2014 Summer Project Week

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

Agenda

Time	Monday, June 23	Tuesday, June 24	Wednesday, June 25	Thursday, June 26	Friday, June 27
	Project Presentations	NA-MIC Update Day		IGT Day	Reporting Day
8:30am		Breakfast	Breakfast	Breakfast	Breakfast
9am-12pm		10-11:30am Breakout Session: DICOM (Steve Pieper) Grier Room (Left)	9:00-10:30am Tutorial Contest Presentations (Sonia Pujol) Grier Rooms ---------------------------------------- 11am-12noon Breakout Session: Slicer for users (Ron Kikinis)	10am-12pm: Breakout Session: Image-Guided Therapy - Neurosurgery (Alexandra Golby, Tina Kapur) Star ---------------------------------------- 12pm Tutorial Contest Winner Announcement Grier Rooms	10am-12pm: Project Progress Updates
12pm-1pm	Lunch	Lunch	Lunch	Lunch	Lunch boxes; Adjourn by 1:30pm
1pm-5:30pm	1-1:05pm: Ron Kikinis: Welcome Grier Rooms ---------------------------------------- 1:05-3:30pm: Project Introductions (all Project Leads) Grier Rooms ---------------------------------------- 3:30-4:30pm Slicer4 Extensions (Jean-Christophe Fillion-Robin) Grier Room (Left)	1-3pm: Breakout Session: QIICR (Andrey Fedorov) Kiva	1-2:30pm: Breakout Session: Contours (Adam Rankin, Csaba Pinter) Kiva	1-3pm: Breakout Session: Image-Guided Therapy - Prostate Interventions (Clare Tempany, Noby Hata) Star ----------------------------------------
5:30pm	Adjourn for the day	Adjourn for the day	Adjourn for the day	Adjourn for the day

Background

Project Week is a hands on activity -- programming using the open source NA-MIC Kit, algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. 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 NA-MIC coverage for all. Subsequent teleconferences 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 are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

A summary of all past NA-MIC Project Events is available here.

Please make sure that you are on the na-mic-project-week mailing list

Projects

• Template for project pages

Image-Guided Therapy

• SlicerIGT extension: testing, tutorials, website (Tamas Ungi, Nobuhiko Hata)
• MR-Ultrasound Registration for Prostate Interventions (Chenxi Zhang, Andriy Fedorov, Andras Lasso)
• Surface approximation from contour points (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
• Robot Control With OpenIGTLink ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)
• Gestural Point of Care Interface for IGT (Saskia, Franklin, Steve, Tobias)
• Steered image registration using intelligent interfaces for minimal user interaction (Marcel Prastawa, Jim Miller, Steve Pieper)
• Image To Mesh Conversion for Brain MRI (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
• An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Ron Kikinis, Nikos Chrisochoides)
• Open-source electromagnetic trackers using OpenIGTLink (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
• Intraoperative Registration of preoperative CT and C-arm CT of the lung (Katharina Breininger, Jay Jagadeesan)
• Making realistic clinical story board for image guided skull base endoscopic surgery (Keryn Palmer, Nobuhiko Hata)
• PathExplorer Extension (code refactoring, documentation, tutorial) (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)
• Tools for Dysplasia Identification in Epilepsy (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)

Huntington's Disease

• Fiber Tract Dispersion and UKF Tractography (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)

TBI

• Interactive segmentation for traumatic brain injury (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

Stroke

• Stroke Imaging Genetics (Adrian Dalca, Ramesh Sridharan, Polina Golland)
• Stroke Super Resolution (Adrian Dalca, Ramesh Sridharan, Polina Golland)

Chronic Obstructive Pulmonary Disease, Lung, Chest

• Pectoralis muscle segmentation (Rola Harmouche, James Ross, Raul San Jose)
• Image Registration with Sliding Motion Constraints (Alexander Derksen, Kanglin Chen, Gregory Sharp)
• Multiscale Non Local Means filter (NLM) for chest CT images (Pietro Nardelli, Raul San Jose)

Head and Neck Cancer / Radiotherapy

• External Beam Planning (Kevin Wang, Greg Sharp, Maxime Desplanques)
• DIR validation tools (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
• Upload H&N data (Greg Sharp, Paolo Zaffino)
• DIR stop and restart (Paolo Zaffino, Greg Sharp, Steve Pieper)
• Interactive Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)
• Proton pencil beam dose calculation (Maxime Desplanques, Kevin Wang, Greg Sharp)

QIICR

• Real world value mapping support (Andrey, Ethan, Andras, Steve, Jim)
• Proper formatting of DICOM Derived Data from CLI (Steve, Andrey, Jim, {Michael and David remotely})
• DICOM SEG conversion to support archival of QIN Grand challenges results (Jayashree, Andrey, Steve, {David remotely})
• Color Bar Support for Slice Views (Alireza, Andrey, Steve, Kevin)
• Slicer DICOM Improvements (Alireza, Andrey, Steve, Ron)

Feature Extraction

• Breast Tumor Segmentation (Vivek Narayan, Jay Jagadeesan)
• Breast Tumor Heterogeneity Analysis (Vivek Narayan, Jay Jagadeesan)
• Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)
• Invariant Feature Methods in Slicer (Matthew Toews, Nicole Aucoin, Sandy Wells)

Additional Brain Image Analysis

• Shape Analysis for the developing murine skull (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
• Slicer Interface to LDDMM shape anlaysis (Saurabh Jain, JHU; Steve Pieper, Isomics; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)
• Atlas Selection (Kanglin Chen, Gregory Sharp)
• CAD Toolbox for Neurological Disorders (Sidong Liu, Siqi Liu, Fan Zhang, Yang Song, Weidong Cai, Sonia Pujol, Ron Kikinis)
• Longitudinal patient-specific DTI analysis using Slicer for neonatal asphyxia (Anuja Sharma, SCI, Utah; Francois Budin, UNC; Martin Styner, UNC; Guido Gerig, SCI, Utah)
• Rapid Visualization of Large Image Collections (Adrian, Ramesh, Polina)

Slicer4 Extensions

• Multidimensional Data (Kevin Wang, Andras Lasso)
• DICOM-SRO import (Kevin Wang)
• Plastimatch extension re-engineering (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)
• Integrating DRAMMS deformable registration into Slicer (Yangming Ou, Steve Pieper, Andriy Fedorov, Tina Kapur, Christos Davatzikos, Ron Kikinis, Randy Gollub, Jayashree Kalpathy-Cramer)

Infrastructure

• Slicer 4.4 Release (JC, Steve, Nicole)
• Chronicle (Steve)
• Post NA-MIC Factory and Testing (Steve, Jc, Ron)
• Volume Registration (Steve, Greg, Marcel, Jim)
• Markups (Nicole Aucoin)
• Pluggable Label Statistics (Andrey , Ethan, Steve, Brad, Jim)
• Subject hierarchy integration (Csaba, Steve, Jc, Andras)
• Contours (Adam Rankin, Csaba, Andras, Steve, Jc)
• Parameter Node Serialization (Kevin Wang, Andras, Steve, Jim, Csaba)
• Self-tests for non-linear transforms (Xining Du)
• Slicer Tutorial Updates (Parth Amin, Farukh Kohistani)

Logistics

• Dates: June 23-27, 2014.
• Location: Stata Center / RLE MIT.
• REGISTRATION: https://www.regonline.com/namic2014summerprojectweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
• Registration Fee: $300.
• Hotel: Similar to previous years, no rooms have been blocked in a particular hotel.
• Room sharing: If interested, add your name to the list: here

Registrants

Do not add your name to this list - it is maintained by the organizers based on your paid registration. (Please click here to register.)

1. Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu
2. Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com
3. Peter Anderson, retired, traneus@verizon.net
4. Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu
5. Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org
6. Francois Budin, NIRAL-UNC, fbudin@unc.edu
7. Saskia Camps, SPL, saskiacamps@gmail.com
8. Lucia Cevidanes, University of Michigan, luciacev@umich.edu
9. Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu
10. Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
11. Adrian Dalca, MIT CSAIL, adalca@mit.edu
12. Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
13. Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it
14. Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
15. Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com
16. Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
17. Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
18. James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com
19. Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu
20. Polina Golland, MIT CSAIL, polina@csail.mit.edu
21. Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu
22. Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com
23. Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu
24. Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
25. Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
26. Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu
27. Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu
28. Ron Kikinis, HMS, kikinis@bwh.harvard.edu
29. Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu
30. Franklin King, Queen's University, franklin.king@queensu.ca
31. Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu
32. Farukh Kohistani, BWH Radiology, kohistan@bc.edu
33. Robin Kouver, BWH/SPL, r.kouver@gmail.com
34. Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca
35. Yangming Li, University of Washington, ymli81@uw.edu
36. Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu
37. Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
38. Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
39. Murat Maga, Seattle Children's Research Institute, maga@uw.edu
40. Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu
41. Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu
42. Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu
43. Jim Miller, GE Research, millerjv@ge.com
44. Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org
45. Vivek Narayan, NCIGT, narayan.vivek9@gmail.com
46. Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu
47. Yangming Ou, MGH, yangming.ou@uphs.upenn.edu
48. Danielle Pace, MIT CSAIL, dfpace@mit.edu
49. Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org
50. Nirav Patel, WPI, napatel@wpi.edu
51. Tobias Penzkofer, SPL, pt@bwh.harvard.edu
52. Steve Pieper, Isomics Inc, pieper@isomics.com
53. Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
54. Marcel Prastawa, GE Research, marcel.prastawa@ge.com
55. Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu
56. Adam Rankin, Queen's University, rankin@queensu.ca
57. Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu
58. Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu
59. Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu
60. Gregory Sharp, MGH, gcsharp@mgh.harvard.edu
61. Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com
62. Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
63. Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu
64. Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
65. Tamas Ungi, Queen's University, ungi@queensu.ca
66. Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca
67. David Welch, University of Iowa, david-welch@uiowa.edu
68. William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu
69. Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu
70. Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu
71. Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org
72. Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
73. Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn
74. Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au