NAMIC Wiki - User contributions [en]

2016 Summer Project Week/Guided Ultrasound Calibration

2016-06-24T14:44:44Z

Chene:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Elvis Chen (Robarts Research Institute)
* Adam Rankin (Robarts Research Institute)
* Tamas Ungi (Queen's University)

==Background==

Ultrasound probe calibration is an active area of research, with many calibration phantoms and their numerical solutions available in the current literature. In the upcoming IPCAI (2016) conference, we present the first ultrasound calibration framework that provides real-time Target Registration Error (TRE) feedback. That is, between successive measurement, our framework suggests the end-user where and how in the US image to collect next phantom measurement so that the TRE is maximally minimized. Refer to the following paper for a detailed description:

* IJCARS Paper: http://link.springer.com/article/10.1007/s11548-016-1390-7

Both theoretical experimental results suggest that sub-millimetre TRE can be achieved with 12 measurements.

The TRE prediction is based on spatial stiffnessm model.

The US calibration is modeled as point-line registration.

Refer to the following video for a demonstration based on the current C++/standalone implementation:
[[IPCAI_edited.mp4]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* A slicer module/GUI for US calibration
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for data (US image and tracker transforms) acquisition
* port existing C++/VTK code into the slicer environment
* There are 2 parts to the development:
** The GUI for the calibration
*** use python for GUI development?
** TRE prediction
*** use numpy for the math. HOWEVER, we need multi-threading
*** alternatively, we can write a CLI module for the computation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer development has been properly set up.
* We ended up developing a python loadable module based on Adam Rankin's prior work, which has a simple/nice interface to fiducial collection as well as OpenIGTLink.
* There are 2 parts to our calibration framework:
** calibration, and
** guidance for calibration based on Target Registration Error, which is computational intensive, and not strictly needed for probe calibration.
Thus the calibration portion will be integrated by the end of the project week, while TRE guidance will be integrated later (requiring multi-threading).
</div>
</div>

2016 Summer Project Week/Guided Ultrasound Calibration

2016-06-20T11:37:48Z

Chene: /* Background */

File:IPCAI edited.mp4

2016-06-20T11:34:53Z

Chene: Current GUI for Guided Ultrasound Calibration, demonstrating the concept of a navigation system for ultrasound calibration

Current GUI for Guided Ultrasound Calibration, demonstrating the concept of a navigation system for ultrasound calibration

2016 Summer Project Week/Guided Ultrasound Calibration

2016-06-20T11:31:37Z

Chene: /* Background */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Elvis Chen (Robarts Research Institute)
* Adam Rankin (Robarts Research Institute)
* Tamas Ungi (Queen's University)

==Background==

Ultrasound probe calibration is an active area of research, with many calibration phantoms and their numerical solutions available in the current literature. In the upcoming IPCAI (2016) conference, we present the first ultrasound calibration framework that provides real-time Target Registration Error (TRE) feedback. That is, between successive measurement, our framework suggests the end-user where and how in the US image to collect next phantom measurement so that the TRE is maximally minimized. Refer to the following paper for a detailed description:

* IJCARS Paper: http://link.springer.com/article/10.1007/s11548-016-1390-7

Both theoretical experimental results suggest that sub-millimetre TRE can be achieved with 12 measurements.

The TRE prediction is based on spatial stiffnessm model.

The US calibration is modeled as point-line registration.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* A slicer module/GUI for US calibration
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for data (US image and tracker transforms) acquisition
* port existing C++/VTK code into the slicer environment
* There are 2 parts to the development:
** The GUI for the calibration
*** use python for GUI development?
** TRE prediction
*** use numpy for the math. HOWEVER, we need multi-threading
*** alternatively, we can write a CLI module for the computation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer development has been properly set up.
</div>
</div>

2016 Summer Project Week/Guided Ultrasound Calibration

2016-05-31T14:02:16Z

Chene:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Elvis Chen (Robarts Research Institute)
* Adam Rankin (Robarts Research Institute)
* Tamas Ungi (Queen's University)

==Background==

Ultrasound probe calibration is an active area of research, with many calibration phantoms and numerical algorithms available in the current literature. In the upcoming IPCAI (2016) conference, we present the first ultrasound calibration framework that provides real-time Target Registration Error (TRE) feedback. That is, between successive measurement, our framework suggests the end-user where and how in the US image to collect next phantom measurement so that the TRE is maximally minimized. Refer to the following paper for a detailed description:

* IJCARS Paper: http://link.springer.com/article/10.1007/s11548-016-1390-7

Both theoretical experimental results suggest that sub-millimetre TRE can be achieved with 12 measurements.

The TRE prediction is based on spatial stiffnessm model.

The US calibration is modeled as point-line registration.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* A slicer module/GUI for US calibration
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for data (US image and tracker transforms) acquisition
* port existing C++/VTK code into the slicer environment
* There are 2 parts to the development:
** The GUI for the calibration
*** use python for GUI development?
** TRE prediction
*** use numpy for the math. HOWEVER, we need multi-threading
*** alternatively, we can write a CLI module for the computation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer development has been properly set up.
</div>
</div>

2016 Summer Project Week/Guided Ultrasound Calibration

2016-05-30T18:20:49Z

Chene:

2016 Summer Project Week/Guided Ultrasound Calibration

2016-05-30T18:17:05Z

Chene:

2016 Summer Project Week/Guided Ultrasound Calibration

2016-05-30T18:16:15Z

Chene:

2016 Summer Project Week/Guided Ultrasound Calibration

2016-05-30T18:13:47Z

Chene:

2016 Summer Project Week

2016-05-10T20:01:05Z

Chene: added registrant

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>
=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

==Logistics==
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
*'''Location:''' Heidelberg, Germany.
**'''Monday''' at German Cancer Research Center - DKFZ
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
*Preparatory Conference Calls:
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**First one on Tuesday, May 10, 3pm Boston time.
==Agenda==
<font color="maroon">Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS</font>
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:15%" |Monday, June 20 <br> DKFZ
!style="width:15%" |Wednesday, June 22 <br> Congress Hall of CARS
!style="width:15%" |Thursday, June 23 <br> Congress Hall of CARS
!style="width:15%" |Friday, June 24 <br> Congress Hall of CARS
!style="width:15%" |Saturday, June 25 <br> Congress Hall of CARS
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! <br> Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''3:00pm-5:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|-
|}

== '''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 23rd Project Week is being held in conjunction with the [http://www.ipcai.org/ IPCAI 2016] conference that is hosted by the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS).

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

==Equipment==
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)

=Projects=
* [[2016_Summer_Project_Week_Template | Template for project pages]]

#[[2016_VRPN_Integration | VRPN Integration]]
#Needle Segmentation from MRI (Tina Kapur, Andre Mastmeyer, Guillaume Pernelle)
#Guided Ultrasound Calibration (Elvis Chen, Robarts Research) http://link.springer.com/article/10.1007/s11548-016-1390-7

= '''Registrants''' =

'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html and then add your name to this list. DKFZ members who will only be attending Monday should only add their name to this list.

#Tina Kapur, BWH/HMS, Boston, USA
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal.
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy
# Steve Pieper, Isomics, Inc., USA
# Nicole Aucoin, Brigham and Women's Hospital
# Simon Drouin, Montreal Neurological Institute
# Thomas Kirchner, German Cancer Research Center
# Elvis Chen, Robarts Research Institute, Canada

2016 Summer Project Week

2016-05-10T19:54:21Z

Chene: /* Projects */

AHM2012-3D-US-Slicer-Breakout

2012-01-03T20:05:30Z

Chene: /* Agenda */

[[AHM_2012#Agenda|Back to AHM Schedule]]

=Objective=
The objective of this break out session is discuss 1) the current Slicer activities related to ultrasound guided therapies, 2) identify shared interest effort overlap, and common unmet needs, 3) produce common statement from participants about the action plans. Everyone is welcome to attend.

=Time/Date/Place=
*In 2012 NA-MIC all hands meeting
*8:10-12:00, Tuesday, January 11, 2012
*Amethyst room, Marriott, Salt Lake City, UT

=Coordinator=
*Nobuhiko Hata, PhD, Brigham and Women's Hospital
*Andras Lasso, PhD, Queens University

=Agenda=

*8:10-8:20, Welcome, Goal of the meeting, Meeting logistics, Note taking in wiki
*X:XX-X:XX, Project introduction 1, PLUS library and/or Canadian projects efforts, Andras Lasso
**Keywords: EKG, Open IGT Link,
*X:XX-X:XX, Project introduction 2, Tamas Ungi, 3D US volume reconstruction
**Keywords:
*X:XX-X:XX, Project introduction 3, Elvis Chen, GPU volume rendering. We have developed (clean room implementation) a stand-along, CUDA-based, VTK class for volume rendering. It is meant to be a drop-in replacement for vtkVolumeMapper. In addition, we implemented multi-dimentional transfer function, allowing much concise pixel-classification and visualization. Video demo will be given, source code will be made available.
**Keywords: CUDA, volume rendering, transfer function
*X:XX-X:XX, Project introduction 4, Laurent Chauvin, 4D US rendering
**Keywords:
*X:XX-X:XX, Project introduction 5, Mehdi Moradi, Prostate 3D US, BWH Efforts on US imaging
**Keywords:
*X:XX-X:XX, Project introduction 6, Junichi Tokuda/Steve Pieper, Related engineering effort: Handling 4D Images in Slicer
**Keywords: ,
*X:XX-X:XX, Project introduction 7, Nobuhiko Hata, review of U.S. US efforts
**Keywords: JHU efforts, BWH efforts, more...
*X:XX-X:XX, Project introduction 8, Anyone who is interested in talking
*X:XX-X:XX, Project introduction 8, Anyone who is interested in talking
*X:XX-X:XX, Project introduction 8, Anyone who is interested in talking
*10:00-10:30, Coffee break and
*10:30-11:00, Summary of current US projects, Breakdown of core technologies
*11:00-11:30, Identifying unmet needs,
*11:30-10:00, Group statement, Action Plan, Plan for the next events

AHM2012-3D-US-Slicer-Breakout

2012-01-03T20:05:01Z

Chene: /* Agenda */

[[AHM_2012#Agenda|Back to AHM Schedule]]

=Objective=
The objective of this break out session is discuss 1) the current Slicer activities related to ultrasound guided therapies, 2) identify shared interest effort overlap, and common unmet needs, 3) produce common statement from participants about the action plans. Everyone is welcome to attend.

=Time/Date/Place=
*In 2012 NA-MIC all hands meeting
*8:10-12:00, Tuesday, January 11, 2012
*Amethyst room, Marriott, Salt Lake City, UT

=Coordinator=
*Nobuhiko Hata, PhD, Brigham and Women's Hospital
*Andras Lasso, PhD, Queens University

=Agenda=

*8:10-8:20, Welcome, Goal of the meeting, Meeting logistics, Note taking in wiki
*X:XX-X:XX, Project introduction 1, PLUS library and/or Canadian projects efforts, Andras Lasso
**Keywords: EKG, Open IGT Link,
*X:XX-X:XX, Project introduction 2, Tamas Ungi, 3D US volume reconstruction
**Keywords:
*X:XX-X:XX, Project introduction 3, Elvis Chen, GPU volume rendering. We have developed (clean room implementation) a stand-along, CUDA-based, VTK class for volume rendering. It is meant to be a drop-in replacement for vtkVolumeMapper. In addition, we implemented multi-dimentional transfer function, allowing much concise pixel-classification and visualization. Video demo will be given, source code will be made available.
**Keywords:
*X:XX-X:XX, Project introduction 4, Laurent Chauvin, 4D US rendering
**Keywords:
*X:XX-X:XX, Project introduction 5, Mehdi Moradi, Prostate 3D US, BWH Efforts on US imaging
**Keywords:
*X:XX-X:XX, Project introduction 6, Junichi Tokuda/Steve Pieper, Related engineering effort: Handling 4D Images in Slicer
**Keywords: ,
*X:XX-X:XX, Project introduction 7, Nobuhiko Hata, review of U.S. US efforts
**Keywords: JHU efforts, BWH efforts, more...
*X:XX-X:XX, Project introduction 8, Anyone who is interested in talking
*X:XX-X:XX, Project introduction 8, Anyone who is interested in talking
*X:XX-X:XX, Project introduction 8, Anyone who is interested in talking
*10:00-10:30, Coffee break and
*10:30-11:00, Summary of current US projects, Breakdown of core technologies
*11:00-11:30, Identifying unmet needs,
*11:30-10:00, Group statement, Action Plan, Plan for the next events

AHM2012-3D-US-Slicer-Breakout

2012-01-03T19:28:19Z

Chene: /* Agenda */

[[AHM_2012#Agenda|Back to AHM Schedule]]

=Objective=
The objective of this break out session is discuss 1) the current Slicer activities related to ultrasound guided therapies, 2) identify shared interest effort overlap, and common unmet needs, 3) produce common statement from participants about the action plans. Everyone is welcome to attend.

=Time/Date/Place=
*In 2012 NA-MIC all hands meeting
*8:10-12:00, Tuesday, January 11, 2012
*Amethyst room, Marriott, Salt Lake City, UT

=Coordinator=
*Nobuhiko Hata, PhD, Brigham and Women's Hospital
*Andras Lasso, PhD, Queens University

=Agenda=

*8:10-8:20, Welcome, Goal of the meeting, Meeting logistics, Note taking in wiki
*X:XX-X:XX, Project introduction 1, PLUS library and/or Canadian projects efforts, Andras Lasso
**Keywords: EKG, Open IGT Link,
*X:XX-X:XX, Project introduction 2, Tamas Ungi, 3D US volume reconstruction
**Keywords:
*X:XX-X:XX, Project introduction 3, Elvis Chen, GPU volume rendering. We have developed (clean room implementation) a stand-along, CUDA-based, VTK class for volume rendering. It is meant to be a drop-in replacement for vtkVolumeMapper. In addition, we implemented multi-dimentional transfer function, allowing much concise pixel-classification and visualization. Video demo will be given. Source code will be made available.
**Keywords:
*X:XX-X:XX, Project introduction 4, Laurent Chauvin, 4D US rendering
**Keywords:
*X:XX-X:XX, Project introduction 5, Mehdi Moradi, Prostate 3D US, BWH Efforts on US imaging
**Keywords:
*X:XX-X:XX, Project introduction 6, Junichi Tokuda/Steve Pieper, Related engineering effort: Handling 4D Images in Slicer
**Keywords: ,
*X:XX-X:XX, Project introduction 7, Nobuhiko Hata, review of U.S. US efforts
**Keywords: JHU efforts, BWH efforts, more...
*X:XX-X:XX, Project introduction 8, Anyone who is interested in talking
*X:XX-X:XX, Project introduction 8, Anyone who is interested in talking
*X:XX-X:XX, Project introduction 8, Anyone who is interested in talking
*10:00-10:30, Coffee break and
*10:30-11:00, Summary of current US projects, Breakdown of core technologies
*11:00-11:30, Identifying unmet needs,
*11:30-10:00, Group statement, Action Plan, Plan for the next events