2008 Winter Project Week

Back to Project Events, AHM_2008, Events

Projects

• 2008 Project Week Template
• Last Year's Projects as a reference
• For hosting projects, we are planning to make use of the NITRC resources. See Information about NITRC Collaboration
• Next Project Week is at MIT -- June 23-27, 2008

Please note that the first four categories below correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.

DBP Harvard Roadmap Project: Brain Segmentation for Velocardio Facial Syndrome (VCFS)

1. Dorsolateral Prefrontal Cortex Segmentation (Marek Kubicki, Sylvain Bouix, John Melonakos, Brad Davis, Polina Golland)

DBP UNC Roadmap Project: Cortical Thickness Measurement for Autism

1. Cortical thickness analysis of pediatric brains (Heather Cody Hazlett, Martin Styner, Clement Vachet)

DBP MIND Roadmap Project: Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus

1. Towards an end to end lesion analysis feature in Slicer3 (Mark Scully, Jeremy Bockholt, Brad Davis, Marcel Prastawa)

DBP JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention

1. Robotic Prostate Interventions (Gabor Fichtinger, David Gobbi, Csaba Csoma)

Structural Analysis

1. Groupwise Registration and Atlas Building (Brad Davis, Serdar Balci, Casey Goodlett)
2. Prostate Segmentation, (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger)
3. Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration (Mert Sabuncu, Kilian)
4. Cortical Surface Parcellation (Thomas Yeo, Mert Sabuncu)

Diffusion Image Analysis

1. Incorporating DTI data into entropy-based particle system for cortical correspondence (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner)
2. Integrating population based DTI tools into NAMIC Kit (Casey Goodlett)
3. Application of population based DTI tools to Schizophrenia (Casey Goodlett, Marek Kubicki)
4. Stochastic tractography of the arcuate fasciculus in schizophrenia (Marek Kubicki, Tri Ngo, Doug Markant)
5. Geodesic Tractography Segmentation, (John Melonakos, Allen Tannenbaum, Marek Kubicki)
6. Fluid Mechanics Based DTI Tractography (Nathan Hageman)

Image Guided Therapy

1. IGSTK-Slicer (Liu, w. Georgetown team, Hata, Tokuda) NA-MIC collaboration | Description
2. Japanese Intelligent Surgical Instrument Project (Hata, Chinzei, Hong)

NA-MIC Kit - Slicer 3

1. MRML Scenes for the Execution Model including Transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
2. Unstructured Grids and Mesh Support(Curt, Alex, Steve, Will, Vince, Bob O'Bara)
3. Python Support in Slicer 3 (Luca, Bryan Smith)
4. Transform hardening in MRML (Luca, Steve)
5. Event broker in Slicer3 (Jim, Steve, Luca)
6. CPack, CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)
7. Drafting Human Interface and Slicer Style Guidelines (Wendy,Sebastien)
8. Shape Descriptor Functions for Dendritic Spine Morphometrics (Bryan Smith, Padma, Martin Styner)
9. Revisit - ROIs in Slicer3 (Wendy, Jim, Nicole, Steve, Ron)
10. Volume rendering (Andy Freudling, Steve Pieper, Grauer)
11. Volume rendering using Cuda (Andy Freudling, Steve Pieper, Grauer)
12. Stereo Displays (Katharina, Curt)
13. 3D W Widgets and Picking (Will, Nicole, Curt, Kiran)
14. MRML support for out of core processing with fMRI and DTI as use cases (Steve, Jim, Wendy, Alex, Will)
15. XNAT Integration (XNAT, Slicer, XCEDE, Batchmake) (Dan Marcus, Steve, Stephen, Jeff, Julien)
16. KWWidgets Roadmap (Sebastien, Wendy, Katie)
17. Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)
18. Astronomical coordinate system support (Mike Halle, Doug Alan)

External Collaborations

1. New Meshing Techniques into NA-MIC [Univ. of Iowa] (Nicole Grosland, Vince Magnotta)
2. Meshing Workflow into Slicer] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta, Kiran, Steve Pieper, Curt Lisle, Brad Davis)
3. Evaluating NA-MIC Tools for Small Animal Imaging Workflows [NCI] (Curt Lisle, Jack Collins, Killian Pohl)
4. GoFigure:High-Level Microscopy Image analysis Application and Algorithms [CalTech-Harvard Medical School] (Alex G, Sean Megason, Arnaud Gelas?)
5. microSlicer3:Doing microscopy image analysis with Slicer3[Ohio State U](Kishore M., Raghu M., Brad Davis,Stephen Aylward, Steve Pieper)
6. fmri image analysis with Slicer 3[Ohio State U](Firdaus J.,Raghu M., Luis Ibanez,Steve Pieper, Wendy Plesniak)

Dates.Venue.Registration

Dates:

• The All Hands Meeting and External Advisory Board Meeting will be held on Thursday, January 10th.
• Project Activities will be held rest of the week between Monday, January 7th and Friday, January 11th.

Venue: The venue for the meeting is Marriot City Center, Salt Lake City, Utah Mariott City Center, Salt Lake City, Utah. (Floorplan). To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

Registration: We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click here for online registration. This registration must be completed by Friday, December 14, 2007.

Please note that this information can also be found here.

(This is a checklist for the onsite planning items)

Introduction to NA-MIC Project Week

Please read the introduction to these events here.

Agenda

Agenda for AHM 2008 and Project Week

Preparation

1. Please make sure that you are on the na-mic-project-week mailing list
2. November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams
3. December 6, 2007: TCON#2 with all participants to Assign/Verify Teams
4. December 13, 2007: TCON#3 with Breakout Session owners to review agendas
5. December 20, 2007: TCON#4 to discuss outstanding projects and teams
6. January 3, 2008: TCON#5 to discuss outstanding projects and teams
7. December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
8. January 3, 2008: 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)
9. By December 17, 2008: 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.
10. 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...

Previous Project Events

A history of all the programming/project events in NA-MIC is available by following this link.