2010 Winter Project Week

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Background

From January 4-8, 2010, the tenth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engange in open source programming using the NA-MIC Kit, algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers (NA-MIC, NCIGT, NAC, Harvard Catalyst, and CIMIT) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

Dates.Venue.Registration

Please click here for Dates, Venue, and Registration for this event.

Agenda

Please click here for the agenda for AHM 2010 and Project Week.

Modules and extensions

• Overview
• Requirements for modules
• User-side explanations
• Developer-side explanations

Projects

Segmentation

1. Spine Segmentation Module in Slicer3 (Martin Loepprich, Sylvain Jaume, Polina Golland, Ron Kikinis, Steve Pieper)
2. The Vascular Modeling Toolkit in 3D Slicer (Daniel Haehn, Luca Antiga, Steve Pieper)
3. Active contour segmentation using robust statistics (Yi Gao, Allen Tannenbaum, GT; Andriy Fedorov, Katie Hayes Ron Kikinis, BWH)
4. High Level Wizard for Segmentation of Images (Mark Scully, Jeremy Bockholt, Steve Pieper)
5. Longitudinal Analyses of Lesions in Lupus (Mark Scully, Jeremy Bockholt, Steve Pieper)
6. Multiscale Analyses of Lupus Patients (Mark Scully, Jeremy Bockholt, Steve Pieper)
7. Prostate segmentation using shape-based method (Andras Lasso, Gabor Fichtinger, Yi Gao, Allen Tannenbaum, Andriy Fedorov)
8. Tubular Tree Segmentation for brain and cardiac imagery (Vandana Mohan, Allen Tannenbaum, GT; Marek Kubicki, BWH)
9. Segmentation of the Endocardial Wall (Behnood Gholami, Yi Gao, Allen Tannenbaum, GT; Rob MacLeod, Josh Blauer, University of Utah)
10. Segmentation on Mesh Surfaces Using Geometric Information (Peter Karasev, Matias Perez, Allen Tannenbaum, GT; Ron Kikinis, BWH)
11. Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI (Marcel Prastawa, Guido Gerig, Ron Kikinis)
12. Cadiac Ablation Scar Segmentation (Michal Depa, Polina Golland, Ehud Schmidt, Ron Kikinis)
13. Rapid Segmentation of Knee Structures for Simulation (Harish Doddi, Saikat Pal, Luis Ibanez, Scott Delp)
14. White Matter Lesion segmentation (Minjeong Kim UNC)

Registration

1. The 3DSlicer Registration Case Library Project (Dominik Meier, Casey Goodlett, Ron Kikinis)
2. Registration Infrastructure (Casey Goodlett, Dominik Meier, Ron Kikinis)
3. Deformation Field and Tensor Visualization (Garrett Larson, Martin Styner)
4. Fusion of Anatomy,MRI and Electrophysiology in Parkinson's (Andrzej Przybyszewski, Dominik Meier, Ron Kikinis)
5. Testbed for Evaluation, Comparison, and Parameter Exploration for 3D Registration (James Fishbaugh, Casey Goodlett, Guido Gerig)
6. HAMMER Registration Algorithm in Slicer 3 (Guorong Wu, Xiaodong Tao, Jim Miller, and Dinggang Shen)

IGT

1. Registration with Varying Elastic Parameters for Tumor Resection (Petter Risholm, Sandy Wells)
2. MRI Reconstruction by Registration for Focused Ultrasound Therapy (Ben Schwartz, Sandy Wells)
3. MRI-guided Robotic Prostate Intervention (Andras Lasso and Junichi Tokuda)
4. Atlas-Based White Matter Segmentation for Neurosurgical Planning (Lauren O'Donnell, C-F Westin, Alexandra J. Golby)
5. Fast Imaging Library, and Siemens EPI for IGT (Scott Hoge, Nick Todd, Dennis Parker, Katie Hayes)

Radiotherapy

1. DicomRT plugin for Slicer (Greg Sharp, others)
2. Adaptive Radiotherapy for Head, Neck, and Thorax (Ivan Kolesov, Vandana Mohan, Greg Sharp, Allen Tannenbaum )

Analysis

1. Vervet MRI Longitudinal Analysis (Andriy Fedorov, Ron Rikinis, Ginger Li, Chris Wyatt)
2. MRSI Module (Bjoern Menze, Polina Golland)
3. Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
4. XNAT Use for Population Analysis (Corentin Hamel, Martin Styner, Clement Vachet)

Informatics

1. XNAT Desktop User Interface (Dan M, Wendy P, Ron K)
2. Slicer 3 XNAT Performance Tuning (Wendy P, Dan M, Tim Olson, Nicole Aucoin)
3. Harvard CTSC XNAT (Yong Gao, Dan M, Tim Olson, John Paulett)
4. xnatfs Integration into XNAT core (Dan Blezek, John Paulett, Tim Olsen)
5. Open Access Whole body CT/MR data set (Dan Marcus, Steve Pieper)
6. Annotation of Medical Images (Kilian Pohl, Yong Zhang, Nicole Aucion, Wendy Plesniak, Steve Pieper)

Diffusion

1. Integration of Real Spherical Harmonic basis for HARDI models (Luke Bloy, C-F Westin)
2. Filtered tractography (James Malcolm, Peter Savadjiev, Yogesh Rathi, C-F Westin, Casey Goodlett)
3. Connectivity Study of Neonatal Brain Data using HARDI Techniques ( Yundi(Wendy) Shi, Deepika Mahalingam, Martin Styner )
4. Tractography Picking and Bundle Editing (Jim Miller, Mahnaz Maddah, Nicole Aucoin, Wendy Plesniak, James Malcolm, Alex Yarmarkovich)
5. DTI Fiber-Tract Statistics (Anuja Sharma, Guido Gerig)
6. Tractography using DTI Atlasing (Gopalkrishna Veni, Ross Whitaker, Sarang Joshi)
7. DTI Quality Control tools integration with NITRC (Hans Johnson, UNC)

NA-MIC Kit Internals

1. Testing for Extensions (Steve, Andriy Fedorov, Jim, Julien Jomier, Katie Hayes, Stuart Wallace)
2. Integration of SPECTRE Java module into 3D Slicer (Nicole Aucoin, Aaron Carass, Min Chen, Jim Miller)
3. VTK 3D Widgets in Slicer3 (Nicole Aucoin, Karthik, Will)
4. Updates to Slicer3 Colors Module (Nicole Aucoin)
5. CMAKE_Build_process (Dave Partyka, Katie Hayes)
6. Integration of XNAT Packaging for Slicer Internals (Dan, Tim Olsen, Steve Pieper, Dave Partyka, Wendy, Randy)
7. Orthogonal planes in reformat widget issues in Slicer3.5 (Michal Depa, Steve Pieper)
8. Slicer Dashboard (Luis, Steve, Bill & All)

(Other possibilities: Plotting, Layouts)

NA-MIC Outreach

1. Tutorial Polishing (Stuart Wallace, Randy Gollub, Sonia Pujol, all contributing tutorial contest developers)

Execution Model

1. Qt-ing the Command Line Module (Jim Miller, Jean-Christophe Fillion-Robin, Julien Finet)
2. Simple Return Types (Jim Miller)

Preparation

1. Please make sure that you are on the na-mic-project-week mailing list
2. Starting Thursday, October 15th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
   • October 15: Engineering Infrastructure Projects
   • October 22: Funded External Collaboration Projects
   • October 29: Funded External Collaboration Projects
   • November 5: DPB Projects
   • November 19: DPB Projects
   • December 3: Other/new collaborations
   • December 10: Finalize Engineering Projects
   • December 17: Loose Ends
3. By December 17, 2010: 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.
4. By December 17, 2009: Create a directory for each project on the NAMIC Sandbox (Zack)
   1. Ask Zack for a Sandbox account
   2. 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)
   3. 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.)
   4. 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)
5. 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...