NAMIC Wiki - User contributions [en]

2015 Summer Project Week

2015-06-08T14:17:53Z

Yrathi: /* Registrants */

__NOTOC__

[[image:PW-Summer2015.png|300px]]
 

'''Welcome to the web page for the 21st Project Week! This is the first Project Week that is being held in conjunction with the [http://www.cars-int.org/ CARS conference].'''

==Logistics==

*'''Dates:''' June 21-24, 2015.
*'''Location:''' [http://www.nh-collection.com/hotel/nh-collection-barcelona-constanza NH Collection Constanza Hotel, Barcelona, Spain]
*'''REGISTRATION:''' Please register by adding your name to the list at the end of this page
*'''Registration Fee:''' None. The organizers will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.
*'''Hotel:''' You are welcome to book a room using the CARS 2015 conference services ([http://www.cars-int.org/fileadmin/templates/download/2015/CARS_2015_accomondation.pdf Click here for form])
*To attend the CARS meeting, please visit [http://www.cars-int.org/ http://www.cars-int.org/]

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Sunday, June 21
!style="width:18%" |Monday, June 22
!style="width:18%" |Tuesday, June 23
!style="width:18%" |Wednesday, June 24
|-
|bgcolor="#ffffdd"|'''10:00am-3:00pm:'''
|rowspan=3 valign=bottom|<hr>'''6pm''' Meeting with All Participants in Hotel Constanza Lobby
|'''10:00-11am:''' Rapid Introduction of all Projects and Teams 
'''11am-3pm''' Work 

|
'''10:00am-11am:''' '''Breakout Session:''' [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis) 
'''11am-3pm''' Work
|'''10am-3pm''' Work 
|-
|bgcolor="#ffffdd"|'''3:00pm-5:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|-
|bgcolor="#ffffdd"|'''5:00-7:00pm'''
|'''5:00-7pm:''' Work
|'''5:00-7:00pm:''' '''Breakout Session:''' [[2015_Summer_Project_Week/SoftwareStack| Open Software Stack]] (Steve Pieper)
|'''5:00-6pm:''' Work 
'''6:00-7pm:''' Report Progress
|-
|bgcolor="#ffffdd"|'''7:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|}

== '''Background''' ==

Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws researchers from around the world. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

The 21st Project Week is being held on conjunction with the [http://www.cars-int.org/ CARS conference].

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2015_Summer_Project_Week_Template | Template for project pages]]

==Image-Guided Therapy==
*[[2015 Orthognatic Surgery|Orthognatic Surgery]] (Dženan Zukić, Kitware)
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]
*[[2015_pilot trajectory planning | Pilot Trajectory Planning(Caroline Essert, Sonia Pujol)]]
*[http://www.na-mic.org/Wiki/index.php/2015_Multi_atlas_based_prostate_segmentation Multi atlas based prostate segmentation] (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)
*[[2015_Summer_Project_Week:SlicerIGT|SlicerIGT tutorials for use cases]] (Tamas Ungi)
*[http://www.na-mic.org/Wiki/index.php/2015_Refinement_Registration_Module Refinement of RegistrationModule] (Peter Behringer, Andrey Fedorov)
*[http://www.na-mic.org/Wiki/index.php/2015_BRAINSFit_registration_in_SimpleITK BRAINSFit registration in SimpleITK] (Peter Behringer, Andrey Fedorov)

==Feature Based Image Analysis==
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan)
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Tina Kapur)
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Tina Kapur)

==Astronomy==
*[[2015_Summer_Project_Week:Astronomy | visualization of HI in galaxies]] (Davide Punzo)

==Infrastructure==
*[[2015_Summer_Project_Week:DCMTK| Integration and testing of new DCMTK with Slicer]] (Michael Onken, Andrey Fedorov)
*[[2015_Summer_Project_Week:Python_scripts_from_command_line|Simplify use of python scripts from the command line]] (Andrey Fedorov, Steve Pieper, Robin Weiss, Artem Mamonov)
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC)
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, ??)
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with "interesting" CLI modules (BRAINSFit, CIP, UKFTractography?) in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin, Jim Miller)
*[[2015_Summer_Project_Week:Update Checker | Update Checker]] (Frankling King, BWH)
*[[2015_Summer_Project_Week:Integrated Virtual Reality Viewer | Integrated Virtual Reality Viewer]] (Frankling King, BWH)
*[[2015_Summer_Project_Week:SegmentationNode| Use new Segmentation node in Editor]] (Andras Lasso, Steve Pieper)
*[[2015_Summer_Project_Week:IGTSliceletBase| Create base classes for IGT slicelet]] (Andras Lasso, Andrey Fedorov)

==Web / DCMJS==
*[[2015_Summer_Project_Week:Dicom parsing with DCMJS | Dicom parsing with DCMJS]] (Nicolas Rannou, Steve Pieper)
*[[2015_Summer_Project_Week:Volume rendering with DCMJS and THREEJS | Volume Rendering with DCMJS and THREEJS]] (Nicolas Rannou, Steve Pieper)

== '''Registrants''' ==

Please add your name to the list. This is the registration mechanism for this project week.
#Tina Kapur, BWH
#Ron Kikinis, BWH & Fraunhofer
#Steve Pieper, Isomics
#Tamas Ungi, Queen's University, Canada
#Andras Lasso, Queen's University, Canada
#Paolo Zaffino, ImagEngLab, Magna Graecia University, Italy
#Salvatore Scaramuzzino, ImagEngLab, Magna Graecia University, Italy
#Giampaolo Pileggi, ImagEngLab, Magna Graecia University, Italy
#Hans Meine, Fraunhofer MEVIS, Bremen, Germany
#Nicole Aucoin, BWH
#Sonia Pujol, BWH
#Dženan Zukić, Kitware, Carrboro, NC
#Jayender Jagadeesan, BWH
#Guido Gerig, Utah
#Sandy Wells, BWH
#Matthew Toews, École de Technologie Supérieure, Montreal, Canada
#Frank Preiswerk, BWH
#Junichi Tokuda, BWH
#Raul San Jose, BWH
#Jorge Onieva, BWH
#Yulong Zhao, Université de Rennes
#Laurent Chauvin, BWH
#Michael Onken, Open Connections
#Tobias Penzkofer, Department of Radiology, Charité Berlin, Germany
#Javier Pascau, Universidad Carlos III de Madrid, Spain
#Angel Torrado-Carvajal, Universidad Rey Juan Carlos, Madrid, Spain
#Nobuhiko Hata, BWH
#Robert H. Owen, BK Medical ApS, Denmark
#Clare Tempany, BWH
#Adam Rankin, Robarts
#Utsav Pardasani, Robarts
#Marcelo Romero, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#J. Jesus Montufar, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
#Andrey Fedorov, BWH
#Nicolas Rannou, BCH
#Mikael Brudfors, Universidad Carlos III de Madrid, Spain
#Laura Sanz, Universidad Carlos III de Madrid, Spain
#Eugenio Marinetto, Universidad Carlos III de Madrid, Spain
#David García, Universidad Carlos III de Madrid, Spain
#Franklin King, Queen's University / BWH
#Jorge García, Universidad Politécnica de Madrid, Spain
#Peter Behringer, BWH
#Caroline Essert, University of Strasbourg
#Pradyumna Reddy, Birla Institute of Technology and Science, Goa-Campus, India.

2010 Summer Project Two Tensor

2010-06-07T18:11:42Z

Yrathi: /* Project */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Stefan Leinhard, James Malcolm, Demian Wassermann, Yogesh Rathi

==Project==
<div style="margin: 10px;">
<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Objective</h3>
1. Implement and test the unscented Kalman filter based two-tensor tractography module in Slicer. We will use Python to implement this module.
2. Another objective is to provide a module that can detect false-positives from the results of the two-tensor tractography module. This module
will also allow for editing (threshold based) fibers and obtaining statistics such as FA, trace, etc on the remaining fibers.
</div>

<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Approach, Plan</h3>
We will use Python/C++ to implement this module.
</div>

<div style="width: 35%; float: left;">
<h3>Progress</h3>
Both the modules are 90% done. We will finish the remaining parts and test the module by the end of the project week.
</div>

2010 Summer Project Two Tensor

2010-06-07T18:10:46Z

Yrathi: Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List </gallery> ==Key Investigators== * BWH: Stefan Leinhard, James Malcolm, Demian Wasse…'

2010 Summer Project Week

2010-06-07T18:05:32Z

Yrathi: /* Diffusion */

__NOTOC__

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. 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 coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and 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 will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanesz)
**3-4pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah, Fill in Dates]]

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
*[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
*[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
*[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
*[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
*[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
*[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* BrainLab-Aurora HybridNav (Isaiah Norton, Dan Marcus)
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
* PerkStation Module (Tamas Ungi)

=== Radiotherapy ===
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)

=== Analysis ===
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
*[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
* [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
* [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason, Badri Roysam)
* [[ITK GPAC level set]] (K. Palaniappan, Kishore Mosaliganti, Sean Megason)
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)

=== Shape Analysis ===
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
* [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)

=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== Diffusion ===
*Fluid Mechanics Based Tractography (Nathan Hageman)
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
*[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)

=== NA-MIC Kit Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)
* [[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
*XNAT Enterprise webservices client for Slicer (Wendy, Mark)
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)

*VTKWidgets (JC, will, Schroeder, Nicole, Ron)
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|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.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). 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.)
## 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)
# 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...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]

# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Eckbo Ryan , BWH
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Haehn Daniel , University of Pennsylvania
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Li Rui , MGH
# Lisle Curtis , KnowledgeVis, LLC
# Liu Haiying , Brigham and Women's Hospital
# Liu Yanling , SAIC-Frederick, Inc.
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , Brigham and Women's Hospital
# Tao Xiaodong , GE Research
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
# Wells Sandy , BWH
# Wu Guorong , University of North Carolina at Chapel Hill

Projects:MultiTensorTractography

2010-05-13T17:35:18Z

Yrathi: /* Publications */

= Multi Tensor Tractography =

We describe a unified framework to simultaneously estimate multiple fibers at
each location and perform tractography. Existing techniques estimate the local fiber orientation at each voxel
independently so there is no running knowledge of confidence in the
estimated fiber model. We formulate fiber tracking as recursive estimation: at each step of tracing
the fiber, the current estimate is guided by the previous.

To do this we model the signal as either a weighted mixture of Gaussian tensors or
Watson directional functions and
perform tractography within a filter framework. Starting from a seed point,
fiber is traced to its termination using an unscented Kalman filter to
simultaneously fit the local model and propagate in the most consistent
direction. Further, we modify the Kalman filter to enforce model, i.e., positive eigenvalues and convex weights. Despite the
presence of noise and uncertainty, this provides a causal estimate of the
local structure at each point along the fiber.

Synthetic experiments demonstrate that this approach significantly improves
the angular resolution at crossings and branchings while consistently
estimating the mixture weights. ''In vivo'' experiments confirm the
ability to trace out fibers in areas known to contain such crossing and
branching while providing inherent path regularization.

[[Image:case01045_2T_tc.png|700px|thumb|left|]]

= Key Investigators =

* Brigham & Women's Hospital: Y. Rathi, J. Malcolm, Sylvain Bouix, Marek Kubicki, Martha E. Shenton, Carl-Fredrik Westin.
* University of Waterloo: O. Michailovich

= Publications =
* J. Malcolm, M. E. Shenton, Y. Rathi. Neural tractography using an unscented Kalman filter. Inf Process Med Imaging,Volume 21, Pages 126-138, 2009 [http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmInfProc09.html (see here for the reference)].

* J. Malcolm, M. E. Shenton, Y. Rathi. Two-Tensor Tractography Using a Constrained Filter. MICCAI, Pages 894-902, 2009 [http://pnl.bwh.harvard.edu/pub/papers_html/Malcolm-MICCAI2009.html (see here for the reference)].

* J. Malcolm, M. Kubicki, M. E. Shenton, Y. Rathi. The Effect of local fiber model on population studies. Workshop on Diffusion modeling (MICCAI), Pages 33-40, 2009 [http://jgmalcolm.com/ (see here for the reference)].

* J. Malcolm, O. Michailovich, S. Bouix, C.F. Westin, M. E. Shenton, Y. Rathi A filtered approach to neural tractography using the Watson directional function. Med Image Analysis, Volume 14, Pages 58-69 2010 [http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmMedImage10.html (see here for the reference)].

Projects:MultiTensorTractography

2010-05-13T17:29:21Z

Yrathi: /* Key Investigators */

= Multi Tensor Tractography =

We describe a unified framework to simultaneously estimate multiple fibers at
each location and perform tractography. Existing techniques estimate the local fiber orientation at each voxel
independently so there is no running knowledge of confidence in the
estimated fiber model. We formulate fiber tracking as recursive estimation: at each step of tracing
the fiber, the current estimate is guided by the previous.

To do this we model the signal as either a weighted mixture of Gaussian tensors or
Watson directional functions and
perform tractography within a filter framework. Starting from a seed point,
fiber is traced to its termination using an unscented Kalman filter to
simultaneously fit the local model and propagate in the most consistent
direction. Further, we modify the Kalman filter to enforce model, i.e., positive eigenvalues and convex weights. Despite the
presence of noise and uncertainty, this provides a causal estimate of the
local structure at each point along the fiber.

Synthetic experiments demonstrate that this approach significantly improves
the angular resolution at crossings and branchings while consistently
estimating the mixture weights. ''In vivo'' experiments confirm the
ability to trace out fibers in areas known to contain such crossing and
branching while providing inherent path regularization.

[[Image:case01045_2T_tc.png|700px|thumb|left|]]

= Key Investigators =

* Brigham & Women's Hospital: Y. Rathi, J. Malcolm, Sylvain Bouix, Marek Kubicki, Martha E. Shenton, Carl-Fredrik Westin.
* University of Waterloo: O. Michailovich

= Publications =
* J. Malcolm, M. E. Shenton, Y. Rathi. Neural tractography using an unscented Kalman filter. Inf Process Med Imaging,Volume 21, Pages 126-138, 2009 [http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmInfProc09.html (see here for the reference)].

* J. Malcolm, M. E. Shenton, Y. Rathi. Two-Tensor Tractography Using a Constrained Filter. MICCAI, Pages 894-902, 2009 [http://pnl.bwh.harvard.edu/pub/papers_html/Malcolm-MICCAI2009.html (see here for the reference)].

* J. Malcolm, O. Michailovich, S. Bouix, C.F. Westin, M. E. Shenton, Y. Rathi A filtered approach to neural tractography using the Watson directional function. Med Image Analysis, Volume 14, Pages 58-69 2010 [http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmMedImage10.html (see here for the reference)].

Projects:MultiTensorTractography

2010-05-13T17:28:36Z

Yrathi: /* Publications */

= Multi Tensor Tractography =

We describe a unified framework to simultaneously estimate multiple fibers at
each location and perform tractography. Existing techniques estimate the local fiber orientation at each voxel
independently so there is no running knowledge of confidence in the
estimated fiber model. We formulate fiber tracking as recursive estimation: at each step of tracing
the fiber, the current estimate is guided by the previous.

To do this we model the signal as either a weighted mixture of Gaussian tensors or
Watson directional functions and
perform tractography within a filter framework. Starting from a seed point,
fiber is traced to its termination using an unscented Kalman filter to
simultaneously fit the local model and propagate in the most consistent
direction. Further, we modify the Kalman filter to enforce model, i.e., positive eigenvalues and convex weights. Despite the
presence of noise and uncertainty, this provides a causal estimate of the
local structure at each point along the fiber.

Synthetic experiments demonstrate that this approach significantly improves
the angular resolution at crossings and branchings while consistently
estimating the mixture weights. ''In vivo'' experiments confirm the
ability to trace out fibers in areas known to contain such crossing and
branching while providing inherent path regularization.

[[Image:case01045_2T_tc.png|700px|thumb|left|]]

= Key Investigators =

* Brigham & Women's Hospital: Y. Rathi, J. Malcolm, Sylvain Bouix, Marek Kubicki, Martha E. Shenton, Carl-Fredrik Westin.

= Publications =
* J. Malcolm, M. E. Shenton, Y. Rathi. Neural tractography using an unscented Kalman filter. Inf Process Med Imaging,Volume 21, Pages 126-138, 2009 [http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmInfProc09.html (see here for the reference)].

* J. Malcolm, M. E. Shenton, Y. Rathi. Two-Tensor Tractography Using a Constrained Filter. MICCAI, Pages 894-902, 2009 [http://pnl.bwh.harvard.edu/pub/papers_html/Malcolm-MICCAI2009.html (see here for the reference)].

* J. Malcolm, O. Michailovich, S. Bouix, C.F. Westin, M. E. Shenton, Y. Rathi A filtered approach to neural tractography using the Watson directional function. Med Image Analysis, Volume 14, Pages 58-69 2010 [http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmMedImage10.html (see here for the reference)].

Projects:MultiTensorTractography

2010-05-13T17:28:13Z

Yrathi: /* Multi Tensor Tractography */

= Multi Tensor Tractography =

We describe a unified framework to simultaneously estimate multiple fibers at
each location and perform tractography. Existing techniques estimate the local fiber orientation at each voxel
independently so there is no running knowledge of confidence in the
estimated fiber model. We formulate fiber tracking as recursive estimation: at each step of tracing
the fiber, the current estimate is guided by the previous.

To do this we model the signal as either a weighted mixture of Gaussian tensors or
Watson directional functions and
perform tractography within a filter framework. Starting from a seed point,
fiber is traced to its termination using an unscented Kalman filter to
simultaneously fit the local model and propagate in the most consistent
direction. Further, we modify the Kalman filter to enforce model, i.e., positive eigenvalues and convex weights. Despite the
presence of noise and uncertainty, this provides a causal estimate of the
local structure at each point along the fiber.

Synthetic experiments demonstrate that this approach significantly improves
the angular resolution at crossings and branchings while consistently
estimating the mixture weights. ''In vivo'' experiments confirm the
ability to trace out fibers in areas known to contain such crossing and
branching while providing inherent path regularization.

[[Image:case01045_2T_tc.png|700px|thumb|left|]]

= Key Investigators =

* Brigham & Women's Hospital: Y. Rathi, J. Malcolm, Sylvain Bouix, Marek Kubicki, Martha E. Shenton, Carl-Fredrik Westin.

= Publications =
* J. Malcolm, M. E. Shenton, Y. Rathi. Neural tractography using an unscented Kalman filter. Inf Process Med Imaging,Volume 21, Pages 126-138, 2009 [http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmInfProc09.html (see here for the reference)].

* J. Malcolm, M. E. Shenton, Y. Rathi. Two-Tensor Tractography Using a Constrained Filter. Medical Image Computing and Computer Assisted Intervention
MICCAI, Pages 894-902, 2009 [http://pnl.bwh.harvard.edu/pub/papers_html/Malcolm-MICCAI2009.html (see here for the reference)].

* J. Malcolm, O. Michailovich, S. Bouix, C.F. Westin, M. E. Shenton, Y. Rathi A filtered approach to neural tractography using the Watson directional function. Med Image Analysis, Volume 14, Pages 58-69 2010 [http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmMedImage10.html (see here for the reference)].

File:Case01045 2T tc.png

2010-05-13T17:21:33Z

Yrathi: Two tensor tractography starting from a seed region in the mid-sagittal plane of the corpus callosum. As is clear, the method is able to trace lateral transcallosal fibers through regions of crossing.

Two tensor tractography starting from a seed region in the mid-sagittal plane of the corpus callosum. As is clear, the method is able to trace lateral transcallosal fibers through regions of crossing.

Projects:MultiTensorTractography

2010-05-13T17:19:53Z

Yrathi:

Projects:MultiTensorTractography

2010-05-13T17:18:12Z

Yrathi:

Projects:MultiTensorTractography

2010-05-13T17:17:41Z

Yrathi: /* Multi Tensor Tractography */

Projects:MultiTensorTractography

2010-05-13T17:15:29Z

Yrathi: Created page with '= Multi Tensor Tractography = We describe a unified framework to simultaneously estimate multiple fibers at each location and perform tractography. Existing techniques estimate …'

DBP2:Harvard

2010-05-13T17:04:34Z

Yrathi: /* Other Harvard-NAMIC Collaboration Projects */

Back to [[DBP2:Main|NA-MIC DBP 2]]
__NOTOC__
= Overview of Harvard DBP 2 =
== Velocardiofacial Syndrome (VCFS) as a Genetic Model for Schizophrenia ==

VCFS is a genetic disorder characterized by a deletion of a small piece of chromosome-22. The features of this syndrome include deficits in neurological psychomotor and perceptual skills, as well as in cognitive domains such as learning and memory. Most importantly, up to 30% of VCFS patients develop schizophrenia, making it the most commonly known single risk factor for the development of psychosis and a unique model for studying neurodevelopmental changes leading to psychotic deficits. We plan to collect new, high resolution DTI, structural and fMRI data, and apply existing NAMIC tools, as well as help to develop new tools to investigate the contribution of genetic variation to brain and behavioral/cognitive abnormalities, thus bridging the gap between neuroimaging studies and genetics.
The NAMIC community will gain access to de-identified imaging data (new, high resolution structural and diffusion data acquired on the 3T magnet at Brigham and Women’s Hospital). Unlike in schizophrenia, subjects with VCFS have concrete cognitive abnormalities, in addition to a well defined chromosomal abnormality, which, taken together, will make it easier to establish scientific protocols that reveal associated anatomical and functional brain abnormalities in this disorder. Interestingly, some anatomical abnormalities will be shared between VCFS and schizophrenia (e.g., connections within working memory circuits), and some will be not (e.g., sensory and motor paths). Neuropsychological and genetic data will also be collected for each individual as part of separate collaboration between PI and the Children's Hospital("Investigation of Genotype/Phenotype Correlations in Velocardiofacial and DiGeorge Syndromes”) and de-dentified dataset containing neuropsychological tests, clinical evaluations and genetic data will be provided to the PI. The NAMIC project with thus enable the PI to apply NAMIC tools to imaging VCFS data, a genetic disorder that is viewed as a genetically mediated subtype of schizophrenia. To date, there have only been a small number of neuroimaging studies of this disorder and no studies have combined neurocognitive, neuroimaging, and genetic investigations in the same study. Importantly, this research will also increase our understanding of schizophrenia, and will help establish a multimodal research project involving an important collaboration between computer scientists, cognitive neuroscientists, radiologists, psychiatrists, and geneticists. The focus on imaging and genes also affords a new window of opportunity for defining further the new area of “imaging genomics”. [[DBP2:Harvard:Introduction|More...]]

Data is provided at the following link: '''[[Data:DBP2:Harvard|Harvard Data]]'''.

= Harvard Roadmap Project =

{| cellpadding="10" border="1" style="background:lightblue;text-align:left;"

| style="width:200px" | [[Image:Arcuate_new.png|200px]]
| style="width:1300px" |

== [[DBP2:Harvard:Brain_Segmentation_Roadmap|Stochastic Tractography for VCSF]] ==

The main goal of this project is to develop end-to-end application that would be used to characterize anatomical connectivity abnormalities in the
brain of patients with velocardiofacial syndrome (VCFS), and to link this information with deficits in schizophrenia. [[DBP2:Harvard:Brain_Segmentation_Roadmap|More...]]

'''New: ''' 12/10/2008 official release of the python Slicer 3 stochastic tractography module

'''New: ''' Collaborative Publication: "Reduced interhemispheric connectivity in schizophrenia-tractography based segmentation of the corpus callosum. Kubicki M, Styner M, Bouix S, Gerig G, Markant D, Smith K, Kikinis R, McCarley RW, Shenton ME. Schizophr Res. 2008 Dec;106(2-3):125-131. Epub 2008 Sep 30.

| style="width:200px" | [[Image:Corpus2.jpg|200px]]

|}

= Other Harvard-NAMIC Collaboration Projects =

; LMI / PNL, Brigham & Women's Hospital 

{| cellpadding="10" border="1" style="background:lightgray;text-align:left;"

| style="width:1700px" |

== [[Projects:WhiteMatterGeometryDTGradients| Local white matter geometry from diffusion tensor gradients]] ==
We are investigating methods for computing local white matter geometrical properties using a differential analysis of diffusion tensor fields. We are also investigating their applications in the context of schizophrenia research.

[[http://pnl.bwh.harvard.edu/pub/papers_html/SavadjievNeuroImage10.html Local white matter geometry from diffusion tensor gradients. P. Savadjiev, G. L. Kindlmann, S. Bouix, M. E. Shenton, C-F Westin, NeuroImage 2010. ]]

|}

{| cellpadding="10" border="1" style="background:lightgray;text-align:left;"

| style="width:1700px" |

== [[Projects:MultiTensorTractography| Multi-Tensor Tractography]] ==
We are developing a novel framework for performing simultaneous multi-fiber model estimation and tractography. This is a unified framework
that allows for using any type of parametric or nonparametric model to perform tractography.

[[http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmInfProc09.html Neural tractography using an unscented Kalman filter. J. Malcolm, M. E. Shenton and Y. Rathi]]

|}

; GA Tech 

{| cellpadding="10" border="1" style="background:lightgray;text-align:left;"

| style="width:1700px" |

== [[Projects:OptimalMassTransportRegistration|EPI distortion correction using optimal mass transport.]] ==
EPI distortion correction using optimal mass transport. (baseline vs. strct t2w). Goal is to use optimal registration for EPI distortion correction in diffusion weigthed scans.

|-
| |

== [[Projects:GeodesicTractographySegmentation| Geodesic Tractography Segmentation]] ==
We are currently investigating Cingulum Bundle fractional anisotropy (FA) differences between a population of 12 schizophrenics and 12 normal controls using this new methodology.

[[http://pnl.bwh.harvard.edu/pub/papers_html/MelmohanMICCAI07.html Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle J. Melonakos, V. Mohan, M. Niethammer, K. Smith, M. Kubicki, A. Tannenbaum miccai 2007 ]]

|-
| |

== [[Projects:TubularSurfaceSegmentationPopStudy| Tubular Surface Segmentation Population Study]] ==
We are currently investigating Cingulum Bundle white matter properties between a population of schizophrenics and controls using using the Tubular Surface Model.

[[http://www.na-mic.org/publications/item/view/1571 Niethammer M., Zach C., Melonakos J., Tannenbaum A. Near-tubular fiber bundle segmentation for diffusion weighted imaging: segmentation through frame reorientation. Neuroimage. 2009 Mar;45(1 Suppl):S123-32. PMID: 19101640. PMCID: PMC2774769. ]]

|-
| |

== [[Projects:LabelSpace| A Coupled Multi-Shape Representation]] ==
We are currently using this technique to build an unbiased atlas for segmentation.

[[http://users.ece.gatech.edu/~malcolm/pubs/malcolm_lss.pdf J. Malcolm, Y. Rathi, and A. Tannenbaum. "Label Space: A Multi-Object Shape Representation." In Combinatorial Image Analysis, 2008.]]

|-
| |

== [[Projects:MultiscaleShapeAnalysis| Shape Analysis of the Caudate]] ==
Multiscale shape analysis

[Y. Gao, D. Nain, M. Styner, M. Niethammer, J. J. Levitt, M E Shenton, G Gerig, A. Bobick, A. Tannenbaum. Framework for the Statistical Shape Analysis of Brain Structures using Spherical Wavelets. In preparation for the Insight Journal, February/March 2007]
|}

; MIT 

{| cellpadding="10" border="1" style="background:lightgray;text-align:left;"

| style="width:1700px" |

== [[Projects:ShapeBasedSegmentationAndRegistration|Shape Based Segmentation and Registration]] ==
We use this segmentation algorithm to process our entire data set.

[[http://pnl.bwh.harvard.edu/pub/papers_html/PohlIEEE07.html A Hierarchical Algorithm for MR Brain Image Parcellation, K. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R. McCarley, R. Kikinis, W. Grimson, M. E. Shenton, W. Wells, IEEE Transactions on Medical Imaging, Volume 26, Number 9, Pages 1201-1212, 2007 ]]

|-
| |

== [[Projects:GroupwiseRegistration| Groupwise Registration]] ==
The goal is to create unbiased atlases throught nonlinear (b-spline) group wise registration.

[[http://www.spl.harvard.edu/publications/item/view/1090 S.K. Balci, P. Golland, M.E. Shenton, W.M. Wells III. Free-Form B-spline Deformation Model for Groupwise Registration. In Proceedings of MICCAI 2007 Statistical Registration Workshop: Pair-wise and Group-wise Alignment and Atlas Formation, 23-30, 2007. ]]

|-
| |

== [[Projects:DTIClustering| DTI Fiber Clustering and Fiber Based Analysis ]] ==
The goal of this project is to provide structural description of the white matter architecture as a partition into coherent fiber bundles and clusters, and to use these bundles for quantitative measurement. We use this method in two ongoing projects- corpus callosum segmentation in chronic schizophrenia sample, and whole brain clustering in sample of first episode psychosis subjects.

[[http://pnl.bwh.harvard.edu/pub/papers_html/odonnellAJNR06.html A Method for Clustering White Matter Fiber Tracts; L. O'Donnell, Kubicki M, M. E. Shenton, M. Dreusicke, W. E. L. Grimson, C.-F. Westin, AJNR Volume 27, Number 5 2006 ]]

|-
| |

== [[Projects:DTIModeling| Fiber Tract Modeling, Clustering, and Quantitative Analysis ]] ==
The goal of this project is to segment and parametrize fiber bundles for more precise group comparison. We use this method to segment and compare between controls and chronic schizophrenia population tracts belonging to inferior semantic processing stream (Inferior Longitudinal fasciculus, Uncinate Fasciculus and Inferior Occipito-Frontal Fasciculus). Manuscript is in preparation.

'''New: '''[[http://pnl.bwh.harvard.edu/pub/papers_html/madahmiccai08.html Findings in Schizophrenia by Tract-Oriented DT-MRI Analysis, M. Maddah, M. Kubicki, W. Wells, C.F. Westin, M.E. Shenton, W.E. Grimson, miccai, Pages 917-924 September, 2008 ]]

|-
| |

== [[Projects:fMRIClustering| fMRI clustering]] ==
The goal of this project is to use resting state fMRI data and clustering algorythm to detect and separate specific functional brain networks. We are in the process of runing the method on group of chronic schizophrenia and matched control subjects.

|}

; UNC 

{| cellpadding="10" border="1" style="background:lightgray;text-align:left;"

| style="width:1700px" |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM| Shape Analysis Framework using SPHARM-PDM]] ==
["Shape Abnormalities of Caudate Nucleus in Schizotypal Personality Disorder" has been accepted by Schizophrenia Research. James J. Levitt, Martin Styner, Marc Niethammer, Sylvain Bouix, Min-Seong Koo, Martina M. Voglmaier, Chandlee C. Dickey, Margaret A. Niznikiewicz, Ron Kikinis, Robert, W. McCarley, Martha E. Shenton.]
 
|}

; Utah 1 

{| cellpadding="10" border="1" style="background:lightgray;text-align:left;"

| style="width:1700px" |

== [[Projects:DTIProcessingTools| Diffusion Tensor Image Processing Tools]] ==
Testing and use of eddy current correction for our DWI scans. 

|}

; Utah 2 

{| cellpadding="10" border="1" style="background:lightgray;text-align:left;"

| style="width:1700px" |

== [[Projects:DTIPopulationAnalysis| Population Analysis from Deformable Registration]] ==
This project uses non-rigid registration of DTI images to produce a common coordinate system for hypothesis testing of diffusion properties. 

|}

;
== Registration Documentation ==

{| cellpadding="10" border="1" style="background:lightgray;text-align:left;"

| style="width:1700px" |

== [[Projects:DBP2:Harvard:Registration_Documentation| Documentation of Slicer3 registration modules]] ==
This page documents the results of using the various registration methods available in Slicer 3. 

|}

File:01045-t2w-restore.nrrd

2009-10-20T13:12:14Z

Yrathi: uploaded a new version of "File:01045-t2w-restore.nrrd"

File:01045-B0.nrrd

2009-10-20T13:10:24Z

Yrathi: uploaded a new version of "File:01045-B0.nrrd"

File:01045-t2w-restore.nrrd

2009-10-20T12:42:39Z

Yrathi:

File:01045-B0.nrrd

2009-10-20T12:36:39Z

Yrathi:

File:Expiration CT.nrrd

2009-10-14T11:24:09Z

Yrathi: uploaded a new version of "File:Expiration CT.nrrd"

[File:[Expiration CT.nrrd]]

File:Std-med.nrrd

2009-10-14T11:23:07Z

Yrathi: uploaded a new version of "File:Std-med.nrrd"

File:Std-med.nrrd

2009-10-13T16:09:00Z

Yrathi:

File:Expiration CT.nrrd

2009-10-13T12:15:36Z

Yrathi:

[File:[Expiration CT.nrrd]]

File:Expiration CT.nrrd

2009-10-13T12:11:25Z

Yrathi: CT images of the lungs during expiration

CT images of the lungs during expiration

2009 Summer Project Week

2009-06-01T18:40:32Z

Yrathi: /* Attendee List */

Back to [[Project Events]], [[Events]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. 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 coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and 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 will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11pm Tutorial Contest Presentations
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Tutorial Contest Winner Announcement and Project Progress using update [[#Projects|Project Wiki pages]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#Liver Ablation in Slicer (Haiying, Ziv)
#SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Grid Wizard+xnat clinic (Clement Vachet)
#?Fluid Mechanincs Module (Nathan Hageman)
#?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
#Cortical Thickness Pipeline (Clement Vachet, Ipek Oguz)
#Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)
#Skull Stripping (Xiaodong, Snehashis Roy)
#FastMarching for brain tumor segmentation (Fedorov, GeorgiaTech)
#Meningioma growth simulation for validation (Fedorov, Marcel, Ron)
#Automatic brain MRI processing pipeline (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#Drunk Monkey Contd (Vidya Rajgopalan, Andrey Fedorov)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#port 4d gated ultrasound code to Slicer - (Danielle)
#integration of stereo video into Slicer (Mehdi)
#multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)
#neuroendoscope workflow presentation (sebastien barre)
#breakout session on Dynamic Patient Models (James Balter)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# EM Segmenter (Sylvain, Nicolas)
# Plug-in 3D Viewer based on XIP (Lining)
# IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien Siebenthal)
# Fix [http://www.na-mic.org/Bug/view.php?id=416 bug 416] in registration (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|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.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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)
## 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.)
## 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)
# 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...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH
#Ferenc Jolesz, BWH
#Clare Tempany, BWH
#Tina Kapur, BWH
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Bill Lorensen, EAB
#Randy Gollub, MGH
#Nicole Aucoin, BWH
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH
#Haiying Liu BWH
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH
#Sonia Pujol, BWH
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH
#Lilla Zollei, MGH
#Lauren O'Donnell, BWH
#Florin Talos, BWH
#Nobuhiko Hata, BWH
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

2008-SCI-tour

2008-01-09T20:42:56Z

Yrathi: /* List of Participants */

__NOTOC__

Back to [[AHM_2008]], [[Events]]

=Tour of the Scientific Computing and Imaging (SCI) Institute=

The SCI Institute (http://www.sci.utah.edu) recently moved into the new Warnock Engineering Building at the University of Utah.

Here is information about our new space:

http://www.sci.utah.edu/stories/2007/Warnock.html

http://www.sci.utah.edu/stories/2007/sci_moving.html

Please join us for a short tour of the SCI Institute.

=Logistics=
We have rented a van/bus that will hold 20 people and take people from the Marriott Hotel to the SCI Institute and then back again to the Hotel.

The van/bus will leave the Marriott Hotel at '''5:00 p.m. on Wednesday, January 9''' and return to the Hotel around 6:15 p.m.

The first 20 people to sign up will be able to ride on the van/bus. Others who would like to join us can car pool.

Here is a map and directions to the SCI Institute (Warnock Engineering Building). It is about a 10 minute drive from the Hotel to the SCI Institute.

http://www.sci.utah.edu/map.html

=List of Participants=
Please add your name to the bottom of the list, if you intend to participate in the tour.
#Ron Kikinis
#Zohara Cohen
#Curtis Lisle
#Martin Styner
#Vincent Magnotta
#Nicole Grosland
#Carl-Fredrik Westin
#Nikos Chrisochoides
#Marek Kubicki
#Sonia Pujol
#Csaba Csoma
#Steve Pieper
#Randy Gollub
#Terry Yoo
#Michael Halle
#Luis Ibanez
#Carlo Pierpaoli
#Sylvain Bouix
#Douglas Alan
#Koen Van Leemput
#Padma Sundaram
#Yogesh Rathi

Algorithm:GATech

2007-04-02T19:24:57Z

Yrathi: /* KPCA, LLE, KLLE Shape Analysis */

= Current Projects =

== Segmentation ==

=== [[Algorithm:GATech:Multiscale_Shape_Segmentation|Multiscale Shape Segmentation Techniques]] ===

To represent multiscale variations in a shape population in order to drive the segmentation of deep brain structures, such as the caudate nucleus or the hippocampus.

'''New: ''' Delphine Nain won the best student paper at [[MICCAI_2006|MICCAI 2006]] in the category "Segmentation and Registration" for her paper entitled "Shape-driven surface segmentation using spherical wavelets" by D. Nain, S. Haker, A. Bobick, A. Tannenbaum.

=== [[Algorithm:GATech:Rule_Based_Segmentation|Rule-Based Segmentation Techniques]] ===

In this work, we provide software to semi-automate the implementation of segmentation procedures based on expert neuroanatomist rules.

'''New: ''' Al-Hakim, et al. Parcellation of the Striatum. SPIE MI 2007.

=== [[Algorithm:GATech:KPCA_Segmentation|Kernel PCA for Segmentation]] ===

Segmentation performances using active contours can be drastically improved if the possible shapes of the object of interest are learnt. The goal of this work is to use Kernel PCA to learn shape priors. Kernel PCA allows for learning non linear dependencies in data sets, leading to more robust shape priors.

'''New: ''' S. Dambreville, Y. Rathi, and A. Tannenbaum. A Framework for Image Segmentation using Image Shape Models and Kernel PCA Shape Priors. PAMI. Submitted to PAMI.

=== [[Algorithm:GATech:Blood_Vessel_Segmentation|Blood Vessel Segmentation]] ===

The goal of this work is to develop blood vessel segmentation techniques for 3D MRI and CT data. The methods have been applied to coronary arteries and portal veins, with promising results.

'''New: '''Y. Yang, S. George, D. Martin, A. Tannenbaum, and D. Giddens. 3D Modeling of Patient-Specific Geometries of Portal Veins Using MR Images. In Proceedings IEEE EMBS, 2006

=== [[Algorithm:GATech:Knowledge_Based_Bayesian_Segmentation|Knowledge-Based Bayesian Segmentation]] ===

This ITK filter is a segmentation algorithm that utilizes Bayes's Rule along with an affine-invariant anisotropic smoothing filter.

'''New: ''' J. Melonakos, Y. Gao, and A. Tannenbaum. Tissue Tracking: Applications for Brain MRI Classification. SPIE Medical Imaging, 2007.

=== [[Algorithm:GATech:Stochastic_Methods_Segmentation|Stochastic Methods for Segmentation]] ===

New stochastic methods for implementing curvature driven flows for various medical tasks such as segmentation.

'''New: ''' Currently under investigation.

== Registration ==

=== [[Algorithm:GATech:Conformal_Flattening_Registration|Conformal Flattening]] ===

The goal of this project is for better visualizing and computation of neural activity from fMRI brain imagery. Also, with this technique, shapes can be mapped to shperes for shape analysis, registration or other purposes. Our technique is based on conformal mappings which map genus-zero surface: in fmri case cortical or other surfaces, onto a sphere in an angle preserving manner.

'''New: ''' Y. Gao, J. Melonakos, and A. Tannenbaum. Conformal Flattening ITK Filter. ISC/NA-MIC Workshop on Open Science at MICCAI 2006.

=== [[Algorithm:GATech:Optimal_Mass_Transport_Registration|Optimal Mass Transport Registration]] ===

The goal of this project is to implement a computationaly efficient Elastic/Non-rigid Registration algorithm based on the Monge-Kantorovich theory of optimal mass transport for 3D Medical Imagery. Our technique is based on Multigrid and Multiresolution techniques. This method is particularly useful because it is parameter free and utilizes all of the grayscale data in the image pairs in a symmetric fashion and no landmarks need to be specified for correspondence.

'''New: ''' Tauseef ur Rehman, A. Tannenbaum. Multigrid Optimal Mass Transport for Image Registration and Morphing. SPIE Conference on Computational Imaging V, Jan 2007.

== DWI Processing ==

=== [[Algorithm:GATech:Finsler_Active_Contour_DWI|Finsler Active Contour DWI Tractography]] ===

In this work, we provide an energy minimization framework which allows one to find optimal curves in direction-dependent data (i.e. where the cost associated with the curve depends both upon its position and orientation)

'''New: ''' J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours for Directional Segmentation. Submitted to IEEE Transactions on Pattern Analysis and Machine Intelligence.

== Shape Analysis ==

=== [[Algorithm:GATech:Multiscale_Shape_Analysis|Multiscale Shape Analysis]] ===

We present a novel method of statistical surface-based morphometry based on the use of non-parametric permutation tests and a spherical wavelet (SWC) shape representation.

'''New: ''' D. Nain, M. Styner, M. Niethammer, J. J. Levitt, M E Shenton, G Gerig, A. Bobick, A. Tannenbaum. Statistical Shape Analysis of Brain Structures using Spherical Wavelets. Accepted in The Fourth IEEE International Symposium on Biomedical Imaging (ISBI ’07) that will be held April 12-15, 2007 in Metro Washington DC, USA.

=== [[Algorithm:GATech:KPCA_LLE_KLLE_Shape_Analysis|KPCA, LLE, KLLE Shape Analysis]] ===

The goal of this work is to study and compare shape learning techniques. The techniques considered are Linear Principal Components Analysis (PCA), Kernel PCA, Locally Linear Embedding (LLE) and Kernel LLE.

'''New: ''' Y. Rathi, S. Dambreville, and A. Tannenbaum. "Comparative Analysis of Kernel Methods for Statistical Shape Learning", In CVAMIA held in conjunction with ECCV, 2006.

 

= Completed Projects =

== Segmentation ==

=== [[Algorithm:GATech:Fast_Marching_Slicer_2|Fast Marching Slicer 2 Module]] ===

The Fast Marching Algorithm was added as a module to Slicer 2.

=== [[Algorithm:GATech:Statistical_Segmentation_Slicer_2|Statistical/PDE Methods for Segmentation]] ===

This flow was added to Slicer 2.

=== [[Algorithm:GATech:Image_Smooth_Slicer_2|Image Smooth Slicer 2 Module]] ===

2D and 3D smoothing of images.

=== [[Algorithm:Affine_Segment_Slicer_2|Affine Segment Slicer 2 Module]] ===

This module can be used to perform edge based segmentation.

Algorithm:GATech

2007-04-02T19:23:55Z

Yrathi: /* KPCA, LLE, KLLE Shape Analysis */

= Current Projects =

== Segmentation ==

=== [[Algorithm:GATech:Multiscale_Shape_Segmentation|Multiscale Shape Segmentation Techniques]] ===

To represent multiscale variations in a shape population in order to drive the segmentation of deep brain structures, such as the caudate nucleus or the hippocampus.

'''New: ''' Delphine Nain won the best student paper at [[MICCAI_2006|MICCAI 2006]] in the category "Segmentation and Registration" for her paper entitled "Shape-driven surface segmentation using spherical wavelets" by D. Nain, S. Haker, A. Bobick, A. Tannenbaum.

=== [[Algorithm:GATech:Rule_Based_Segmentation|Rule-Based Segmentation Techniques]] ===

In this work, we provide software to semi-automate the implementation of segmentation procedures based on expert neuroanatomist rules.

'''New: ''' Al-Hakim, et al. Parcellation of the Striatum. SPIE MI 2007.

=== [[Algorithm:GATech:KPCA_Segmentation|Kernel PCA for Segmentation]] ===

Segmentation performances using active contours can be drastically improved if the possible shapes of the object of interest are learnt. The goal of this work is to use Kernel PCA to learn shape priors. Kernel PCA allows for learning non linear dependencies in data sets, leading to more robust shape priors.

'''New: ''' S. Dambreville, Y. Rathi, and A. Tannenbaum. A Framework for Image Segmentation using Image Shape Models and Kernel PCA Shape Priors. PAMI. Submitted to PAMI.

=== [[Algorithm:GATech:Blood_Vessel_Segmentation|Blood Vessel Segmentation]] ===

The goal of this work is to develop blood vessel segmentation techniques for 3D MRI and CT data. The methods have been applied to coronary arteries and portal veins, with promising results.

'''New: '''Y. Yang, S. George, D. Martin, A. Tannenbaum, and D. Giddens. 3D Modeling of Patient-Specific Geometries of Portal Veins Using MR Images. In Proceedings IEEE EMBS, 2006

=== [[Algorithm:GATech:Knowledge_Based_Bayesian_Segmentation|Knowledge-Based Bayesian Segmentation]] ===

This ITK filter is a segmentation algorithm that utilizes Bayes's Rule along with an affine-invariant anisotropic smoothing filter.

'''New: ''' J. Melonakos, Y. Gao, and A. Tannenbaum. Tissue Tracking: Applications for Brain MRI Classification. SPIE Medical Imaging, 2007.

=== [[Algorithm:GATech:Stochastic_Methods_Segmentation|Stochastic Methods for Segmentation]] ===

New stochastic methods for implementing curvature driven flows for various medical tasks such as segmentation.

'''New: ''' Currently under investigation.

== Registration ==

=== [[Algorithm:GATech:Conformal_Flattening_Registration|Conformal Flattening]] ===

The goal of this project is for better visualizing and computation of neural activity from fMRI brain imagery. Also, with this technique, shapes can be mapped to shperes for shape analysis, registration or other purposes. Our technique is based on conformal mappings which map genus-zero surface: in fmri case cortical or other surfaces, onto a sphere in an angle preserving manner.

'''New: ''' Y. Gao, J. Melonakos, and A. Tannenbaum. Conformal Flattening ITK Filter. ISC/NA-MIC Workshop on Open Science at MICCAI 2006.

=== [[Algorithm:GATech:Optimal_Mass_Transport_Registration|Optimal Mass Transport Registration]] ===

The goal of this project is to implement a computationaly efficient Elastic/Non-rigid Registration algorithm based on the Monge-Kantorovich theory of optimal mass transport for 3D Medical Imagery. Our technique is based on Multigrid and Multiresolution techniques. This method is particularly useful because it is parameter free and utilizes all of the grayscale data in the image pairs in a symmetric fashion and no landmarks need to be specified for correspondence.

'''New: ''' Tauseef ur Rehman, A. Tannenbaum. Multigrid Optimal Mass Transport for Image Registration and Morphing. SPIE Conference on Computational Imaging V, Jan 2007.

== DWI Processing ==

=== [[Algorithm:GATech:Finsler_Active_Contour_DWI|Finsler Active Contour DWI Tractography]] ===

In this work, we provide an energy minimization framework which allows one to find optimal curves in direction-dependent data (i.e. where the cost associated with the curve depends both upon its position and orientation)

'''New: ''' J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours for Directional Segmentation. Submitted to IEEE Transactions on Pattern Analysis and Machine Intelligence.

== Shape Analysis ==

=== [[Algorithm:GATech:Multiscale_Shape_Analysis|Multiscale Shape Analysis]] ===

We present a novel method of statistical surface-based morphometry based on the use of non-parametric permutation tests and a spherical wavelet (SWC) shape representation.

'''New: ''' D. Nain, M. Styner, M. Niethammer, J. J. Levitt, M E Shenton, G Gerig, A. Bobick, A. Tannenbaum. Statistical Shape Analysis of Brain Structures using Spherical Wavelets. Accepted in The Fourth IEEE International Symposium on Biomedical Imaging (ISBI ’07) that will be held April 12-15, 2007 in Metro Washington DC, USA.

=== [[Algorithm:GATech:KPCA_LLE_KLLE_Shape_Analysis|KPCA, LLE, KLLE Shape Analysis]] ===

'''New: ''' The goal of this work is to study and compare shape learning techniques. The techniques considered are Linear Principal Components Analysis (PCA), Kernel PCA, Locally Linear Embedding (LLE) and Kernel LLE.

 

= Completed Projects =

== Segmentation ==

=== [[Algorithm:GATech:Fast_Marching_Slicer_2|Fast Marching Slicer 2 Module]] ===

The Fast Marching Algorithm was added as a module to Slicer 2.

=== [[Algorithm:GATech:Statistical_Segmentation_Slicer_2|Statistical/PDE Methods for Segmentation]] ===

This flow was added to Slicer 2.

=== [[Algorithm:GATech:Image_Smooth_Slicer_2|Image Smooth Slicer 2 Module]] ===

2D and 3D smoothing of images.

=== [[Algorithm:Affine_Segment_Slicer_2|Affine Segment Slicer 2 Module]] ===

This module can be used to perform edge based segmentation.

Projects:AffineSegmentSlicer2

2007-04-02T16:28:49Z

Yrathi:

= Objective =
This module can be used to perform semi-automatic segmentation by evolving an initial surface in 3D. The method uses a 3D
affine invariant edge detector to create potential well where the evolving surface converges. Use fiducials to create
initial contours (spheres) inside the object of interest. Use the expand button to inflate the initial contours for several
iterations untill it converges to the object boundary. To make the surface smooth, use the smooth button for a few iterations.
Technical details about this method can be found in the paper mentioned here.

= Links =
* [Y. Rathi, P. Olver, G. Sapiro, and A. Tannenbaum. '''Affine''' Invariant Surface Evolutions for 3D Image Segmentation. In IS&T/SPIE Electronic Imaging, 2006]

Projects:KPCA LLE KLLE ShapeAnalysis

2007-04-02T16:27:02Z

Yrathi:

Projects:KPCA LLE KLLE ShapeAnalysis

2007-04-02T16:26:38Z

Yrathi:

Projects:KPCA LLE KLLE ShapeAnalysis

2007-04-02T16:26:07Z

Yrathi:

File:Table2.png

2007-04-02T16:24:46Z

Yrathi:

File:Table1.png

2007-04-02T16:24:34Z

Yrathi:

Projects:KPCA LLE KLLE ShapeAnalysis

2007-04-02T16:24:21Z

Yrathi:

Projects:KPCA LLE KLLE ShapeAnalysis

2007-04-02T16:20:34Z

Yrathi: /* Key Investigators */

Projects:KPCA LLE KLLE ShapeAnalysis

2007-04-02T15:22:02Z

Yrathi:

Projects:KPCA LLE KLLE ShapeAnalysis

2007-04-02T15:18:12Z

Yrathi:

== Objective ==
To compare various shape representation techniques like linear PCA (LPCA), kernel PCA (KPCA), locally linear embedding (LLE) and
kernel locally linear embedding (KLLE).

== Overview ==

=== Shape Representation ===
The surfaces are represented as the zero level set of a signed distance function and shape learning is performed on the embeddings of these shapes. We carry out some experiments to see how well each of these methods can represent a shape, given the training set. We tested the performance of these methods on shapes of left caudate nucleus and left hippocampus. The training set of left caudate nucleus consisted of 26 data sets and the test set contained 3 volumes. Error between a particular shape representation and
ground truth was calculated by computing the number of mislabeled voxels using each of the methods. Figure 1 gives the error
using each of the methods. Similar tests were done on a training set of 20 hippocampus data with 3 test volumes. Figure 2 gives the error table for each of the methods [1].

[[Image:Table1.png|thumb|200px|Figure 1: Steps of the Shape Representation using Spherical Wavelets]]
[[Image:Table2.png|thumb|200px|Figure 2: A shape is represented using spherical wavelet coefficients]]

=== Segmentation ===
Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner.

=== Results ===
We applied our algorithm to the caudate nucleus, a brain structure of interest in the study of schizophrenia [2]. Our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model (ASM) algorithm, by capturing finer shape details.

== References ==
* [1] Nain D, Haker S, Bobick A, Tannenbaum A. Multiscale 3D Shape Analysis using Spherical Wavelets. Proc MICCAI, Oct 26-29 2005; p 459-467 [1]
* [2] Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven 3D Segmentation using Spherical Wavelets. Proc MICCAI, Oct 2-5, 2006. PDF of paper

== Key Investigators ==
* Core 1:
** Georgia Tech: Delphine Nain, Aaron Bobick, Allen Tannenbaum
** Harvard SPL: Steven Haker

== Collaborators ==

* Core 1: Martin Styner (UNC)
* Core 2: Jim Miller (GE), Luis Ibanez (Kitware)
* Core 3: James Levitt, Marc Niethammer, Sylvain Bouix, Martha Shenton (Harvard PNL)

== Links: ==
* Paper presented in [[MICCAI_2006|MICCAI 2006, Copenhagen, October 2 - 4, 2006 ]]
* Code: [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]]
* [[Algorithm:GATech|Georgia Tech Summary Page]]
* [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

Y. Rathi, S. Dambreville, and A. Tannenbaum. "Comparative Analysis of Kernel Methods for Statistical Shape Learning", In CVAMIA held in conjunction with ECCV, 2006.

File:Table2.PNG

2007-04-02T15:11:48Z

Yrathi: Number of mislabelled voxels using each of the methods for left hippocampus

Number of mislabelled voxels using each of the methods for left hippocampus

File:Table1.PNG

2007-04-02T15:11:16Z

Yrathi: Number of mislabelled voxels using each of the methods.

Number of mislabelled voxels using each of the methods.

Projects:KPCA LLE KLLE ShapeAnalysis

2007-04-02T15:05:04Z

Yrathi:

== Objective ==
To compare various shape representation techniques like linear PCA (LPCA), kernel PCA (KPCA), locally linear embedding (LLE) and
kernel locally linear embedding (KLLE).

== Overview ==

=== Shape Representation ===
The surfaces are represented as the zero level set of a signed distance function and shape learning is performed on the embeddings of these shapes. We carry out some experiments to see how well each of these methods can represent a shape, given the training set. We tested the performance of these methods on shapes of left caudate nucleus and left hippocampus. The training set of left caudate nucleus consisted of 26 data sets and the test set contained 3 volumes. Error between a particular shape representation and
ground truth was calculated by computing the number of mislabeled voxels using each of the methods. Figure 1 gives the error
using each of the methods. Similar tests were done on a training set of 20 hippocampus data with 3 test volumes. Figure 2 gives the error table for each of the methods [1].

[[Image:Gatech_SW_representation.png|thumb|200px|Figure 1: Steps of the Shape Representation using Spherical Wavelets]]
[[Image:Gatech_SW_mscale_shape.png|thumb|200px|Figure 2: A shape is represented using spherical wavelet coefficients]]

=== Segmentation ===
Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner.

=== Results ===
We applied our algorithm to the caudate nucleus, a brain structure of interest in the study of schizophrenia [2]. Our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model (ASM) algorithm, by capturing finer shape details.

== References ==
* [1] Nain D, Haker S, Bobick A, Tannenbaum A. Multiscale 3D Shape Analysis using Spherical Wavelets. Proc MICCAI, Oct 26-29 2005; p 459-467 [1]
* [2] Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven 3D Segmentation using Spherical Wavelets. Proc MICCAI, Oct 2-5, 2006. PDF of paper

== Key Investigators ==
* Core 1:
** Georgia Tech: Delphine Nain, Aaron Bobick, Allen Tannenbaum
** Harvard SPL: Steven Haker

== Collaborators ==

* Core 1: Martin Styner (UNC)
* Core 2: Jim Miller (GE), Luis Ibanez (Kitware)
* Core 3: James Levitt, Marc Niethammer, Sylvain Bouix, Martha Shenton (Harvard PNL)

== Links: ==
* Paper presented in [[MICCAI_2006|MICCAI 2006, Copenhagen, October 2 - 4, 2006 ]]
* Code: [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]]
* [[Algorithm:GATech|Georgia Tech Summary Page]]
* [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

Y. Rathi, S. Dambreville, and A. Tannenbaum. "Comparative Analysis of Kernel Methods for Statistical Shape Learning", In CVAMIA held in conjunction with ECCV, 2006.

Projects:KPCA LLE KLLE ShapeAnalysis

2007-04-02T14:37:24Z

Yrathi:

Y. Rathi, S. Dambreville, and A. Tannenbaum. "Comparative Analysis of Kernel Methods for Statistical Shape Learning", In CVAMIA held in conjunction with ECCV, 2006.

Projects:AffineSegmentSlicer2

2007-04-02T14:33:52Z

Yrathi: /* Links */

= Links =
This module can be used to perform semi-automatic segmentation by evolving an initial surface in 3D. The method uses a 3D
affine invariant edge detector to create potential well where the evolving surface converges. Use fiducials to create
initial contours (spheres) inside the object of interest. Use the expand button to inflate the initial contours for several
iterations untill it converges to the object boundary. To make the surface smooth, use the smooth button for a few iterations.
Technical details about this method can be found in the paper mentioned here.
* [Y. Rathi, P. Olver, G. Sapiro, and A. Tannenbaum. '''Affine''' Invariant Surface Evolutions for 3D Image Segmentation. In IS&T/SPIE Electronic Imaging, 2006]