2011 Winter Project Week

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To AHM 2011

Welcome to the web page for the 12th Project Week!

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Summary

The 12th PROJECT EVENT was held on January 10-14, 2011 in Salt Lake City, UT. It recorded 106 registered attendees, who worked on 59 projects. These attendees represented 20 academic sites (Brigham and Women's Hospital, UPenn, University of Utah, UNC Chapel Hill, UCLA, JHU, UCSF, MIT, MD Anderson, Georgia Tech, University of Iowa, Queen's University, Rutgers, Children's Hospital Boston, Massachusetts General Hospital, University of Western Australia, UCSD, SRI, WUSTL, Robarts) and 9 companies (Kitware, Isomics, GE Research, Radnostisc, Cosmo, AZE, Knowledgevis, Covidien, Physical Sciences).

A summary of all past Project Events.

Projects

Segmentation

• Extension of ABC (Atlas-Based Classification) to detect pathology categories, with tests on TBI images (Bo Wang, Jack Van Horn, Andrei Irimia, Micah Chambers, Marcel Prastawa, Guido Gerig).
• Segmentation of the left atrial wall for atrial fibrillation ablation therapy (Behnood Gholami, Yi Gao, and Allen Tannenbaum)
• The Vascular Modeling Toolkit in 3D Slicer (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
• TubeTK for vascular image segmentation and analysis (Stephen Aylward, Danielle Pace, Steve Pieper)
• A stenosis detector in Slicer4 using VMTK (Suares Tamekue, Daniel Haehn, Luca Antiga, Ron Kikinis)
• Surface Region Segmentation for Surgical Planning and Mapping (Peter Karasev, Karol Chudy, Allen Tannenbaum)
• Integration of SPECTRE into Slicer (Nicole Aucoin, Min Chen)
• Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)

Registration

• The 3DSlicer Registration Case Library (Dominik Meier,Ron Kikinis)
• Voxel Anisotropy and Bias Field Effects on Slicer Image Registration (Dominik Meier, Andriy Fedorov, William Wells) (tentative)
• DTI registration & resampling wizard (Dominik Meier, Hans Johnson, Francois Budin, Mark Scully)
• Efficient co-registration of multiple MR modalities using the ABC (atlas-based classification) framework, joint visualization of multiple co-registered modalities (Bo Wang, Jack Van Horn, Andrei Irimia, Micah Chambers, Marcel Prastawa, Guido Gerig).
• Longitudinal DTI Analysis for TBI and HD data for individual patients' follow-up images (Anuja Sharma, Guido Gerig)
• Atlas Registration in Slicer3 (Daniel Haehn, Dominik Meier, Kilian Pohl, Ryan Eckbo)
• Registration in the presence of anatomic variation (sliding organ registration) (Danielle Pace, Marc Niethammer, Petter Risholm, Tina Kapur, Sandy Wells, Stephen Aylward)
• Visualizing registration uncertainty in Slicer3 (Petter Risholm, William Wells)
• Landmark-based registration with analytic regularization (Nadya Shusharina, Gregory Sharp)
• DTI registration/processing pipeline in Slicer3 (Francois Budin, Clement Vachet)

IGT

• Two-tensor full brain tractography pipeline - Lauren O'Donnell, Yogesh Rathi, C-F Westin
• OpenIGTLink 2.0 (Junichi Tokuda, Nobuhiko Hata)
• Osteormark, navigation tool for Osteotomy (Laurent Chauvin, Nobuhiko Hata)
• Detection and compensation for prostate motion during MR-guided prostate biopsy (A.Fedorov, Andras Lasso)
• Thin Client QT Interface for IGT (Nicholas Herlambang, Nobuhiko Hata, Steve Pieper, Julien Finet, JC)
• Transform recorder and (surgical) procedure annotation module (Tamas Ungi, Junichi Tokuda)
• Surgical Tools Tracking (Martin Rajchl, Feng Li)
• Slicer IGT Looking forward (Junichi Tokuda, Nobuhiko Hata, Andriy Fedorov, Sandy Wells, Danielle Pace, Andras Lasso, Tamas Ungi)

Radiotherapy

• Segmentation of the eye structures for Adaptive Radiotherapy (Ivan Kolesov, Gregory Sharp, and Allen Tannenbaum)
• DICOM-RT export (Greg Sharp, Steve Pieper)

Analysis

• GAMBIT - Cortical thickness analysis - Clement Vachet, Martin Styner
• Particle shape analysis incorporating surface normals - Beatriz Paniagua, Martin Styner
• NAMIC shape analysis pipeline in Slicer 3 - Lucile Bompard, Martin Styner, Clement Vachet, Chris Gloschat
• Particle Systems for Shape Analysis - Josh Cates, Manasi Datar, Ross Whitaker
• MRSI module and SIVIC interface - Bjoern Menze, Jason Crane, Beck Olson, Polina Golland
• Porting the IA-FEMesh Module to Slicer4 - Curtis Lisle, Steve Pieper, Vince Magnotta

Informatics

• Share all UIowa Traveling Human Phantom DTI data with NAMIC - Mark Scully, Hans Johnson, Zack M.
• Recode FetchMI API to work with XNAT 1.5 API - Dan Marcus, Misha Milchenko
• Engineer XNAT infrastructure for handling slicer scene files - Dan Marcus, Misha Milchenko

Diffusion

• Test suite for DicomToNrrdConverter - Mark Scully, Zach Mullen, Xiaodong Tao, Joy Matsui, Hans Johnson
• Requirements gathering for refactoring DicomToNrrdConverter - Mark Scully, Xiaodong Tao, Joy Matsui, Hans Johnson
• Documentation and 1st Draft Tutorial for DTIPrep - Joy Matsui, Clement Vachet, Mark Scully, Hans Johnson
• Voxelwise fiber distribution from tractography - Yinpeng Li, Martin Styner
• Finsler tractography in ITK - Antonio Tristan-Vega, C-F Westin
• Statistical analysis of WM tracts generated by Tractography and Volumetric framework - Gopal Veni, Ross Whitaker

NA-MIC Kit Internals

• Command line module logic redesign (passing paramenters, tie into workflows) - Jim, Steve
• 64bit Windows Builds - David Partyka
• Dashboards: Factory machine, subprojects, and CDash@Home - David P, Zack M, Steve, and Stephen
• MIDAS for data hosting - Zach M and Hans
• vtkWidgets JC and Will, Nicole Aucoin
• Annotation module in Slicer4: Display widget intersections (Daniel Haehn, Nicole Aucoin, Steve Pieper)
• Python and Slicer4: Workflows, Scripting, and Porting - JC, Jim, Steve, Danielle and Demian
• Improve Performance of Slice Rendering in slicer3 and slicer4 (Steve, Will, Jc, J2, Jim, Luca)
• Real-Time Volume Rendering for Virtual Colonoscopy (Steve, Alex)
• Slicer4 - ITK4 Integration (Bill, Luis)

Execution Model

• Extract SlicerExecutionModel (SEM) into separate entity. SEM is the only component needed to build modules compatible with Slicer3D, so it should be easy incorporate into external applications without all of Slicer3D. Jim, Hans
• Extend SEM xml to include sections for explicit grant acknowledgements, pointers to documentation, and pointers to examples. - Hans, Andriy
• Create a formal schema for the SEM xml so that eternal tools (i.e. nipype) can validate the xml. - Hans Johnson, Jim Miller, Tim Olsen
• Improve documentation extractor script that converts XML to MediaWiki format so that it can directly push this information into the Slicer3D MediaWiki. - (Wiki Systems Admin), Hans Johnson, Steve Pieper, Stephen Aylward
• Improve merging strategies between software that is part of externals tools and part of Slicer. - Mark Scully, Hans Johnson

Workflows and Integration

• Workflows and Service Oriented Architecture Solutions for Slicer3 Modules (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)

Agenda

Please click here for the agenda for AHM 2011 and Project Week.

Background

From January 10-14, 2011, the twelfth 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 engage 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.

Preparation

1. Please make sure that you are on the NA-MIC Project Week mailing list.
2. Starting Thursday, October 28th, 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 28: Engineering Infrastructure Projects
   • November 4: Engineering Infrastructure Projects
   • November 11: DPB Projects: Iowa, Outcomes from Alg Core Retreat
   • November 18: DPB Projects: MGH
   • November 25: DBP Projects, Funded External Collaborations
   • December 2: Funded External Collaborations
   • December 9: Other External Collaborations
   • December 16:Finalize Engineering Projects
   • January 6: Loose Ends
3. By December 16, 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 16, 2010: 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...