NAMIC Wiki - User contributions [en]

2010 Summer Project Week Best Regularization Term for Demons Registration Algorithm

2010-06-25T03:31:37Z

Rli: /* References */

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

==Key Investigators==
* MGH: Rui Li, Greg Sharp

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Show comparison of the demons algorithm performance with different regularization terms.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our plan is to find a way to convert the current research code into an itk module that can
be loaded into slicer.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

The research code is a mixture of MATLAB and C code. Thanks to the discussion with Luis, we have
successfully implemented itkCurvatureDemonsFilter.* and itkCurvatureDemonsFunction.* for a variant of
the Demons algorithm with the curvature regularization term.

Our next steps after this project week are: (1). implement locally adaptive curvature based Demons algorithm.
(2). implement Demons algorithm that uses L1-regularization term, this step will take more time and effort.
itkPDEDeformableRegistrationFilter.* and itkPDEDeformableRegistrationFunction.* need to be rewritten.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==
All the implementations will be included into plastimatch.

==References==
* ''Demons algorithms for fluid and curvature registration''. Cahill, N.D., Noble, J.A., Hawkes, D.J. ISBI 2009.
* ''A Demons Algorithm for Image Registration with Locally Adaptive Regularization''. Cahill, N.D., Noble, J.A., Hawkes, D.J.. MICCAI 2009.
* ''High Accuracy Optical Flow Estimation Based on a Theory for Warping''. Brox, T. et al., ECCV 2004
</div>

2010 Summer Project Week Best Regularization Term for Demons Registration Algorithm

2010-06-25T03:28:49Z

Rli: /* References */

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

==Key Investigators==
* MGH: Rui Li, Greg Sharp

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Show comparison of the demons algorithm performance with different regularization terms.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our plan is to find a way to convert the current research code into an itk module that can
be loaded into slicer.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

The research code is a mixture of MATLAB and C code. Thanks to the discussion with Luis, we have
successfully implemented itkCurvatureDemonsFilter.* and itkCurvatureDemonsFunction.* for a variant of
the Demons algorithm with the curvature regularization term.

Our next steps after this project week are: (1). implement locally adaptive curvature based Demons algorithm.
(2). implement Demons algorithm that uses L1-regularization term, this step will take more time and effort.
itkPDEDeformableRegistrationFilter.* and itkPDEDeformableRegistrationFunction.* need to be rewritten.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==
All the implementations will be included into plastimatch.

==References==
<div>
[1]. ''Demons algorithms for fluid and curvature registration''. Cahill, N.D., Noble, J.A., Hawkes, D.J. ISBI 2009.
</div>
<div>
[2]. ''A Demons Algorithm for Image Registration with Locally Adaptive Regularization''. Cahill, N.D., Noble, J.A., Hawkes, D.J.. MICCAI 2009.
</div>
<div>
[3]. ''High Accuracy Optical Flow Estimation Based on a Theory for Warping''. Brox, T. et al., ECCV 2004
</div>

2010 Summer Project Week Best Regularization Term for Demons Registration Algorithm

2010-06-25T03:28:13Z

Rli: /* References */

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

==Key Investigators==
* MGH: Rui Li, Greg Sharp

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Show comparison of the demons algorithm performance with different regularization terms.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our plan is to find a way to convert the current research code into an itk module that can
be loaded into slicer.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

The research code is a mixture of MATLAB and C code. Thanks to the discussion with Luis, we have
successfully implemented itkCurvatureDemonsFilter.* and itkCurvatureDemonsFunction.* for a variant of
the Demons algorithm with the curvature regularization term.

Our next steps after this project week are: (1). implement locally adaptive curvature based Demons algorithm.
(2). implement Demons algorithm that uses L1-regularization term, this step will take more time and effort.
itkPDEDeformableRegistrationFilter.* and itkPDEDeformableRegistrationFunction.* need to be rewritten.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==
All the implementations will be included into plastimatch.

==References==
<div>
[1]. '''''Demons algorithms for fluid and curvature registration''.''' Cahill, N.D., Noble, J.A., Hawkes, D.J. ISBI 2009.
</div>
<div>
[2]. '''''A Demons Algorithm for Image Registration with Locally Adaptive Regularization''.''' Cahill, N.D., Noble, J.A., Hawkes, D.J.. MICCAI 2009.
</div>
<div>
[3]. '''''High Accuracy Optical Flow Estimation Based on a Theory for Warping''.''' Brox, T. et al., ECCV 2004
</div>

2010 Summer Project Week Best Regularization Term for Demons Registration Algorithm

2010-06-25T03:27:13Z

Rli: /* References */

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

==Key Investigators==
* MGH: Rui Li, Greg Sharp

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Show comparison of the demons algorithm performance with different regularization terms.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our plan is to find a way to convert the current research code into an itk module that can
be loaded into slicer.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

The research code is a mixture of MATLAB and C code. Thanks to the discussion with Luis, we have
successfully implemented itkCurvatureDemonsFilter.* and itkCurvatureDemonsFunction.* for a variant of
the Demons algorithm with the curvature regularization term.

Our next steps after this project week are: (1). implement locally adaptive curvature based Demons algorithm.
(2). implement Demons algorithm that uses L1-regularization term, this step will take more time and effort.
itkPDEDeformableRegistrationFilter.* and itkPDEDeformableRegistrationFunction.* need to be rewritten.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==
All the implementations will be included into plastimatch.

==References==
[1]. '''''Demons algorithms for fluid and curvature registration''.''' Cahill, N.D., Noble, J.A., Hawkes, D.J. ISBI 2009.
[2]. '''''A Demons Algorithm for Image Registration with Locally Adaptive Regularization''.''' Cahill, N.D., Noble, J.A., Hawkes, D.J.. MICCAI 2009.
[3]. '''''High Accuracy Optical Flow Estimation Based on a Theory for Warping''.''' Brox, T. et al., ECCV 2004
</div>

2010 Summer Project Week Best Regularization Term for Demons Registration Algorithm

2010-06-25T03:18:05Z

Rli: /* Key Investigators */

2010 Summer Project Week Best Regularization Term for Demons Registration Algorithm

2010-06-25T03:17:49Z

Rli: /* Delivery Mechanism */

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

==Key Investigators==
* MGH: Rui Li, Greg Sharp

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Show comparison of the demons algorithm performance with different regularization terms.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our plan is to find a way to convert the current research code into an itk module that can
be loaded into slicer.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

The research code is a mixture of MATLAB and C code. Thanks to the discussion with Luis, we have
successfully implemented itkCurvatureDemonsFilter.* and itkCurvatureDemonsFunction.* for a variant of
the Demons algorithm with the curvature regularization term.

Our next steps after this project week are: (1). implement locally adaptive curvature based Demons algorithm.
(2). implement Demons algorithm that uses L1-regularization term, this step will take more time and effort.
itkPDEDeformableRegistrationFilter.* and itkPDEDeformableRegistrationFunction.* need to be rewritten. (3). All
the filters will be included in plastimatch as open source.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==
All the implementations will be included into plastimatch.

==References==

</div>

2010 Summer Project Week Best Regularization Term for Demons Registration Algorithm

2010-06-25T03:16:26Z

Rli: /* Key Investigators */

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

==Key Investigators==
* MGH: Rui Li, Greg Sharp

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Show comparison of the demons algorithm performance with different regularization terms.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our plan is to find a way to convert the current research code into an itk module that can
be loaded into slicer.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

The research code is a mixture of MATLAB and C code. Thanks to the discussion with Luis, we have
successfully implemented itkCurvatureDemonsFilter.* and itkCurvatureDemonsFunction.* for a variant of
the Demons algorithm with the curvature regularization term.

Our next steps after this project week are: (1). implement locally adaptive curvature based Demons algorithm.
(2). implement Demons algorithm that uses L1-regularization term, this step will take more time and effort.
itkPDEDeformableRegistrationFilter.* and itkPDEDeformableRegistrationFunction.* need to be rewritten. (3). All
the filters will be included in plastimatch as open source.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

==References==

</div>

2010 Summer Project Week Best Regularization Term for Demons Registration Algorithm

2010-05-13T13:44:31Z

Rli: Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List </gallery> ==Key Investigators== * MGH: Rui Li, Greg Sharp <div style="margin: 20px…'

2010 Summer Project Week

2010-05-13T13:36:32Z

Rli: /* Registration */

__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==

'''PLEASE NOTE THAT THIS IS A TENTATIVE AGENDA. IT WILL BE CONFIRMED IN MAY 2010.
'''
=== 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 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)
**1-5pm: Breakout Session: Prostate Interventions (Junichi Tokuda)
**3-4pm: Breakout Session: VTK Widgets (Nicole, Kilian, JC)
**3-5pm: Breakout Session: QA Training (Luis Ibanesz)
** 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: GWE (Marco Ruiz)
** 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/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, ?)

=== 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]] (Greg Sharp, Nadya Shusharina)
*[[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)

=== IGT ===
* Liver Ablation (Ziv Yaniv, Haiying Liu)

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

=== Analysis ===
*[[Microscopy Image Analysis]] (Arnaud Gelas)
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)

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

=== Diffusion ===

=== Python ===

=== Slicer Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)

=== Execution Model ===

===Other NA-MIC Kit Internals===
*VTKWidgets (JC, Nicole)
*Superbuild (Dave Partika)

== 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].