2014 Summer Project Week

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

Summary

The most recent project week was the 19th event in the series. It was held June 23-27, 2014 at MIT. It recorded 81 registered attendees, who worked on 66 projects. These attendees represented 21 academic sites (Brigham and Women’s Hospital, Massachusetts General Hospital, MIT, WPI, Univ of Utah, Univ of Iowa, Univ of Michigan, Univ of North Carolina at Chapel Hill, Queen’s Univ, Univ of Sydney, Univ Magna Graecia of Catanzaro, Old Dominion Univ, Univ of CA San Diego, Johns Hopkins Univ, Stony Brook Univ, Univ of Washington, NIH, Seattle Children's Research Institute, Univ College Cork, Ben-Gurion Univ, Princess Margaret Cancer Centre) and 4 companies (GE Global Research, Kitware, Fraunhofer MEVIS, Isomics Inc).

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 (Stata Building 4th Floor R&D Common Dining Area)
9am-12pm		10-11:30am Breakout Session: DICOM (Steve Pieper) Star	11am-12noon Breakout Session: Slicer for users (Ron Kikinis)	9:00-10:30am Tutorial Contest Presentations (Sonia Pujol) Grier Rooms ---------------------------------------- 10am-12pm: Breakout Session: Image-Guided Therapy - Neurosurgery (Alexandra Golby, Tina Kapur) Star	10am-12pm: Project Progress Updates (Stata Building 4th Floor R&D Common Dining Area) ---------------------------------------- 12pm Tutorial Contest Winner Announcement (Stata Building 4th Floor R&D Common Dining Area)
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, Tina Kapur)
• Robot Control With OpenIGTLink ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)
• Visual Guidance for Neurosurgery US Data Recording (Alireza, Isaiah, Rahul, Matthew, Tina, Steve, Sandy, Alex Golby)
• Gestural Point of Care Interface for IGT (Saskia, Franklin, Steve, Tobias, Andras)
• Steered image registration using intelligent interfaces for minimal user interaction (Marcel Prastawa, Jim Miller, Steve Pieper)
• CBC 3D I2M Conversion (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)
• MR-Ultrasound Registration for Prostate Interventions (Andriy Fedorov, Chenxi Zhang, Andras Lasso)
• Surface approximation from contour points (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
• Tools for Dysplasia Identification in Epilepsy (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)
• Focused Ultrasound Pressure Sensor (Robin Kouver, Nassim Alikacem)
• Focused Ultrasound Positioner (Nassim Alikacem, Robin Kouver)
• Searching for Software Platform for Robotic Surgery (Yangming Li)
• Rapid Visualization of Large Image Collections (Adrian, Ramesh, Polina)
• Ventriculostomy Guidance with Transcranial Ultrasound (Jason White, Kirby Vosburgh, Can Meral, Alex Golby)
• Calibration of EM-tracked US acquisition using Plus (Andrey Fedorov, Tamas Ungi, Andras Lasso, Jay Jagadeesan)

Huntington's Disease

• Fiber Tract Dispersion and UKF Tractography (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)
• 4D Segmentation for Longitudinal Consistency (Regina Kim, James Fishbaugh, Guido Gerig, Hans Johnson)
• Automated Prior-driven Segmentation QA (Dave Welch, Hans Johnson)
• Manual Segmentation QA (Dave Welch, Hans Johnson)
• Update BRAINSTools (BRAINSFit and DWIConvert) in Slicer (Hans Johnson, Dave Welch, Kent Williams, JC, Brad)
• Cardiac Agatston Scoring Extension (Jessica Forbes, Hans Johnson)

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)

Cardiac

• MRI segmentation for congenital heart disease (Danielle Pace, Adrian Dalca, 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

• ScalarBar vtk6 migration (Kevin Wang, Nicole)
• Upload H&N data (Greg Sharp, Paolo Zaffino)
• DIR stop and restart (Paolo Zaffino, Greg Sharp, Steve Pieper)
• Proton pencil beam dose calculation (Maxime Desplanques, Kevin Wang, Greg Sharp)

QIICR

• Real world value mapping support (Ethan, Andrey, 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, Hans Johnson, 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)
• Pipeline Visualization (Ramesh, Adrian, Polina)

Slicer4 Extensions

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

TMJOA RO1 - Collaboration with NAMIC

• TMJOA (Francois Budin, Beatriz Paniagua, Lucia Cevidanes, Nicole Aucoin, Steve Pieper, Jean-Christophe Fillion-Robin, Alex Yarmarkovich)

Infrastructure

• 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, Steve, Jim, Jc, Matt, Nicole)
• Self-tests for non-linear transforms (Xining Du)
• Slicer Tutorial Updates (Parth Amin, Farukh Kohistan, Sonia Pujol)

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 Cancer Institute :: hugo_aerts at dfci.harvard.edu
2. Nassim Alikacem :: Brigham and Women's Hospital :: Nassim.Alikacem at gmail.com
3. Parth Amin :: Wentworth Institute of Technology :: aminp at wit.edu
4. Peter Anderson :: Retired :: traneus at verizon.net
5. Nicole Aucoin :: Brigham and Women's Hospital :: nicole at bwh.harvard.edu
6. Eva Breininger :: Brigham and Women's Hospital :: ebreininger at partners.org
7. Francois Budin :: University of North Carolina :: fbudin at unc.edu
8. Saskia Camps :: Brigham and Women's Hospital :: saskiacamps at gmail.com
9. Lucia Cevidanes :: University of Michigan :: luciacev at umich.edu
10. Laurent Chauvin :: Brigham and Women's Hospital :: lchauvin at bwh.harvard.edu
11. Kanglin Chen :: Fraunhofer MEVIS, Bremen :: kanglin.chen at mevis.fraunhofer.de
12. Adrian Dalca :: Massachusetts Institute of Technology :: adalca at MIT.EDU
13. Alexander Derksen :: Fraunhofer MEVIS, Bremen :: alexander.derksen at mevis.fraunhofer.de
14. Maxime Desplanques :: Massachusetts General Hospital :: maxime.desplanques at cnao.it
15. Fotis Drakopoulos :: Old Dominion University :: fdrakopo at gmail.com
16. Sneha Durgapal :: Brigham and Women's Hospital :: durgapalsneha at gmail.com
17. Andriy Fedorov :: Brigham and Women's Hospital :: fedorov at bwh.harvard.edu
18. Jean-Christophe Fillion-Robin :: Kitware, Inc. :: jchris.fillionr at kitware.com
19. James Fishbaugh :: University of Utah :: jfishbau at sci.utah.edu
20. Jessica Forbes :: University of Iowa :: jessica-forbes at uiowa.edu
21. Polina Golland :: Massachusetts Institute of Technology :: polina at csail.mit.edu
22. Jeffrey Grethe :: UCSD :: jgrethe at ncmir.ucsd.edu
23. Rola Harmouche :: Brigham and Women's Hospital :: rolaharmouche at gmail.com
24. Nobuhiko Hata :: Brigham and Women's Hospital :: hata at bwh.harvard.edu
25. Jayender Jagadeesan :: Brigham and Women's Hospital :: jayender at bwh.harvard.edu
26. Saurabh Jain :: Johns Hopkins University :: saurabh at cis.jhu.edu
27. Hans Johnson :: University of Iowa :: hans-johnson at uiowa.edu
28. Jayashree Kalpathy-Cramer :: Massachusetts General Hospital :: kalpathy at nmr.mgh.harvard.edu
29. Tina Kapur :: Brigham and Women's Hospital :: tkapur at bwh.harvard.edu
30. Ron Kikinis :: Brigham and Women's Hospital :: kikinis at bwh.harvard.edu
31. Eun Young Regina Kim :: University of Iowa :: eunyoung-kim at uiowa.edu
32. Franklin King :: Queen's University :: franklin.king at queensu.ca
33. Tassilo Klein :: Brigham and Women's Hospital :: TJKlein at bwh.harvard.edu
34. Farukh Kohistani :: Brigham and Women's Hospital :: kohistan at bc.edu
35. Ivan Kolesov :: Stony Brook University :: ivan.kolesov1 at gmail.com
36. Robin Kouver :: Brigham and Women's Hospital :: r.kouver at gmail.com
37. Andras Lasso :: Queen's University :: lasso at queensu.ca
38. Yangming Li :: University of Washington :: ymli81 at uw.edu
39. Sidong Liu :: University of Sydney :: sliu at bwh.harvard.edu
40. Siqi Liu :: University of Sydney :: sliu4512 at uni.sydney.edu.au
41. Bradley Lowekamp :: National Library of Medicine :: blowekamp at mail.nih.gov
42. Murat Maga :: Seattle Children's Research Institute :: maga at uw.edu
43. Katie Mastrogiacomo :: Brigham and Women's Hospital :: kmast at bwh.harvard.edu
44. Alireza Mehrtash :: Brigham and Women's Hospital :: mehrtash at bwh.harvard.edu
45. Dominik Meier :: Brigham and Women's Hospital :: meier at bwh.harvard.edu
46. James Miller :: General Electric :: millerjv at ge.com
47. Luiz Otavio Murta :: Brigham and Women's Hospital :: lmurta at partners.org
48. Vivek Narayan :: Brigham and Women's Hospital :: narayan.vivek9 at gmail.com
49. Pietro Nardelli :: University College Cork :: pietro at bwh.harvard.edu
50. Isaiah Norton :: Brigham and Women's Hospital :: isaiah.norton at gmail.com
51. Jorge Onieva :: Brigham and Women's Hospital :: jorgeonieva at gmail.com
52. Yangming Ou :: Massachusetts General Hospital :: yangming.ou at uphs.upenn.edu
53. Danielle Pace :: Massachusetts Institute of Technology :: dfpace at mit.edu
54. Keryn Palmer :: Brigham and Women's Hospital :: kpalmer5 at partners.org
55. Nirav Patel :: Worcester Polytechnic Institute :: napatel at wpi.edu
56. Tobias Penzkofer :: Brigham and Women's Hospital :: pt at bwh.harvard.edu
57. Steve Pieper :: Isomics, Inc. :: pieper at isomics.com
58. Csaba Pinter :: Queen's University :: csaba.pinter at queensu.ca
59. Marcel Prastawa :: General Electric :: marcel.prastawa at ge.com
60. Somia Pujol :: Brigham and Women's Hospital :: spujol at bwh.harvard.edu
61. Adam Rankin :: Queen's University :: rankin at queensu.ca
62. Aymeric Reshef :: Brigham and Women's Hospital :: areshef at bwh.harvard.edu
63. Tammy Riklin Raviv :: Ben-Gurion University :: rrtammy at ee.bgu.ac.il
64. Rahul Sastry :: Brigham and Women's Hospital :: rahul_sastry at hms.harvard.edu
65. Peter Savadjiev :: Brigham and Women's Hospital :: petersv at bwh.harvard.edu
66. Gregory Sharp :: Massachusetts General Hospital :: gcsharp at mgh.harvard.edu
67. Emylin Sousa :: Brigham and Women's Hospital :: emylin.sousa at gmail.com
68. Ramesh Sridharan :: Massachusetts Institute of Technology :: rameshvs at csail.mit.edu
69. Clare Tempany :: Brigham and Women's Hospital :: ctempany at bwh.harvard.edu
70. Matthew Toews :: Brigham and Women's Hospital :: mt at bwh.harvard.edu
71. Ethan Ulrich :: University of Iowa :: ethan-ulrich at uiowa.edu
72. Tamas Ungi :: Queen's University :: ungi at queensu.ca
73. Kevin Wang :: Princess Margaret Cancer Centre :: kevin.wang at rmp.uhn.ca
74. David Welch :: University of Iowa :: david-welch at uiowa.edu
75. Sandy Wells :: Brigham and Women's Hospital :: sw at bwh.harvard.edu
76. Jason White :: Brigham and Women's Hospital :: white at bwh.harvard.edu
77. Alexander Yarmarkovich :: Isomics, Inc. :: alexy at bwh.harvard.edu
78. Ryan Young :: Seattle Children's Research Institute :: ryan.young at seattlechildrens.org
79. Paolo Zaffino :: Magna Græcia University of Catanzaro :: p.zaffino at unicz.it
80. Chenxi Zhang :: Brigham and Women's Hospital :: chenxizhang at fudan.edu.cn
81. Fan Zhang :: University of Sydney :: fzha8048 at uni.sydney.edu.au