2015 Summer Project Week

Welcome to the web page for the 21st Project Week!

The 21st PROJECT EVENT was held June 21-24, 2015 in Barcelona, Spain in conjunction with the CARS conference (http://www.cars-int.org/). It recorded 55 registered attendees, who worked on 39 projects. These attendees represented 20 academic sites (Boston Children’s Hospital, Brigham and Women’s Hospital, Charité University Hospital Berlin (Germany), École de Technologie Supérieure, (Canada), École supérieure d'informatique (Belgium), Fraunhofer (Germany), Leibniz Universität Hannover (Germany), Magna Graecia University (Italy),Massachusetts General Hospital, Queen’s University (Canada), Robarts Research Institute (Canada), Semmelweis University (Hungary), Universidad Autonoma del Estado de Mexico, Universidad Carlos III de Madrid, University of Groningen (Netherlands), Universidad de la Republica (Uruguay), Universidad Rey Juan Carlos (Madrid), Universidad Politécnica de Madrid, University of Strasbourg (France), University of Utah, and 7 companies (Kitware, Isomics Inc,Open Connections, Galgo Medical, BK Medical ApS, ICM, Perk Lab)

Logistics

• Dates: June 21-24, 2015.
• Location: NH Collection Constanza Hotel, Barcelona, Spain
• REGISTRATION: Please register by adding your name to the list at the end of this page
• Registration Fee: None. The organizers will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.
• Hotel: You are welcome to book a room using the CARS 2015 conference services (Click here for form)
• To attend the CARS meeting, please visit http://www.cars-int.org/
• Premium Network at Berlin Room:
  • username: EVENT/CARS2015
  • Password=CARS

• Please get a badge for CARS, even if you did not register for the CARS conference. Otherwise you will not be able to come in tomorrow.

Agenda

Time	Sunday, June 21	Monday, June 22 Room Berlin	Tuesday, June 23 Room Berlin	Wednesday, June 24 Room Berlin
9:00am-3:00pm:	6pm Meeting with All Participants in Hotel Constanza Lobby	10:00-11am: Rapid Introduction of all Projects and Teams 11am-3pm Work	10:00am-11am: Breakout Session: - Ask expert physicians (Ron Kikinis, Clare Tempany) 11am-3pm Work	Work
1:00pm-3:00pm		Lunch Places to Eat	Lunch Places to Eat	Lunch Places to Eat
4:00-7:00pm		Work	5:00-7:00pm: Breakout Session: Open Software Stack (Steve Pieper) 4pm-6pm: Registration Desk Open for CARS attendees. Please pick up badges.	4:00-5:00pm: Work 4:30-6pm: Report Progress
7:00pm		Adjourn for the day Places to Eat	Adjourn for the day Sant Joan Festival	6:00pm Adjourn Project Week and relocate to CARS Opening 7:30pm CARS Welcome Reception

• Please note that start, end, and mealtimes have been set to match local schedules in Barcelona.
• Here is a list of locally recommended places to eat in the vicinity of the conference hotel. All participants are responsible for their own meals.

Background

Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded NCBC program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform 3D Slicer, built using VTK, ITK, CMake, and CDash, and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

Project Week is a semi-annual event which draws researchers from around the world. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include NAC, NCIGT, QIICR, OCAIRO, and NCI Funded Image-Guided Fellowship Program.

A summary of all previous Project Events is available here.

This project week is an event endorsed by the MICCAI society.

The 21st Project Week is being held on conjunction with the CARS conference.

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

Projects

• Template for project pages

Equipment

• Specialized equipment people are going to bring (Please add to this list if you are bringing anything)

Image-Guided Therapy

• SlicerIGT tutorials for use cases (Tamas, Andras, Jay, Steve, Alvaro, Javier, Adam, Caroline, Noby, Tina)
• Refinement of RegistrationModule (Peter Behringer, Andrey Fedorov)
• Create base classes for IGT slicelet (Andras Lasso, Andrey Fedorov, Adam Rankin)
• BRAINSFit registration in SimpleITK (Peter Behringer, Andrey Fedorov, Dženan Zukić)
• Multi atlas based prostate segmentation (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)
• Multimodal Guidance for Breast Cancer Surgery (Mikael Brudfors, David García, Javier Pascau)
• Pilot Trajectory Planning(Caroline Essert, Sonia Pujol)
• Linear Feature Registration (Matthew Holden)
• Integration of a KUKA robot using OpenIGTLink (Sebastian Tauscher, Junichi Tokuda)
• Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer (Frank Preiswerk, Laurent Chauvin)
• Orthognathic Surgery (Dženan Zukić, Kitware)
• SlicerTAVI (Adam Rankin)
• pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)
• Open-source MRI-TRUS Fusion for Prostate biopsy (Andrey Fedorov, Andras Lasso, Clare Tempany)
• Trackerless MRI - US Registration (Utsav Pardasani)
• Sordina LINAC Guidance (Eugenio Marinetto)
• US Reconstruction (Steve Pieper, Tamas Ungi,Mikael Brudfors)

Feature Based Image Analysis

• LungCAD (Jayender Jagadeesan, Tobias Penzkofer, Sandy Wells, Clara Meinzer, Raúl San José Estepar, Jorge Onieva)
• Texture Analysis for Prostate Imaging (Tobias Penzkofer, Jay Jagadeesan, Matthew Toews, Tina Kapur)
• Big Data Medical Image Analysis using Local Features (Matthew Toews, William Wells, Raul San Jose Estepar, Tina Kapur)
• Automatic Cephalometric Analysis (J. Jesus Montufar, Marcelo Romero)

Chest Imaging Platform

• Slicer CIP: advanced features and deployment (Raúl San José, Alex Yarmarkovich, Jorge Onieva)
• PAA Ratio Module (Jorge Onieva,Raúl San José)
• Planning for tracheal stents (Raúl San José, Jorge Onieva, George Cheng)
• Volumetric Quantification of Atelectasis (Ángel Torrado-Carvajal, Carolina Romero, Norberto Malpica)

QIICR

• Dynamic Susceptibility Contrast (DSC) MRI for brain (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)
• T1 mapping for Dynamic Contrast Enhanced (DCE) MRI (Xiao Da, Yangming Ou, Andriy Fedorov, Jayashree Kalpathy-Cramer)
• Integration and testing of new DCMTK with Slicer (Michael Onken, Andrey Fedorov, Steve Pieper)

Infrastructure

• Return fiducials from CLIs (Nicole Aucoin,Hans Meine)
• Integrated Virtual Reality Viewer (Franklin King, Utsav Pardasani)
• Use new Segmentation node in Editor (Andras Lasso, Steve Pieper)
• Integrate Conda Python in Slicer (Jorge Onieva, Raúl San José, Utsav Pardasani, Steve Pieper)

Web

• Dicom parsing with DCMJS (Nicolas Rannou, Yves Martelli, Michael Onken, Steve Pieper)
• Volume Rendering with DCMJS and THREEJS (Nicolas Rannou, Steve Pieper)
• CTK for the web and touch devices (Nicolas Rannou, Yves Martelli, Steve Pieper)
• Slicer for mobile-based vr goggles (Utsav Pardasani, Adam Rankin)
• Python developer tutorial (Adam Rankin)

Astronomy

• Visualization of HI in galaxies (Davide Punzo)

Registrants

Please add your name to the list. This is the registration mechanism for this project week.

1. Tina Kapur, BWH
2. Ron Kikinis, BWH & Fraunhofer
3. Steve Pieper, Isomics
4. Tamas Ungi, Queen's University, Canada
5. Andras Lasso, Queen's University, Canada
6. Paolo Zaffino, ImagEngLab, Magna Graecia University, Italy
7. Salvatore Scaramuzzino, ImagEngLab, Magna Graecia University, Italy
8. Giampaolo Pileggi, ImagEngLab, Magna Graecia University, Italy
9. Nicole Aucoin, BWH
10. Sonia Pujol, BWH
11. Dženan Zukić, Kitware, Carrboro, NC
12. Jayender Jagadeesan, BWH
13. Guido Gerig, Utah
14. Sandy Wells, BWH
15. Matthew Toews, École de Technologie Supérieure, Montreal, Canada
16. Frank Preiswerk, BWH
17. Raul San Jose, BWH
18. Jorge Onieva, BWH
19. Yulong Zhao, Université de Rennes
20. Laurent Chauvin, BWH
21. Michael Onken, Open Connections
22. Tobias Penzkofer, Department of Radiology, Charité Berlin, Germany
23. Javier Pascau, Universidad Carlos III de Madrid, Spain
24. Angel Torrado-Carvajal, Universidad Rey Juan Carlos, Madrid, Spain
25. Nobuhiko Hata, BWH
26. Robert H. Owen, BK Medical ApS, Denmark
27. Clare Tempany, BWH
28. Adam Rankin, Robarts
29. Utsav Pardasani, Robarts
30. Marcelo Romero, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
31. J. Jesus Montufar, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
32. Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
33. Andrey Fedorov, BWH
34. Nicolas Rannou, BCH
35. Mikael Brudfors, Universidad Carlos III de Madrid, Spain
36. Laura Sanz, Universidad Carlos III de Madrid, Spain
37. Eugenio Marinetto, Universidad Carlos III de Madrid, Spain
38. David García, Universidad Carlos III de Madrid, Spain
39. Franklin King, Queen's University / BWH
40. Jorge García, Universidad Politécnica de Madrid, Spain
41. Peter Behringer, BWH
42. Caroline Essert, University of Strasbourg
43. Sebastian Tauscher, Institute of Mechatronic Systems, Leibniz Universität Hannover, Germany
44. Matthew Holden, Queen's University, Canada
45. Sara Fernandez Vidal, ICM, France
46. Laszlo Kanyasi, Perk Lab affiliate, Hungary
47. Xiao Da, MGH
48. Arnaud De Bruecker, École supérieure d'informatique, Brussels, Belgium
49. Ali Gottschalk, École supérieure d'informatique, Brussels, Belgium
50. Christophe Teixeira Pereira, École supérieure d'informatique, Brussels, Belgium
51. Tsotne Shonia, École supérieure d'informatique, Brussels, Belgium
52. Clara Meinzer, Semmelweis University, Hungary
53. Yves Martelli, Galgo Medical, Barcelona, Spain
54. Alvaro Gomez (Universidad de la Republica, Uruguay)
55. Alfredo Higueras, Galgo Medical, Barcelona, Spain