2012 Winter Project Week

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Agenda and Project List

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Background

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy 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.

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

Projects

Traumatic Brain Injury

• Segmentation of Serial MRI of TBI patients using Personalized Atlas Construction (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
• Registration and analysis of white matter tract changes in TBI (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
• Validation, visualization and analysis of segmentation for TBI (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
• Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Stephen Aylward)
• Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
• Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

Predict Huntington's Disease

• SPIE DTI Workshop Preparation: Perform DTI Quality Control (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
• DTI tractography phantom: a software for evaluating tractography algorithms (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
• FiberViewerLight: a fiber bundle visualization and clustering tool (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
• DTIAtlasFiberAnalyzer (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
• Pairwise DTI registration: DTI-Reg (Clement Vachet, Hans Johnson, Martin Styner)
• Morphometric analysis in subcortical structures in HD (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
• Applying our DTI pipeline to analyse HD data (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
• Longitudinal change modeling of fiber tracts in serial HD DTI data (Anuja Sharma, Hans Johnson, Guido Gerig)
• Continuous 4d shape models from time-discrete data: Subcortical structures in HD (James Fishbaugh, Hans Johnson, Guido Gerig)

Atrial fibrillation

• Endocardial Segmentation in DE-MRI for AFib (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
• Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
• Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
• OpenIGT for realtime MRI-guided RF ablation (Gene Payne, Rob MacLeod, and Junichi Tokuda)
• Graph based segmentation on LGE-MRI data (Gopal Veni, Ross Whitaker)

Head and Neck Cancer

• A patch-based approach to the segmentation of organs of risk (Christian Wachinger, Polina Golland)
• Label fusion with pairwise interactions (Ramesh Sridharan, Christian Wachinger, Polina Golland)
• RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)
• Interactive editing tools for segmentation (Greg Sharp, Steve Pieper)
• Interactive 3D Level-Set Segmentation (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)
• Segmentation of polymodal images of GBM's in Slicer (Misha Milchenko, Dan Marcus, Andrey Fedorov, Jan Egger)

IGT for Surgery and Radiation Treatments

• OpenIGTLink interface for Slicer4 (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
• Live ultrasound in Slicer4 using Plus and OpenIGTLink (Tamas Ungi, Elvis Chen)
• 4D Ultrasound Storage and Volume Rendering on Slicer 3.6 (Laurent, Noby)
• Integration of BK Ultrasound into PLUS and Slicer (Mehdi Moradi, Isaiah Norton, Tamas Ungi)
• Deformable prostate registration: 3D ultrasound to MRI (Mehdi Moradi, Jan Egger, Andrey Fedorov)
• iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Kanokpis Townamchai, Tina Kapur, Akila Viswanathan)
• Needle Detection in MR Images for Brachytherapy in AMIGO (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Stephen Aylward)
• Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer for Neurosurgery (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Jens Sommer, Christopher Nimsky, Alexandra Golby, Tina Kapur)
• RT tools for Slicer4 (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
• RT structure set data representation (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

Musculoskeletal System

• Spine Segmentation & Osteoporosis Screening In CT Imaging Studies (Anthony Blumfield)

Registration

• Framework for Cranio-Maxillo Facial registration in Slicer3 (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
• Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)
• Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)
• Fast Image Interpolation Given Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)
• Register liver CT images for tumor progress monitoring (Karl Diedrich, Nobuhiko Hata, Atsushi Yamada)

Shape Analysis

• Principal Nested Spheres Normal Consistency in ShapeWorks (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
• Porting of White Matter Geometric Indices Module to Slicer4 (Peter Savadjiev)
• Slicer end-to-end particle correspondence wrapper module (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

NA-MIC Kit Internals

• Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
• Slicer4 extensions (JC)
• Slicer4 documentation (JC)
• Slicer4 GUI Testing (Benjamin Long, JC, J2)
• Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
• Slicer4 Scene Views Module (Nicole Aucoin, Ron Kikinis, Julien Finet)
• Annotations Module File Format Refactor (Nicole Aucoin)
• QT 3D Text rendering proof of concept (Julien Finet, Steve Pieper, Nicole Aucoin)
• DICOM Networking, Database, and Slicer Integration (Steve, Andrey, Andras)
• Editor Extension Examples and Debugging (Steve, Andrey, Jc, Hans, Satra)
• General minor GUI redesign (Wendy Plezniak, Julien Finet, Ron Kikinis)
• Redesign of the slice viewer control panels (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
• Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)
• Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
• Batch Processing with Slicer Modules (Steve, Andrey, JC, Hans, Satra)
• Support for 4D Images in Slicer4 (Andrey, Steve, Junichi, Alex)
• QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations (Andrey, Steve, Nicole, Jayashree)

Preparation

1. Please make sure that you are on the na-mic-project-week mailing list
2. Starting Thursday, October 27th, 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 27: MGH DBP
   • November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
   • November 10: Utah Atrial Fibrillation DBP
   • November 17: UCLA TBI DBP
   • November 24: No call. thanksgiving.
   • December 1:
   • December 8:
   • December 15:Finalize Projects
   • January 5: Loose Ends
3. By December 15: 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 15: 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. MIDAS, xNAT). 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...