2014 Winter Project Week

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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.

Dates.Venue.Registration

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

AGENDA and Project List

Please:

• Click here for the agenda for AHM 2014 and Project Week.
• Click here to jump to Project list

Background and Preparation

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

TBI

• Multimodal neuroimaging for the quantification of brain atrophy at six months following severe traumatic brain injury (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
• Systematic evaluation of axonal demyelination subsequent to traumatic brain injury using structural T1- and T2-weighted magnetic resonance imaging (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
• Mapping the effect of traumatic brain injury upon white matter connections in the human brain using 3D Slicer (Andrei Irimia, John D. Van Horn)
• Patient-specific longitudinal DTI analysis in traumatic brain injury (Anuja Sharma, Andrei Irimia, Bo Wang, John D. Van Horn, Martin Styner, Guido gerig)
• Testing the interactive segmentation algorithm for traumatic brain injury (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

Atrial Fibrillation

• DEMRI LA Segmentation via Image Fusion (MRA) (Josh, Salma, Alan)
• LA Fibrosis / Scar Visualization (Josh, Salma, Alan)
• CARMA Extension Documentation Project (Josh, Salma)
• LA Segmentation module using multi-column Graph Cuts (Gopal, Salma, Josh, Rob, Ross)
• Joint Image and Shape Analysis for Fibrosis Distribution(Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
• Grow cut, level set integration for interactive LA segmentation ( Liangjia Zhu, Ivan Kolesov, Yi Gao, Allen Tannenbaum)

Huntington's Disease

• DWI Dispersion (Hans, CF, Peter Savadjiev)
• DTI Compressed Sensing? (Hans, CF)
• Slicer module scripting? (Dave)
• DWIConverter? (Hans, Kent)
• Slicer Based Surface Template Estimation (Saurabh Jain, Steve Pieper, Hans Johnson, Josh Cates)
• 4D shape analysis: application to HD (James Fishbaugh,Hans Johnson, Guido Gerig)
• Shape registration and regression in Slicer4 (James Fishbaugh,Hans Johnson, Guido Gerig)

Head and Neck Cancer

• DIR Validation (Nadya and Greg)
• Hybrid B Spline (Nadya, Greg, Steve)
• Interactive Segmentation (Ivan, LiangJia, Nadya, Yi, Greg, Allen)

Slicer4 Extensions

• Surface Visualization - ShapePopulationViewer (Alexis Girault, Francois Budin, Beatriz Panaigua, Martin Styner)
• DTI Analysis Pipeline as Slicer4 Extensions (Francois Budin, Martin Styner)

Cardiac

• Monitoring engrafted stem cells in cardiac tissue with time series manganese enhanced MRI (Karl Diedrich)
• Whole-heart segmentation of cardiac MR images in congenital heart defect cases (Danielle Pace, Polina Golland)

Stroke

• Multi-Tissue Stroke Segmentation (Ramesh, Polina B., Polina G.)

Brain Segmentation

• Multi-Atlas based Multi-Image Segmentation (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)

Image-Guided Interventions

• OpenIGTLink Interface: New data types and structures (Junichi Tokuda, Andras Lasso, Steve Piper, ???)
• Ultrasound Visualization and Navigation in Neurosurgery (Matthew Toews, Alireza Mehrtash, Csaba Pinter, Andras Lasso, Steve Pieper, William M. Wells III)
• Percutaneous Approach Analysis (Atsushi Yamada, Junichi Tokuda, Koichiro Murakami, ??)
• Endoscope Console (Atsushi Yamada, Junichi Tokuda, ??)
• Statistical Shape Model for robotic spine surgery (Marine Clogenson, ???)
• Immersive VR devices (Franklin King, Andras Lasso)

Radiation Therapy

• DICOM RT Export (Greg Sharp, Kevin Wang, others??)
• DICOM Spatial Registration Export (Greg Sharp, Kevin Wang, others??)
• Interactive Registration and Evaluation (Kevin Wang, Steve Pieper, Greg Sharp)
• External Beam Planning Visualization (Kevin Wang, Greg Sharp, Csaba Pinter)

TMJ-OA

• Constrain Fiducial along Suface (Vinicius Boen, Nicole Aucoin, Beatriz Paniagua)
• Cropping multiple surfaces simultaneously (Alexander, Jc, Steve, Vinicius, Beatriz Paniagua)
• Color Coded Tables (Vinicius Boen, Beatriz Paniagua, Nicole Aucoin, Steve Pieper, Francois Budin)
• 4DShape Analysis of mandibular changes (Vinicius Boen, James Fishbaugh, Guido Gerig)

Chronic Obstructive Pulmonary Disease

• Chest Imaging Platform (CIP) - Core Infrastructure (Raul San Jose, Rola Harmouche, Pietro Nardelli, James Ross)
• CIP Testing and SuperBuild (James Ross, Raul San Jose)
• Slicer CIP- MRML consolidation (Pietro Nardelli, Rola Harmouche, James Ross, Raul San Jose)
• Slicer CIP- Modules (Rola Harmouche, Pietro Nardelli, James Ross, Raul San Jose)

QIICR

• 4D NIfTI Multivolume Support (Jayashree, Andrey, Jim, John)
• RT and ITK Format Conversions (Jayashree, Andras, Csaba. John)
• Python Scripting Slicer DICOM read/write to convert segmentation objects (Jayashree, Andrey, Alireza, Steve, Jc, Hans, John)
• User module for DCE modeling (Andrey, Jayashree, Jim, Alireza, Steve, Ron)
• DICOM enhanced multiframe object support (Andrey, Alireza, David Clunie, Jayashree, Steve, Reinhard, Jim)
• Quantitative Index Computation (Ethan Ulrich, Reinhard Beichel, Nicole, Andrey, Jim)
• TCIA Browser Extension in Slicer (Alireza, Andrey, Steve, Ron)

Infrastructure

• MRML Scene speed up (Jc, Andras Lasso)
• Multidimensional data support (Andras Lasso, Andriy Fedorov, Steve Pieper, JC, Kevin Wang)
• Markups Module (Nicole Aucoin)
• Logging (standardization, logging to file) (Nicole Aucoin, Steve Pieper, Jc, Andras Lasso, Csaba Pinter, ???)
• CLI (Jim Miller)
• Steered Registration (LandmarkRegistration module) (Steve, Greg, Kevin, Vinicius, Marcel)
• MRB Extension Dependencies (Steve, Jc, Jim, Nicole, Alex)
• Subject hierarchy (Csaba Pinter, Andras Lasso, Steve Pieper, Jc, Jayashree, John, Alireza, Andrey)
• Integration of Contour object (Csaba Pinter, Andras Lasso, Steve Pieper, ???)
• Integration nonlinear transforms (Alex Yarmarkovich, Csaba Pinter, Andras Lasso, Steve Pieper, ???)
• JSON Parameter Serialization (Matt McCormick, Steve Pieper, Jim Miller)
• 3DSlicer annotations in XNAT (Erwin Vast, Nicole Aucoin, Andrey Fedorov)
• Planar Images (Franklin King, Csaba Pinter, Andras Lasso)