [[Events]]
-To [[Engineering:Programming_Events|All Hands on Project Events]]
+A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].
 =Welcome to the web page for the 1st Project Week!

@@ Line 2: / Line 2: @@
 Back to [[Events]]
-=Welcome to the web page for the 1st Project Week!=
+To [[Engineering:Programming_Events|All Hands on Project Events]]
 === Summary ===
 The first NA-MIC Programming Week was successfully concluded on July 1, 2005 at MIT.  Results are summarized [[Engineering:2005_Programming_Week_Results|here]].

@@ Line 2: / Line 2: @@
 Back to [[Events]]
-[[image:Summer Project Week 2005.jpg|300px|thumb|left]]
+=Welcome to the web page for the 1st Project Week!=
 === Summary ===
+The first NA-MIC Programming Week was successfully concluded on July 1, 2005 at MIT.  Results are summarized [[Engineering:2005_Programming_Week_Results|here]].
 === Logistics ===
@@ Line 269: / Line 268: @@
 === [http://www.slicer.org/slicerWiki/index.php/Main_Page Slicer3.0 Architecture Kickoff] ===
 === Computer Resources ===
@@ Line 282: / Line 280: @@
 === Social stuff ===
 * Pictures from [[http://www.cs.unc.edu/~styner/pics/2005_namic_prog_week/2005_namic_prog_week.html Martin's Treo camera]]

@@ Line 1: / Line 1: @@
-[[image:Summer Project Week 2005.jpg|300px|thumb|right]]
+__NOTOC__
 === Summary ===
@@ Line 176: / Line 180: @@
 We are now beyond capacity (35) for this workshop. '''Please don't add any more names to this list.''' If you are still interested in attending, please identify the team that you will work with and send an email to tkapur at epiphanymedical com and hopefully we will be able to figure something out.
-When you add a name to this list, please also make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list].
+When you add a name to this list, please also make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week NA-MIC Programming Week mailing list].
 # John Melonakos (Georgia Tech, Core 1)

← Older revision		Revision as of 22:19, 18 December 2013
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	=== Summary ===		=== Summary ===

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 ==== [[Engineering:Project:Pipelining_ITK_Modules|(Star)Pipelining ITK modules(Jags, Pieper)]] ====
-=== [[Engineering:Project:Slicer3.0|Slicer3.0 Architecture Kickoff]] ===
+=== [http://www.slicer.org/slicerWiki/index.php/Main_Page Slicer3.0 Architecture Kickoff] ===
 <br />