NAMIC Wiki - User contributions [en]

OpenIGTLink/ProtocolV2/Type/ImageMeta

2010-07-01T19:30:05Z

ZivYaniv: /* Comments */

[[OpenIGTLink/ProtocolV2/Draft | << Version 2 Draft Page]]

=Summary=
The IMGMETA message is used to transfer image meta information which are not available in IMAGE message type, such as patient name, medical record number, modality etc. An IMGMETA message can contain meta data for multiple images. This message type may be used to obtain a list of images available in the remote system, such as image database or commercial image-guided surgery (IGS) system.

=Message Types=
==IMGMETA==

{| border="1" cellpadding="5" cellspacing="0" align="center"
|-
| align="left style="background:#e0e0e0;" | Data
| align="left style="background:#e0e0e0;" | Type
| align="left style="background:#e0e0e0;" | Description
|-
| align="left" | Name/Description
| align="left" | char[64]
| align="left" | Name or description of the image
|-
| align="left" | Id
| align="left" | char[20]
| align="left" | Id to query the IMAGE and COLORT
|-
| align="left" | Modality
| align="left" | char[32]
| align="left" | String which specifies the modality
|-
| align="left" | Patient name
| align="left" | char[64]
| align="left" | Name of the patient
|-
| align="left" | Patient id
| align="left" | char[64]
| align="left" | Id of the patient
|-
| align="left" | Timestamp
| align="left" | 64 bit unsigned
| align="left" | Scan time, see [[OpenIGTLink/Timestamp]]
|-
| align="left" | RI, RJ, RK
| align="left" | 16 bit unsigned
| align="left" | Number of pixels in each direction (same as in IMAGE)
|-
| align="left" | S
| align="left" | 8 bit unsigned
| align="left" | Scalar type (e.g. 3:uint8, 5:uint16, same as in IMAGE)
|-
| align="left" | --
| align="left" | 8 bit unsigned
| align="left" | Reserved
|-
|}

* More than one item can be transmitted. The number is bodySize/itemSize.
* To get the IMAGE, GET_IMAGE is used with the Id in the device name field.

==GET_IMGMETA==
{| border="1" cellpadding="5" cellspacing="0" align="center"
|-
| align="left style="background:#e0e0e0;" | Data
| align="left style="background:#e0e0e0;" | Type
| align="left style="background:#e0e0e0;" | Description
|-
|}

==STT_IMGMETA==

N/A

==STP_IMGMETA==

N/A

=Implementations=
IMGMETA message type is implemented in the following source code.
*[http://svn.na-mic.org/NAMICSandBox/trunk/OpenIGTLink/Source/igtlImageMetaMessage.h igtlImageMetaMessage.h]
*[http://svn.na-mic.org/NAMICSandBox/trunk/OpenIGTLink/Source/igtlImageMetaMessage.cxx igtlImageMetaMessage.cxx]

=Contributors=
Alexander Schaal

=Comments=

Ziv Yaniv:<br>
The fixed size of "Patient name" and "Patient id" can potentially lead to buffer overflow. If treating the king of Spain you will need all 64 characters "Juan Carlos Alfonso Víctor María de Borbón y Borbón-Dos Sicilias". Possibly separate each field into two, something like "Patient Name Length" (unsigned int - 16 bits) and then "Patient Name". I believe that all names are shorter than 65535 characters.

OpenIGTLink/ProtocolV2/Type/ImageMeta

2010-07-01T19:29:51Z

ZivYaniv: /* Comments */

OpenIGTLink/ProtocolV2/Type/ImageMeta

2010-07-01T19:28:34Z

ZivYaniv: /* Comments */

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2009-06-11T16:54:28Z

ZivYaniv: /* Publications */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to:
# Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions
# Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists.
# Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed.
# Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures.
# Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Haying Liu, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].
Current (12/08) proposed workflow is [[media:NAVRFAWorkflow.ppt | here]].

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==
# "Electromagnetic Tracking in the Clinical Environment", Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, Med. Phys., Vol. 36(3), pp. 876-892, 2009. PMID: 19378748
# "Interfacing Proprietary Hardware with the Image-Guided Surgery Toolkit (IGSTK): a Case for the OpenIGTLink Protocol", S. Ordas, Z. Yaniv, P. Cheng, J. Tokuda, H. Liu, N. Hata, K. Cleary, SPIE Medical Imaging: Visualization, Image-Guided Procedures, and Display, 2009.
#"OpenIGTLink: An open network protocol for image-guided therapy environment," J. Tokuda et al., International Journal of Medical Robotics and Computer Assisted Surgery, to appear.

==Meetings==
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, July 30, 2008]]
*[[2008_IGT_Project_Week_RF_Ablation_System| Semi-annual project meeting, Dec 8, 2008]]

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2009-06-11T16:54:00Z

ZivYaniv: /* Publications */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to:
# Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions
# Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists.
# Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed.
# Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures.
# Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Haying Liu, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].
Current (12/08) proposed workflow is [[media:NAVRFAWorkflow.ppt | here]].

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==
# "Electromagnetic Tracking in the Clinical Environment", Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, Med. Phys., Vol. 36(3), pp. 876-892, 2009. PMID: 19378748
# "Interfacing Proprietary Hardware with the Image-Guided Surgery Toolkit (IGSTK): a Case for the OpenIGTLink Protocol", S. Ordas, Z. Yaniv, P. Cheng, J. Tokuda, H. Liu, N. Hata, K. Cleary, SPIE Medical Imaging: Visualization, Image-Guided Procedures, and Display, 2009.
#J. Tokuda et al., "OpenIGTLink: An open network protocol for image- guided therapy environment," International Journal of Medical Robotics and Computer Assisted Surgery, to appear.

==Meetings==
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, July 30, 2008]]
*[[2008_IGT_Project_Week_RF_Ablation_System| Semi-annual project meeting, Dec 8, 2008]]

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2009-06-11T16:53:48Z

ZivYaniv: /* Publications */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to:
# Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions
# Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists.
# Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed.
# Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures.
# Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Haying Liu, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].
Current (12/08) proposed workflow is [[media:NAVRFAWorkflow.ppt | here]].

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==
# "Electromagnetic Tracking in the Clinical Environment", Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, Med. Phys., Vol. 36(3), pp. 876-892, 2009. PMID: 19378748

# "Interfacing Proprietary Hardware with the Image-Guided Surgery Toolkit (IGSTK): a Case for the OpenIGTLink Protocol", S. Ordas, Z. Yaniv, P. Cheng, J. Tokuda, H. Liu, N. Hata, K. Cleary, SPIE Medical Imaging: Visualization, Image-Guided Procedures, and Display, 2009.

#J. Tokuda et al., "OpenIGTLink: An open network protocol for image- guided therapy environment," International Journal of Medical Robotics and Computer Assisted Surgery, to appear.

==Meetings==
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, July 30, 2008]]
*[[2008_IGT_Project_Week_RF_Ablation_System| Semi-annual project meeting, Dec 8, 2008]]

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

2009 Summer Project Week Liver Ablation Slicer

2009-06-11T16:45:03Z

ZivYaniv: /* References */

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:originalSegmentation.png|Segmentation showing no pass zones (ribs)and tumor.
Image:segmentationAfterDilation.png|Segmented tumor region is dilated according to physician prescribed ablation margin.
</gallery>

==Key Investigators==
* BWH: Haiying Liu, Noby Hata
* Georgetown: Ziv Yaniv

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

<h3>Objective</h3>
Implement a complete workflow:
#Load data.
#Manually mark regions (tumor, entry, critical structure).
#Process segmentation and export information to planning module (executable plugin with command line options).
#Load results of the optimization program.
#Configure OpenIGTLink module on Slicer and run OpenIGTLink IGSTK client.
#Navigate.
</div>

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

<h3>Approach, Plan</h3>
#Integrate code from Georgetown for step 3 into Slicer.
#Decide on appropriate format for describing the output of the optimization (set of trajectories and ablations along each trajectory).
#Implement a stub executable plugin as a stand in for the optimization program.
#Test the integrated workflow.
</div>

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

<h3>Progress</h3>
A new module is being created in Slicer3.

</div>
</div>

==References==
*Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, "Electromagnetic Tracking in the Clinical Environment", Med. Phys., Vol. 36(3), pp. 876-892, 2009. PMID: 19378748
*J. Tokuda et al., "OpenIGTLink: An open network protocol for image- guided therapy environment," International Journal of Medical Robotics and Computer Assisted Surgery, to appear.

2009 Summer Project Week Liver Ablation Slicer

2009-06-11T16:40:30Z

ZivYaniv: /* Key Investigators */

2009 Summer Project Week Liver Ablation Slicer

2009-06-11T16:39:27Z

ZivYaniv:

File:SegmentationAfterDilation.png

2009-06-11T16:38:09Z

ZivYaniv: Liver RFA, segmentation after tumor has been dilated to include ablation margin.

Liver RFA, segmentation after tumor has been dilated to include ablation margin.

2009 Summer Project Week Liver Ablation Slicer

2009-06-11T16:37:15Z

ZivYaniv:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:originalSegmentation.png|Segmentation showing no pass zones (ribs)and tumor.
</gallery>

==Key Investigators==
* BWH: Haiying Liu, Noby Hata
* Georgetown: Ziv Yaniv

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

<h3>Objective</h3>
Implement a complete workflow:
#Load data.
#Manually mark regions (tumor, entry, critical structure).
#Process segmentation and export information to planning module (executable plugin with command line options).
#Load results of the optimization program.
#Configure OpenIGTLink module on Slicer and run OpenIGTLink IGSTK client.
#Navigate.
</div>

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

<h3>Approach, Plan</h3>
#Integrate code from Georgetown for step 3 into Slicer.
#Decide on appropriate format for describing the output of the optimization (set of trajectories and ablations along each trajectory).
#Implement a stub executable plugin as a stand in for the optimization program.
#Test the integrated workflow.
</div>

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

<h3>Progress</h3>
A new module is being created in Slicer3.

</div>
</div>

File:OriginalSegmentation.png

2009-06-11T16:33:51Z

ZivYaniv:

2009 Summer Project Week Liver Ablation Slicer

2009-06-11T15:15:33Z

ZivYaniv: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Haiying Liu, Noby Hata
* Georgetown: Ziv Yaniv

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

<h3>Objective</h3>
Implement a complete workflow:
#Load data.
#Manually mark regions (tumor, entry, critical structure).
#Process segmentation and export information to planning module (executable plugin with command line options).
#Load results of the optimization program.
#Configure OpenIGTLink module on Slicer and run OpenIGTLink IGSTK client.
#Navigate.
</div>

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

<h3>Approach, Plan</h3>
#Integrate code from Georgetown for step 3 into Slicer.
#Decide on appropriate format for describing the output of the optimization (set of trajectories and ablations along each trajectory).
#Implement a stub executable plugin as a stand in for the optimization program.
#Test the integrated workflow.
</div>

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

<h3>Progress</h3>
A new module is being created in Slicer3.

</div>
</div>

2009 Summer Project Week

2009-05-28T18:12:51Z

ZivYaniv: /* Collaboration Projects */

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) ([[NA-MIC/Projects/Theme/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]]
** 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: TBD
** 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_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#[[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)
#gpu based registration acceleration (James Balter, Greg Sharp, Alark Joshi?, Aditya K., Yogesh Rathi?, Jimi Malcolm, Sandy Wells, Tina Kapur)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Xnat user interface improvements for NA-MIC (Dan M, Tina, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Xnat user clinic - combine with data clinic
#xnat programmer clinic
#Grid Wizard+xnat clinic (Clement)
#?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, Ipek)
#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)

===IGT Projects:===
#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)
#slicer integration of mri compatible prostate biopsy robot(sid, queens)
#breakout session on Dynamic Patient Models (James Balter)
#gpu acceleration of 2d-3d registration (james balter, greg sharp, sandy wells, noby hata, terry peters proxy)

===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]] (Jim Miller, Ross Whitaker, Samuel Gerber)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien Siebenthal, Ran Tao )
# 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

== 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]]

2009 Summer Project Week

2009-05-27T19:13:30Z

ZivYaniv: /* 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) ([[NA-MIC/Projects/Theme/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]]
** 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: TBD
** 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_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#Liver Ablation in Slicer (Haiying, Georgetown?)
#SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#gpu based registration acceleration (James Balter, Greg Sharp, Alark Joshi?, Aditya K., Yogesh Rathi?, Jimi Malcolm, Sandy Wells, Tina Kapur)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Xnat user interface improvements for NA-MIC (Dan M, Tina, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Xnat user clinic - combine with data clinic
#xnat programmer clinic
#Grid Wizard+xnat clinic (Clement)
#?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, Ipek)
#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)

===IGT Projects:===
#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)
#slicer integration of mri compatible prostate biopsy robot(sid, queens)
#breakout session on Dynamic Patient Models (James Balter)
#gpu acceleration of 2d-3d registration (james balter, greg sharp, sandy wells, noby hata, terry peters proxy)

===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)
# VTK 3d Widgets in Slicer3 (Nicole, Will/Karthik)
# Update 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]] (Jim Miller, Ross Whitaker, Samuel Gerber)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien Siebenthal, Ran Tao )
# 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

== 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]]

2009 Winter Project Week NAVRFA

2009-01-06T19:48:28Z

ZivYaniv: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|
|
|}

__NOTOC__

===Key Investigators===
* Georgetown: Kevin Cleary, Ziv Yaniv
* BWH: Noby Hata

<div style="margin: 20px;">

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

<h1>Objective</h1>
Develop an initial worklow based interface for guidance during Liver RFA.

</div>

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

<h1>Approach, Plan</h1>
Use a workflow based on existing Slicer modules for segmentation and registration and implement modules specific to the optimal planning and guidance.

</div>

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

<h1>Progress</h1>
Basic OpenIGTLink client program capable of broadcasting data from all IGSTK trackers is currently in IGSTK cvs. Georgetown will rework the program so that it deals with the use of a dynamic reference frame (which can then be ignored on the Slicer side), and switch from a command line based program to a GUI based one. BWH is currently developing the workflow based on the agreed specifications (posted on project wiki page).
</div>

<br style="clear: both;" />

</div>

===References===
*"Electromagnetic Tracking in the Clinical Environment", Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, Med. Phys, accepted for publication.
*"Interfacing Proprietary Hardware with the Image-Guided Surgery Toolkit (IGSTK): a Case for the OpenIGTLink Protocol", S. Ordas, Z. Yaniv, P. Cheng, J. Tokuda, H. Liu, N. Hata, K. Cleary, to appear SPIE Medical Imaging 2009.

2009 Winter Project Week NAVRFA

2008-12-17T21:31:07Z

ZivYaniv: New page: {| |Project Week Main Page ]] | | |} __NOTOC__ ===Key Investigators=== * Georgetown: Kevin Cleary, Ziv Yaniv * ...

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|
|
|}

__NOTOC__

===Key Investigators===
* Georgetown: Kevin Cleary, Ziv Yaniv
* BWH: Noby Hata

<div style="margin: 20px;">

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

<h1>Objective</h1>
Develop an initial worklow based interface for guidance during Liver RFA.

</div>

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

<h1>Approach, Plan</h1>
Use a workflow based on existing Slicer modules for segmentation and registration and implement modules specific to the optimal planning and guidance.

</div>

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

<h1>Progress</h1>
Basic OpenIGTLink client program capable of broadcasting data from all IGSTK trackers is currently in IGSTK cvs. Georgetown will rework the program so that it deals with the use of a dynamic reference frame (which can then be ignored on the Slicer side), and switch from a command line based program to a GUI based one. BWH is currently developing the workflow based on the agreed specifications (posted on project wiki page).
</div>

<br style="clear: both;" />

</div>

===References===
*"Electromagnetic Tracking in the Clinical Environment", Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, revised version under review, Med. Phys.
*"Interfacing Proprietary Hardware with the Image-Guided Surgery Toolkit (IGSTK): a Case for the OpenIGTLink Protocol", S. Ordas, Z. Yaniv, P. Cheng, J. Tokuda, H. Liu, N. Hata, K. Cleary, to appear SPIE Medical Imaging 2009.

2009 Winter Project Week

2008-12-17T21:22:09Z

ZivYaniv: /* External Collaborations */

Back to [[Project Events]], [[AHM_2009]], [[Events]]

==Introduction to NA-MIC Project Week==

Please read an introduction about these events [[Project_Events#Introduction|here]].

== Dates.Venue.Registration ==

Please [[AHM_2009#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2009#Agenda|click here for the agenda for AHM 2009 and Project Week]].

==Projects==
Please note:
*Please use the [[2009_Winter_Project_Week_Template|'''2009 Project Week Template''']] to create a page for your project(s)
*[[2008_Summer_Project_Week#Projects|Last Event'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]]
*Next Project Week is at MIT -- June 22-26, 2009
The following is a list of all projects that will be pursued at this meeting.

===NA-MIC DBP Roadmap Projects===
Please note that these projects correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.

#[[DBP2:Harvard:Brain_Segmentation_Roadmap|Harvard Roadmap Project: Stochastic Tractography for VCFS]]
##[[2009_Winter_Project_Week:GT_TubularSurfaceSeg|Tubular Surface Segmentation for fiber bundle extraction]] (Vandana Mohan GATech, Allen Tannenbaum GATech, Marek Kubicki BWH, Stephen Aylward Kitware)
##[[2009_Winter_Project_Week_StochasticTractography |Stochastic Tractograhy Tool for Slicer]] (Marek Kubicki BWH, Julien de Siebenthal BWH, Steve Pieper Isomics)
##[[2009_Winter_Project_Week_Slicer3Functioning |Evaluation of basic Slicer 3.0 Functionality from a User Perspective]] (Doug Terry BWH, Marek Kubicki BWH, Sylvain Bouix BWH, Steve Pieper, Wendy Plesniak, Nicole Aucoin)
##[[2009_Winter_Project_Week:DTIGroupAnalysis |Group analysis of DTI fiber bundles]] (Casey Goodlett, Guido Gerig, Marek Kubicki, Sylvain Bouix)
#[[DBP2:UNC:Cortical_Thickness_Roadmap|UNC Roadmap Project: Cortical Thickness Measurement for Autism]]
##[[2009_Winter_Project_Week:LocalCorticalThicknessPipeline|Local Cortical Thickness Pipeline]] (Clement Vachet, Martin Styner, Heather Cody Hazlett, Marc Niethammer, Ipek Oguz)
##[[2009_Winter_Project_Week:RegionalCorticalThicknessPipeline|Regional Cortical Thickness Pipeline]] (Cedric Mathieu, Clement Vachet, Martin Styner, Heather Cody Hazlett)
#[[DBP2:MIND:Roadmap|MIND Roadmap Project: Brain Lesion Analysis in Lupus]]
##[[2009_Winter_Project_Week:HighLevelWizard|Slicer High Level Wizard Project]](Steve Pieper, Mark Scully, Jeremy Bockholt)
##[[2009_Winter_Project_Week:LesionAlgorithms|Review of Lesion Algorithms]](Ross Whitaker, Vincent Magnotta, Marcel Prastawa, Mark Scully, Jeremy Bockholt)
##[[2009_Winter_Project_Week:LongitudinalLesions|Determine Requirements of Longitudinal Lesion Analyses]](Jeremy Bockholt, Marcel Prastawa, Mark Scully, Andriy Fedorov)
#[[DBP2:JHU:Roadmap|JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]
##[[2009_Winter_Project_Week:SterotacticFrameModel|Generating a Model of a Stereotactic Frame for Neurosurgery]] (Rares Crisan, Queens, Gabor Fichtinger, Queens, Katie Hayes, BWH)

===Other NA-MIC Projects===
#[[2009_Winter_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#UCLA BrainLab/Slicer Neurosurgery Preoperative Tumor Planning - using Slicer and its link to BrainLab to investigate whether different tractography methods aid in preoperative planning of tumor resection.(Nathan Hageman UCLA)
#Development of FEM / FVM solver library in ITK/VTK (and/or Python?) (Nathan Hageman UCLA, Vince, Luca, Steve)
#[[2009_Winter_Project_Week_Transform_Management | Transform Management]](Jim Miller)
#Interactive 3D Widgets - Introduce new interactors into Slicer; extensions to current widgets to support Slicer (Karthik, Will Schroeder, Nicole Aucoin)
#[[2009_Winter_Project_Week_vtkITK_Pipeline | Using ITK in VTK Pipelines]] (Jim, Steve)
#[[2009_Winter_Project_Week_SlicerLayouts | User Interface Flexible Layouts]] (Wendy, Jim, Steve, Sebastien, Ron)
#[[2009_Winter_Project_Week_Python | Python interface completion and packaging - Fortran and openssl problems]] (Luca, Steve, Demian)
#[[Two-tensor tractography in Slicer using Python and Teem]] (Madeleine Seeland, C-F Westin, Xiaodong Tao)
#[[2009_Winter_Project_Week_Rotation_Tangents | Diffusion Tensor Invariant gradients and rotation tangents in Python and Teem]] (Peter Savadjiev, C-F Westin, Luis Ibanez)
#Automated GUI testing (Sebastien, Interested User: Vince)
#[[2009_Winter_Project_Week_ColorModule | Slicer Colors Module update ]](Nicole)
#[[Volume Rendering]] (Alex, Curt, Nicholas)
#[[2009_Winter_Project_Week_XND | XNAT Desktop BatchMake integration & Slicer interface]] (Dan Marcus, Stephen Aylward, Wendy Plesniak, Curt Lisle)
#Cortical correspondence using DTI (Ipek, Martin, Xiaodong)
#[[2009_Winter_Project_Week_Command_Line_Program_Testing |Command Line Program Testing]] (Lorensen, Ron)
#[[2009_Winter_Project_Week_Slicer_VMTK |Vessel Segmentation in Slicer using VMTK]] ([[User:haehn|Daniel Haehn]], [[User:lantiga| Luca Antiga]])
#[[2009_Winter_Project_Week_fMRI_Clustering |Exploring Functional Connectivity in fMRI via Clustering]] (Archana Venkataraman, Marek Kubicki, Polina Golland)
#[[2009_Winter_Project_Week_Compiler_Warnings:Slicer3_Graffiti |Compiler Warnings:Slicer3's Graffiti]] (Lorensen, NA-MIC)
#[[2009_Winter_Project_Week_ChangeTracker |Measuring dynamics of tumor growth in Slicer3 with ChangeTracker]] (Andriy Fedorov)
#[[2009_Winter_Project_Week_GWE_Catalogs |GWE integration with catalog files]] (Marco)
#[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti)
#[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard)
#[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas)
#[[2009_Winter_Project_Week_UtahPlugins | Integration of Utah registration and segmentation methods as Slicer plugins]] (Marcel Prastawa)
#[[2009_Winter_Project_Week_OMTRegistration | DWI to MRI Registration Using Optimat Mass Transport]] (Sylvain Bouix, Ivan Kolesov GATech)

===External Collaborations===
* [[Iowa Meshing Tutorial]]
*Wake Forest - Virginia Tech
** [[2009_Winter_Project_Week_WFU1 | Move to All Slicer3 Workflow]]
** [[2009_Winter_Project_Week_WFU2 | Development of deformation based morphometry module]]
*Georgetown U: [[2009_Winter_Project_Week_NAVRFA | Prototype RF Lesion Ablation Workflow prototyped in Slicer]]
*UNC:
**[[2009_UNC_HAMMER | MR-image registration algorithm to be extended and added to namic kit]]
**[[2009_UNC_White_Matter_Lesion | white matter lesion segmentation]]
* [[Stanford SIMBIOS: Whole Body Segmentation for Simulation]]
* [[2009_Winter_Project_Week_MRSI | MRSI Module for Slicer (Bjoern Menze)]]
*[[NCI Evaluating NA-MIC Tools for Image Analysis]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# Starting Thursday, October 16th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 16: Engineering Infrastructure Projects
#*October 23: Funded External Collaboration Projects
#*November 6: DPB Projects
#*November 20: New Collaborations
#*December 4: Other Projects
#*December 18: Loose Ends
#By December 17, 2008: [[2009_Winter_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 December 17, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## 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)
# FINAL TCON: December 18th 3pm ET to tie loose ends
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== Previous Project Events ==

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

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-12-17T14:31:34Z

ZivYaniv: /* Projects */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to:
# Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions
# Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists.
# Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed.
# Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures.
# Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Haying Liu, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].
Current (12/08) proposed workflow is [[media:NAVRFAWorkflow.ppt | here]].

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==
# "Electromagnetic Tracking in the Clinical Environment", Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, revised version under review, Med. Phys.
# "Interfacing Proprietary Hardware with the Image-Guided Surgery Toolkit (IGSTK): a Case for the OpenIGTLink Protocol", S. Ordas, Z. Yaniv, P. Cheng, J. Tokuda, H. Liu, N. Hata, K. Cleary, to appear SPIE Medical Imaging 2009.

==Meetings==
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, July 30, 2008]]
*[[2008_IGT_Project_Week_RF_Ablation_System| Semi-annual project meeting, Dec 8, 2008]]

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-12-17T14:31:14Z

ZivYaniv: /* Projects */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to:
# Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions
# Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists.
# Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed.
# Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures.
# Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Haying Liu, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].
Current (12/08) proposed workflow is [[media:NAVRFAWorkflow.ppt | here]]

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==
# "Electromagnetic Tracking in the Clinical Environment", Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, revised version under review, Med. Phys.
# "Interfacing Proprietary Hardware with the Image-Guided Surgery Toolkit (IGSTK): a Case for the OpenIGTLink Protocol", S. Ordas, Z. Yaniv, P. Cheng, J. Tokuda, H. Liu, N. Hata, K. Cleary, to appear SPIE Medical Imaging 2009.

==Meetings==
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, July 30, 2008]]
*[[2008_IGT_Project_Week_RF_Ablation_System| Semi-annual project meeting, Dec 8, 2008]]

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-12-17T14:30:39Z

ZivYaniv: /* Projects */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to:
# Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions
# Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists.
# Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed.
# Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures.
# Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Haying Liu, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].
Current (12/08) proposed workflow is [[ Image:NAVRFAWorkflow.ppt |here]]. [[media:NAVRFAWorkflow.ppt ]]

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==
# "Electromagnetic Tracking in the Clinical Environment", Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, revised version under review, Med. Phys.
# "Interfacing Proprietary Hardware with the Image-Guided Surgery Toolkit (IGSTK): a Case for the OpenIGTLink Protocol", S. Ordas, Z. Yaniv, P. Cheng, J. Tokuda, H. Liu, N. Hata, K. Cleary, to appear SPIE Medical Imaging 2009.

==Meetings==
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, July 30, 2008]]
*[[2008_IGT_Project_Week_RF_Ablation_System| Semi-annual project meeting, Dec 8, 2008]]

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-12-17T14:29:57Z

ZivYaniv: /* Projects */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to:
# Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions
# Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists.
# Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed.
# Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures.
# Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Haying Liu, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].
Current (12/08) proposed workflow is [[ Image:NAVRFAWorkflow.ppt |here]]. [[media::NAVRFAWorkflow.ppt]]

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==
# "Electromagnetic Tracking in the Clinical Environment", Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, revised version under review, Med. Phys.
# "Interfacing Proprietary Hardware with the Image-Guided Surgery Toolkit (IGSTK): a Case for the OpenIGTLink Protocol", S. Ordas, Z. Yaniv, P. Cheng, J. Tokuda, H. Liu, N. Hata, K. Cleary, to appear SPIE Medical Imaging 2009.

==Meetings==
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, July 30, 2008]]
*[[2008_IGT_Project_Week_RF_Ablation_System| Semi-annual project meeting, Dec 8, 2008]]

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-12-17T14:27:16Z

ZivYaniv: /* Projects */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to:
# Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions
# Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists.
# Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed.
# Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures.
# Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Haying Liu, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].
Current (12/08) proposed workflow is [[ Image:NAVRFAWorkflow.ppt |here]].

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==
# "Electromagnetic Tracking in the Clinical Environment", Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, revised version under review, Med. Phys.
# "Interfacing Proprietary Hardware with the Image-Guided Surgery Toolkit (IGSTK): a Case for the OpenIGTLink Protocol", S. Ordas, Z. Yaniv, P. Cheng, J. Tokuda, H. Liu, N. Hata, K. Cleary, to appear SPIE Medical Imaging 2009.

==Meetings==
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, July 30, 2008]]
*[[2008_IGT_Project_Week_RF_Ablation_System| Semi-annual project meeting, Dec 8, 2008]]

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-12-16T20:55:29Z

ZivYaniv: /* Projects */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to:
# Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions
# Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists.
# Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed.
# Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures.
# Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Haying Liu, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].
Current (12/08) proposed workflow is [[ NAVRFAWorkflow.ppt |here]].

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==
# "Electromagnetic Tracking in the Clinical Environment", Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, revised version under review, Med. Phys.
# "Interfacing Proprietary Hardware with the Image-Guided Surgery Toolkit (IGSTK): a Case for the OpenIGTLink Protocol", S. Ordas, Z. Yaniv, P. Cheng, J. Tokuda, H. Liu, N. Hata, K. Cleary, to appear SPIE Medical Imaging 2009.

==Meetings==
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, July 30, 2008]]
*[[2008_IGT_Project_Week_RF_Ablation_System| Semi-annual project meeting, Dec 8, 2008]]

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

File:NAVRFAWorkflow.ppt

2008-12-16T20:53:15Z

ZivYaniv:

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-12-16T14:10:59Z

ZivYaniv: /* Key Personnel */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to:
# Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions
# Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists.
# Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed.
# Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures.
# Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Haying Liu, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==
# "Electromagnetic Tracking in the Clinical Environment", Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, revised version under review, Med. Phys.
# "Interfacing Proprietary Hardware with the Image-Guided Surgery Toolkit (IGSTK): a Case for the OpenIGTLink Protocol", S. Ordas, Z. Yaniv, P. Cheng, J. Tokuda, H. Liu, N. Hata, K. Cleary, to appear SPIE Medical Imaging 2009.

==Meetings==
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, July 30, 2008]]
*[[2008_IGT_Project_Week_RF_Ablation_System| Semi-annual project meeting, Dec 8, 2008]]

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

2008 IGT Project Week RF Ablation System

2008-12-15T21:51:09Z

ZivYaniv:

Back to [[2008_IGT_Project_Week#Projects]]

'''Team:''' Haiying Liu, Ziv Yaniv, Noby Hata, Paul Morrison

'''Goals:''' Create navigated RFA workflow based slicer module with stubs for all procedure steps:
#Load CT data set.
#Segment the volume using a semi-automatic approach (liver, tumor, ribs, blood vessels).
#Manually denote regions as one of:
##Tumor
##Entry region
##No touch - RFA probe cannot pass or ablate this region.
##No pass - RFA probe cannot pass through this region but can ablate.
#Export segmentation to planning module via text file.
#Import plan into Slicer.
#Manually localize fiducials.
#Start IGSTK based tracking process.
#Localize fiducials on patient and perform rigid registration.
#Navigation GUI.

'''Approach:''' Implement during IGT and NAMIC project weeks.

'''Results:'''
'''Summary by Noby Hata'''
#Preliminary work toward addition of OpenIGTLink support in IGSTK. To be released in Feb 2009, at SPIE Medical Imaging
#Concurrent release of IGSTK book in SPIE meeting. Junichi was offered to write a chapter on OpenIGTLink. Noby offered to come to SPIE to present the book chapter. The meeting will be held in Orlando, FL in February 2009.
'''Detailed description of work done'''
#Created an application and code to acquire tracking data
##Uses xml files to configure tracker type and configuration (specifying tools).
##Supports all tracking devices currently supported by IGSTK.
##Support broadcasting (specific request from Noby's colleagues in Japan).
##Currently program is command line and receives as input the xml file. Will work on a GUI for users that do not work with command line.
#Completed architecure for the RF ablation system.
#Completed workflow design for the system.

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-12-15T21:49:54Z

ZivYaniv: /* Publications */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to:
# Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions
# Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists.
# Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed.
# Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures.
# Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==
# "Electromagnetic Tracking in the Clinical Environment", Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, revised version under review, Med. Phys.
# "Interfacing Proprietary Hardware with the Image-Guided Surgery Toolkit (IGSTK): a Case for the OpenIGTLink Protocol", S. Ordas, Z. Yaniv, P. Cheng, J. Tokuda, H. Liu, N. Hata, K. Cleary, to appear SPIE Medical Imaging 2009.

==Meetings==
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, July 30, 2008]]
*[[2008_IGT_Project_Week_RF_Ablation_System| Semi-annual project meeting, Dec 8, 2008]]

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-12-15T21:45:04Z

ZivYaniv: /* Meetings */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to:
# Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions
# Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists.
# Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed.
# Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures.
# Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==

==Meetings==
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, July 30, 2008]]
*[[2008_IGT_Project_Week_RF_Ablation_System| Semi-annual project meeting, Dec 8, 2008]]

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

2008 IGT Project Week RF Ablation System

2008-12-12T14:41:23Z

ZivYaniv:

Back to [[2008_IGT_Project_Week#Projects]]

'''Team:''' Haiying Liu, Ziv Yaniv, Noby Hata, Paul Morrison

'''Goals:''' Create navigated RFA workflow based slicer module with stubs for all procedure steps:
#Load CT data set.
#Segment the volume using a semi-automatic approach (liver, tumor, ribs, blood vessels).
#Manually denote regions as one of:
##Tumor
##Entry region
##No touch - RFA probe cannot pass or ablate this region.
##No pass - RFA probe cannot pass through this region but can ablate.
#Export segmentation to planning module via text file.
#Import plan into Slicer.
#Manually localize fiducials.
#Start IGSTK based tracking process.
#Localize fiducials on patient and perform rigid registration.
#Navigation GUI.

'''Approach:''' Implement during IGT and NAMIC project weeks.

'''Results:'''
#Created an application to acquire tracking data (committed to IGSTK cvs, will be part of the upcoming IGSTK release 4.0):
##Uses xml files to configure tracker type and configuration (specifying tools).
##Supports all tracking devices currently supported by IGSTK.
##Support broadcasting (specific request from Noby's colleagues in Japan).
##Currently program is command line and receives as input the xml file. Will work on a GUI for users that do not work with command line.
#Completed architecure for the RF ablation system.
#Completed workflow design for the system.

2008 IGT Project Week RF Ablation System

2008-12-12T14:40:19Z

ZivYaniv:

Back to [[2008_IGT_Project_Week#Projects]]

'''Team:''' Haiying Liu, Ziv Yaniv, Noby Hata, Paul Morrison

'''Goals:''' Create navigated RFA workflow based slicer module with stubs for all procedure steps:
#Load CT data set.
#Segment the volume using a semi-automatic approach (liver, tumor, ribs, blood vessels).
#Manually denote regions as one of:
##Tumor
##Entry region
##No touch - RFA probe cannot pass or ablate this region.
##No pass - RFA probe cannot pass through this region but can ablate.
#Export segmentation to planning module via text file.
#Import plan into Slicer.
#Manually localize fiducials.
#Start IGSTK based tracking process.
#Localize fiducials on patient and perform rigid registration.
#Navigation GUI.

'''Approach:''' Implement during IGT and NAMIC project weeks.

'''Results:'''
#Created an application to acquire tracking data (committed to IGSTK cvs, will be part of the upcoming IGSTK release 4.0):
##Uses xml files to configure tracker type and configuration (specifying tools)
##Supports all tracking devices currently supported by IGSTK.
##Support broadcasting (specific request from Noby's colleagues in Japan)
##Currently program is command line and receives as input the xml file. Will work on a GUI for users that do not work with command line.
#Completed architecure for the RF ablation system
#Completed workflow design for the system

2008 IGT Project Week RF Ablation System

2008-12-03T16:45:40Z

ZivYaniv:

Back to [[2008_IGT_Project_Week#Projects]]

Team: Haying Liu, Patrick Cheng, Ziv Yaniv, Noby Hata

Goals: Create navigated RFA workflow based slicer module with stubs for all procedure steps:
#Load CT data set.
#Segment the volume using a semi-automatic approach (liver, tumor, ribs, blood vessels).
#Manually denote regions as one of:
##Tumor
##Entry region
##No touch - RFA probe cannot pass or ablate this region.
##No pass - RFA probe cannot pass through this region but can ablate.
#Export segmentation to planning module via text file.
#Import plan into Slicer.
#Manually localize fiducials.
#Start IGSTK based tracking process.
#Localize fiducials on patient and perform rigid registration.
#Navigation GUI.

Approach: Implement during IGT and NAMIC project weeks.

Results (to be completed and presented at the end of the week):

2008 IGT Project Week

2008-12-01T21:09:46Z

ZivYaniv: /* Confirmed Attendees */

=Introduction=
<gallery perrow="4" widths="200px">
Image:NCIGTlogo.gif|[http://www.ncigt.org National Center for Image Guided therapy]
Image:NAMIC 380x463.jpg|[http://www.na-mic.org National Alliance for Medical Image Computing]
Image:Nac.png|[http://nac.spl.harvard.edu/ Neuroimage Analysis Center]
Image:Cimit_logo.gif|[http://www.cimit.org CIMIT]
</gallery>
'''Dates: Monday, December 8th to Friday, December 12th'''

Location: SPL facility at 1249 Boylston Street, Boston MA ([http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. Directions]) (See here for information about area [[Boston_Hotels|hotels]].)

IGT Project Week is a hands-on event that will involve various scientific, clinical, and engineering activities that are part of building image-guided therapy systems. Please note that is '''not''' a week long session of lectures and/or slide presentations. Instead, active researchers in the field will gather for a week to get actual work done on projects that they have identified ahead of time. A fair amount of effort will be put into phone calls between the hosts and the participants in the month leading upto the event to ensure that every participant belongs to a project that makes sense to be pursued in such a collaborative setting. Depending on the needs of the projects, the hosts, NCIGT at Brigham and Women's Hospital, will reserve time at appropriate research imaging and therapy equipment.

A week before the event, a teleconference will be held with confirmed participants to review the scope of the work that they will collaboratively pursue during this week. The event itself will start with short presentation by each project team to allows all participants to be acquainted with others who are doing similar work. In the rest of the week, most of the time will be spent doing hands-on programming, imaging, algorithm design, phantom or animal experiments or other validation in small project teams. Given that this is the first stand-alone IGT event of this kind, we expect to have about 5-10 teams of size 3-4 each. To facilitate this work, a conference room will be setup with several tables, with internet and power access, to allow teams to either work on their own laptops. Based on the project requirements, times will also be reserved on the research imaging equipment and therapy equipment at Brigham and Women's Hospital. 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 modeled after the [http://www.na-mic.org/Wiki/index.php/Project_Events NA-MIC Project Week] and its main goal is to foster a hand-on image-guided therapy systems community. The first event is being organized by NCIGT and several other NIH funded grants, and the outcome at this meeting will determine the format and frequency of future events. Unfortunately, no travel support is available from NCIGT for this event; it must be sponsored by their host institution/grant.

If you are interested in joining this event, please send an email to Tina Kapur: tkapur at bwh.harvard.edu

=Agenda=

==Monday==
Please note that Monday's session will be held at The Ledge Building located at One Brigham Circle Room BC-4-004 F

*1:30-3:30pm: Presentation of all Projects
*3:30-5pm: Start Project Work

==Tuesday==
Please note that the rest of the week will be held at the 2nd floor conference room, 1249 Boylston Street.

*9am: Breakfast
*10am-noon: Non-rigid Registration Breakout session
*noon: lunch
*1-5pm: Work
*3pm: coffee

==Wednesday==
*9am: Breakfast
*9am-noon: Work
*noon: lunch
*1pm: Journal Club Talk: James Balter, University of Michigan: "Finding the truth: Surrogates and Sampling for Setup and monitoring of treatment"
*2-5pm: Work
*3pm: coffee

==Thursday==
*9am: Breakfast
*10am-noon: Tissue Characterization Breakout Session
*9am-noon: Work
*noon: lunch
*1-5pm: Work
*3pm: coffee

==Friday==
*9am: Breakfast
*10am: Review of Progress
*12pm: adjourn

=Projects=

This is a working list of projects for this week.

#Fast Imaging Library (Scott Hoge,Bob Kraft)
#Nonrigid MR-ULS Registration Algorithms development for neurosurgery (Sandy Wells, Stephen Aylward, Tina Kapur, Matt Toews, Louis Collins)
#Nonrigid registration methods for tracking targets during Prostate MRgFUS (Nathan McDannold, Ben Schwartz, Sandy Wells, Steve Haker, Nicu Archip)
#Dynamic control of the MRI acquisition based on US-based signals. This would be to apply existing technologies developed for IGT (such as optical-based tracking of a biopsy or ablation probe). (Nathan McDannold, Ben Schwartz, Ehud Schmidt)
#Analysis of dynamic contrast enhanced imaging for (Team TBD)
##Developing models of BBB disruption to optimize drug delivery;
##Mapping of tissue perfusion for modeling tissue parameters for treatment planning for MRgFUS;
##Distinguishing between residual tumor and the edge of the ablated region after MRgFUS.
#RF Ablation System (Ziv Yaniv Georgetown, Noby Hata)
#Volume Rendering for IGT using CUDA (Xenios Papademeteris, Noby Hata)
#Realtime Tractography for Neurosurgery (Noby Hata, Haiying Liu, Alex Golby, Isaiah Norton)
#Prostate Robotics (Junichi Tokuda, Noby Hata, Clif Burdette, Jack Blevins, Clare Tempany)
#Work-flow based Slicer Module for IGT application (Andinet Enquobahrie, Noby Hata)
#Tissue Characterization (Sharon Peled, and others?)

=Confirmed Attendees=
#Ziv Yaniv, Georgetown - Monday 11:00pm-Wednesday 3pm
#Andinet Enquobahrie, Kitware- Monday 1:30pm-Friday noon
#Michel Audette - Monday 1:30pm-Friday noon
#Xenios Papademetris, Yale- Monday 1:30pm-Tuesday 5pm.
#John Onofrey, Yale-Monday 1:30pm-Tuesday 5pm
#Sandy Wells, BWH- Monday 1:30pm-Friday noon
#Louis Collins, MNI- Tuesday 9am -Wednesday 5pm
#Tina Kapur, BWH - Monday 1:30pm-Friday noon
#Matt Towes, BWH - Monday 1:30pm-Friday noon
#Noby Hata, BWH - Monday 1:30pm-Friday noon
#Steve Pieper, BWH - Monday 1:30pm-Friday noon
#Katie Hayes, BWH - Monday 1:30pm-Friday noon
#Scott Hoge, BWH - Monday 1:30pm-Friday noon
#Nathan McDannold, BWH - Tuesday 9am -Friday noon
#Ben Schwartz, BWH - Tuesday 9am -Friday noon
#Ron Kikinis, BWH- Monday 1:30pm-Friday noon
#Clare Tempany, BWH- Monday 1:30pm-3:30pm, Friday 10am-noon
#Ferenc Jolesz, BWH- Monday 1:30pm-3:30pm, Friday 10am-noon
#Junichi Tokuda, BWH - Monday 1:30pm-Friday noon
#Haiying Liu, BWH- Monday 1:30pm-Friday noon
#Greg Fischer, WPI- Monday 1:30pm-Friday noon
#Clif Burdette, AcousticMed Systems- Monday 1:30pm-Friday noon
#Jack Blevins, AcousticMed Systems- Monday 1:30pm-Friday noon
#Iulian Iordachita, JHU- Monday 1:30pm-Friday noon
#Sam Song, JHU- Monday 1:30pm-Friday noon
#Andriy Fedorov, BWH/W&M- Monday 1:30pm-Friday noon
#Haytham Elhawary, BWH- Monday 1:30pm-Friday noon
#Bob Kraft, Wake Forest Univ- Monday 1:30pm-Friday noon
#James Balter, U Michigan- Wednesday 9am-Thursday 5pm
#Paul Morrison, BWH - Monday 1:30pm-Friday noon

Liver RFA project mtg 7 30 2008

2008-07-31T15:23:00Z

ZivYaniv: /* Action Items */

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008 <br>
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0 semi-auto segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker client application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
[rankdir="LR"]
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Fully integrated system. Using Slicer 3.0 as front end, implement segmentation and navigation in Slicer, integrate optimization, and talk to IGSTK tracker client using OpenIGTLink
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorough documentation page on how to setup the Slicer-RFA, detailed step-by-step guide for user
*## Publications
*# Segmentation
*## Using CT image (Georgetown has liver data base and segmented the liver, need to segment ribs and vascular tree)
*## Sota working on the segmentation using slicer, identify the problems and tackle/present them in the NCIGT workshop next January

=== Action Items ===
Georgetown:
# IGSTK-OpenIGTLink client and tutorial [Finish before next meeting in Boston, Dec 2008]
# Process all liver image in the data base.
# Run the segmented data through optimization and compare the planning results between different doctors and optimization. Publish 1 paper out of this study
# Publish results on animal study: validation of the RFA study is big problem

Slicer-IGT:
# Sota will segment 3~5 cases using Slicer and pass the results through optimization. Identify the limitation in Slicer segmentation method
# Implement IGSTK navigation interface in Slicer

Liver RFA project mtg 7 30 2008

2008-07-31T15:15:17Z

ZivYaniv: /* Day 2 */

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008 <br>
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0 semi-auto segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker client application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
[rankdir="LR"]
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Fully integrated system. Using Slicer 3.0 as front end, implement segmentation and navigation in Slicer, integrate optimization, and talk to IGSTK tracker client using OpenIGTLink
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorough documentation page on how to setup the Slicer-RFA, detailed step-by-step guide for user
*## Publications
*# Segmentation
*## Using CT image (Georgetown has liver data base and segmented the liver, need to segment ribs and vascular tree)
*## Sota working on the segmentation using slicer, identify the problems and tackle/present them in the NCIGT workshop next January

=== Action Items ===
Georgetown:
# IGSTK-OpenIGTLink client and tutorial [Finish before next meeting in Boston, Dec 2008]
# Process all liver image in the data base.
# Run the segmented data through optimization and study the outcomes. Publish 1 paper out of this study
# Publish results on animal study: validation of the RFA study is big problem
# Compare the planning results between different doctors and optimization

Slicer-IGT:
# Sota will segment 3~5 cases using Slicer and pass the results through optimization. Identify the limitation in Slicer segmentation method
# Implement IGSTK navigation interface in Slicer

Liver RFA project mtg 7 30 2008

2008-07-31T15:03:50Z

ZivYaniv: /* Day 1 */

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008 <br>
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0 semi-auto segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker client application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
[rankdir="LR"]
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Fully integrated system. Using Slicer 3.0 as front end, implement segmentation and navigation in Slicer, integrate optimization, and talk to IGSTK tracker client using OpenIGTLink
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorogh documentation page on how to setup the Slicer-RFA, detialed step-by-step guide for user
*## Publications
*# Segmentation
*## Using traditional CT image first instead of cone-beam CT (Georgetown has liver data base and segmented the liver, need to segment ribs and vascular tree)
*## Sota working on the segmentation using slicer, indentify the problem and tacle those problems in the NCIGT workshop next January

=== Action Items ===
Georgetown:
# IGSTK-OpenIGTLink client and tutorial [Finish before next meeting in Boston, Dec 2008]
# Process all liver image in the data base.
# Run the segmented data through optimization and study the outcomes. Publish 1 paper out of this study
# Publish results on animal study: validation of the RFA study is big problem
# Compare the planning results between different doctors and optimization

Slicer-IGT:
# Sota will segment 3~5 cases using Slicer and pass the results through optimization. Identify the limitation in Slicer segmentation method
# Implement IGSTK navigation interface in Slicer

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-07-31T13:29:33Z

ZivYaniv: /* Grant# */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to: 1) Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions 2) Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists. 3) Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed. 4) Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures. 5) Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==

==Meetings==

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-07-31T13:29:01Z

ZivYaniv: /* Grant# */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to: 1) Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions 2) Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists. 3) Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed. 4) Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures. 5) Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==

==Meetings==

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

2008 July RFA Experiment Georgetown

2008-07-24T20:31:09Z

ZivYaniv:

'''Date''': July 30 - August 1, 2008

'''Location''': Imaging Science and Information Systems (ISIS) Center, Department of Radiology, Georgetown University Medical Center, 2115 Wisconsin Avenue, Suite 603, Washington, DC, 20007

=Participants=
*Noby Hata (BWH)
*Haiying Liu (BWH)
*Enrique Campos-Nanez (GWU)
*Teo Popa (GU)
*Patrick Cheng (GU)
*Emmanuel Wilson (GU)
*Sebastian Ordas (GU)
*Kevin Cleary (GU)
*Filip Banovac (GU)
*Ziv Yaniv (GU)

=Agenda=
*Do RFA phantom experiment on 07/30 (will start around 5pm if all goes well).
*Work on the IGSTK/OpenIGTLink/Slicer interface for sending the transforms so that a working example may be built that sends transforms from IGSTK to Slicer and that this program is configurable, supporting all of the IGSTK trackers.
**Patient to image registration (using Landmarks) in Slicer?
*Hammer out the details of how to communicate a segmentation performed in slicer to the path planning component and then upload the plan back to Slicer.
*It would be nice to create stubs that allow us to go through the whole workflow in Slicer so that we have an initial module into which the actual content can be added later.

=Equipment for Experiment=
# Navigation, segmentation, and data translation software between segmentation and Enrique's input format.
# George phantom, liver phantom (inside George), bird seed, pump, fiducials.
# Aurora tracking system with four SIU's and needles.
# Path planning, optimization software.
# Computers to run segmentation, navigation, pump and optimization (Enrique's computer).

=Experiment protocol=
#Place fiducial's on George, attach pump and start breathing.
#Stop breathing, acquire CBCT scan.
#Transfer scan to navigation/segmentation computer and have Fil segment it.
#Translate resulting segmentation to input format for optimization (Teo).
#Perform optimization (Enrique).
#Transfer plan to navigation station.
#Start George breathing and register.
#Fil navigates to the prescribed locations according to plan.
#Optional: After each needle positioning, stop George's breathing and acquire a CBCT scan with needle in place. After the fact register the regions of interest to the planning CBCT and compute the distances between the planned needle location and the actual location.

=Results=

2008 July RFA Experiment Georgetown

2008-07-24T20:08:38Z

ZivYaniv: /* Participants */

NAV-RFA workflow and requirements

2008-06-26T16:05:45Z

ZivYaniv: /* NAV-RFA Workflow */

== NAV-RFA Workflow ==
#Place fiducials on patient.
#Acquire volumetric data set, CT or cone-beam CT (corresponding modality DICOM tags are either CT or XA) at end expiration.
#Segment the volume using a semi-automatic approach.
#Enable manual segmentation to correct the semi-automatic results.
#Export the segmentation to the planning module.
#Import the plan back into 3D Slicer.
#Start IGSTK based tracking process.
#Localize fiducials on 3D data set.
#Digitize fiducials using calibrated needle.
#Perform rigid registration.
#Show navigation GUI with current ablation path and target.

===Additional comments===
#Needle calibration - requires implementation in IGSTK.
#Interaction with planning/optimization module should be done using an xml file format.
#Setup of the tracker process should be performed using an xml file. This should be output provided by Slicer.
The XML file will contain:
#ip address to which we write data.
#All communication settings required for the Aurora (COM port, baud rate, etc.).
#For each tool:
##The desired ip and port to which the data should be written.
##The physical port on the control box that corresponds to this tool.
##Optional, the physical channel on the port
##Optional, the SROM file for the tool.

#Expected GUI:
##Axial, off axial, off sagittal, and down the barrel views (see [http://public.kitware.com/IGSTKWIKI/index.php/ImageSliceRepresentation#Appendix this] page for definitions).
##Axial, off-axial and sagittal views display the planned trajectory and the needle projection.
##Down-the-barrel view displays concentric circles denoting needle tip hub and target. In addition a depth gauge displaying the distance from the target.
##Respiratory signal as estimated from tracking data.
##Allow user to choose each trajectory and show ablation targets starting with the one farthest from the entry point along the trajectory.

NAV-RFA workflow and requirements

2008-06-26T15:37:02Z

ZivYaniv: New page: == NAV-RFA Workflow == #Place fiducials on patient. #Acquire volumetric data set, CT or cone-beam CT (corresponding modality DICOM tags are either CT or XA) at end expiration. #Segment the...

This

2008-06-26T15:36:24Z

ZivYaniv: /* NAV-RFA Use Case */

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-06-26T15:33:52Z

ZivYaniv: /* Projects */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to: 1) Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions 2) Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists. 3) Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed. 4) Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures. 5) Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==

==Meetings==

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

This

2008-06-26T15:29:12Z

ZivYaniv: New page: == NAV-RFA Use Case == #Place fiducials on patient. #Acquire volumetric data set, CT or cone-beam CT (corresponding modality DICOM tags are either CT or XA) at end expiration. #Segment the...

== NAV-RFA Use Case ==
#Place fiducials on patient.
#Acquire volumetric data set, CT or cone-beam CT (corresponding modality DICOM tags are either CT or XA) at end expiration.
#Segment the volume using a semi-automatic approach.
#Enable manual segmentation to correct the semi-automatic results.
#Export the segmentation to the planning module.
#Import the plan back into 3D Slicer.
#Start IGSTK based tracking process.
#Localize fiducials on 3D data set.
#Digitize fiducials using calibrated needle.
#Perform rigid registration.
#Show navigation GUI with current ablation path and target.

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-06-26T15:20:41Z

ZivYaniv: /* Projects */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to: 1) Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions 2) Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists. 3) Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed. 4) Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures. 5) Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Ziv Yaniv

==Projects==

[[This]] page describes the expected system workflow.

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==

==Meetings==

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-06-26T15:19:40Z

ZivYaniv: /* Projects */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to: 1) Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions 2) Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists. 3) Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed. 4) Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures. 5) Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Ziv Yaniv

==Projects==

[[Use Case]]

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==

==Meetings==

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-06-26T15:18:39Z

ZivYaniv: /* Projects */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to: 1) Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions 2) Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists. 3) Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed. 4) Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures. 5) Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Ziv Yaniv

==Projects==

Use Case

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==

==Meetings==

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

People

2008-06-26T15:16:10Z

ZivYaniv: /* NA-MIC Collaborators */

== Personnel at least partially funded by NA-MIC ==

#Leadership Core
## [[User:Kikinis|Ron Kikinis]], Harvard (BWH SPL) PI
## [[User:Naucoin|Nicole Aucoin]], Harvard (BWH SPL)
## [[User:Marianna| Marianna Jakab]], Harvard (BWH SPL)
## [[User:Tkapur|Tina Kapur]], Harvard (BWH SPL)
## [[User:Mastrogiacom|Katie Mastrogiacomo]], Harvard (BWH SPL)
## Wendy Plesniak, Harvard (BWH SPL)
# Algorithms Core
## [http://www.cs.utah.edu/~whitaker/ Ross Whitaker], Utah PI
## [[Eric_Grimson|Eric Grimson]], MIT (CSAIL)
## [[Polina_Golland|Polina Golland]], MIT (CSAIL) PI
## [[User:Styner|Martin Styner]], UNC PI
## Ipek Oguz, UNC
## Gary Long, UNC
## Allen Tannenbaum, Georgia Tech, PI
## Oleg Michailovich, Georgia Tech
## Preston T. Fletcher, Utah
## Ran Tao, Utah
## [http://www.cs.unc.edu/~gerig/ Guido Gerig], Utah
## [[User:Gcasey|Casey Goodlett]], Utah (Guido)
## [http://www.massgeneral.org/ncs/neuro_faculty_Kennedy.htm/ David Kennedy], Ph.D, Harvard (MGH) PI
## Bruce Fischl, Ph.D, Harvard (MGH)
## [[User:nicks|Nick Schmansky]], Harvard (MGH)
## Daniel Marcus, Washington University at St. Louis
# Engineering Core
## [[User:Will| Will Schroeder]], Kitware PI
## [[User:Ibanez|Luis Ibanez]], Kitware
## [http://www.kitware.com/profile/team/hoffman.html/ William Hoffman], Kitware
## [[User:Barre|Sebastien Barre]], Kitware
## [[User:Millerjv|Jim Miller]], GE PI
## [[User:Taox|Xiaodong Tao]], GE
## Dan Blezek, GE
## [[User:Pieper|Steve Pieper]], Isomics PI
## Alex Yarmakovich, Isomics
## Arthur W. Toga, UCLA PI
## Jia Wei Tam, UCLA
## [[User:Jags|Jagadeeswaran Rajendiran]], UCLA
## Mark Ellisman, UCSD PI
## Jeff Grethe, UCSD
## [http://www.cse.ucsd.edu/~ncjones/bio.html/ Neil Jones], UCSD
## Bryan W. Smith, UCSD
# Driving Biological Problems (DBP)
##[http://media.cs.queensu.ca/purang/ Purang Abolmaesumi], Queen's University
## Jonathan Boisvert, Queen's University
## Jeremy Bockholt, The Mind Institute
## [http://www.cisst.org/~gabor/ Gabor Fichtinger], Queen's University
## Chuck Gasparovic, The Mind Institute
## [http://imaging.robarts.ca/~dgobbi/ David Gobbi], Queen's University
## [http://www.med.unc.edu/psych/directories/hazlett.htm/ Heather Cody Hazlett], UNC
## Usman Khan, Harvard (BWH)
## [http://lmi.bwh.harvard.edu/~kubicki/ Marek Kubicki], Harvard (BWH)
## Gary Long, UNC
## Rachel Gimpel Smith, UNC
## Clement Vachet, UNC
# Service Core
## [[User:Will|Will Schroeder]], Kitware PI
## Brad Davis, Kitware
## Ken Martin, Kitware
# Training Core
## Guido Gerig, Utah
## [[User:Randy|Randy Gollub]], Harvard (MGH) PI
## [[User:SPujol|Sonia Pujol]], Harvard (BWH SPL)
## Martha Shenton, Harvard (BWH PNL) PI
## [http://www.cs.utah.edu/~whitaker/ Ross Whitaker], Utah
# Dissemination Core
## [[User:Tkapur|Tina Kapur]], Harvard (BWH SPL) co-PI
## [[User:Pieper|Steve Pieper]], Isomics co-PI
# Management Core
## Rachana Manandhar, Harvard (BWH SPL)
## [[User:Sanjay|Sanjay Manandhar]], Harvard (BWH SPL)

== NA-MIC Collaborators ==
These NA-MIC collaborators are funded under the "Collaboration with NCBC" PAR.
#Nicole Grosland, UIowa
#Vincent Magnotta, UIowa
#Steve Pieper, Isomics
#James Daunais, Wake Forest
#Robert Kraft, Wake Forest
#Chris Wyatt, Virginia Tech
#Kilian Pohl, Harvard (BWH SPL)
#Sandy Wells, Harvard (BWH SPL)
#Kevin Cleary, Georgetown
#Enrique Campos-Nanez, George Washington U.
#Patrick (Peng) Cheng, Georgetown
#Ziv Yaniv, Georgetown
#Nobuhiko Hata, Harvard (BWH)

== NA-MIC alumni ==
* [http://marchingcubes.org Bill Lorensen]
* [[User:Lzollei|Lilla Zollei]], MIT (CSAIL)
* Lauren O'Donnell, MIT (CSAIL)
* [http://people.csail.mit.edu/wanmei/ Wanmei Ou], MIT (CSAIL)
* [[Mahnaz_Maddah|Mahnaz Maddah]], MIT (CSAIL)
* Ramsey Al-Hakim, Georgia Tech
* [[User:Melonakos|John Melonakos]], Georgia Tech
* [[User:Lankton|Shawn Lankton]], Georgia Tech
* [[User:Nain|Delphine Nain]], Georgia Tech
* Xavier Le Faucheur, Georgia Tech
* [[User:Mohan|Vandana Mohan]], Georgia Tech
* Tom Fletcher, Utah
* [http://www.sci.utah.edu/cgi-bin/SCIpersonnel.pl?username=tolga Tolga Tasdizen], Utah
* [http://www.cs.utah.edu/~sbasu/ Saurav Basu], Utah
* Josh Snyder, Harvard (MGH)
* [[User:DavidTuch|David Tuch]], Harvard (MGH)
* [[User:Karthik|Karthik Krishnan]],Kitware
* [http://www.kitware.com/profile/team/cedilnik.html/ Andy Cedilnik], Kitware
* [[User:Mathieu|Mathieu Malaterre]], Kitware
* [http://www.stat.ucla.edu/~dinov/ Ivo Dinov], UCLA
* [[User:MichaelPan|Michael Pan]], UCLA
* Brendan Flaherty, UCSD
* [[User:Adamc|Adam Cohen]], Harvard (BWH PNL)
* [[User:Markd|Mark Dreusicke]], Harvard (BWH PNL)
* Martha Shenton, Harvard (BWH PNL) PI
* [http://lmi.bwh.harvard.edu/~sylvain/ Sylvain Bouix], Harvard (BWH PNL)
* [http://lmi.bwh.harvard.edu/~marc/ Marc Niethammer], Harvard (BWH PNL)
* [http://synapse.hitchcock.org/bios/saykin.shtml Andy Saykin], Dartmouth PI
* Bob Roth, Dartmouth
* [http://synapse.hitchcock.org/bios/flashman.shtml Laura Flashman], Dartmouth
* [http://www.dhmc.org/providers/dhmc_provider_634.html Thomas McAllister], Dartmouth
* Alan Green, Dartmouth
* John West, Dartmouth
* [http://synapse.hitchcock.org/bios/mchugh.shtml/ Tara McHugh], Dartmouth
* [http://synapse.hitchcock.org/bios/pixley.shtml Heather Pixley], Dartmouth
* Stephen Guerin, Dartmouth
* John MacDonald, Dartmouth
* [http://www.bic.uci.edu/faculty/sgpotkin.htm/ Steve Potkin], UCI PI
* [[User:Jfallon|James Fallon]], UCI
* Jessica Turner, UCI
* Martina Panzenboeck, UCI
* David Medina, UCI
* [http://www.ics.uci.edu/~smyth/ Padhraic Smyth], UCI
* [http://www.ics.uci.edu/~sternh/ Hal Stern], UCI
* Diane Highum, UCI
* [http://www.ess.uci.edu/~yu/ Yi Jin], UCI
* Liv Trondsen, UCI
* Fabio Macciardi, Toronto
* [http://www.utpsychiatry.ca/dirsearch.asp?id=130 Jim Kennedy], Toronto
* Aristotle Voineskos, Toronto

== "Friends and Family" ==

=== NIH ===

* [[User:Lysterp|Peter M. Lyster]]

=== mBIRN ===

* [[User:Akolasny|Anthony Kolasny]]
* [[User:Dmarcus|Dan Marcus]]
* [[User:Kikinis|Ron Kikinis]]

=== fBIRN ===

* [[User:Kikinis|Ron Kikinis]]

=== IGT ===

* [[User:Ibanez|Luis Ibanez]]
* [[User:Noby| Nobuhiko Hata]]

=== Other ===

2007 December Slicer IGT Programming

2007-12-06T17:32:20Z

ZivYaniv: /* Confirmed Attendees */

__NOTOC__
==Dates.Location.Hotels==
December 12-14, 2007

SPL at 1249 Boylston Street, Boston MA. ([http://www.spl.harvard.edu/Directions#Getting_to_1249_Boylston_Street Directions])

Area hotels: [[Boston_Hotels]]

==Goal==
*Continued [[Leadership:SlicerIGT_2007|'''discussion''']] of Slicer IGT infrastructure, applications, and timelines
*Introduce each team's effort in Slicer in the context of IGT
*active funding&future submissions
*on-going technical development
*find unmet needs

=Agenda=
==Wednesday, December 12 ==
'''Theme: Where are we?'''
*12noon: lunch
*12:55pm: Welcome (Ferenc Jolesz)
*1-2pm:
**Slicer: overview of architecture, current status, and future plans (Pieper, Hata)
***History
***Clinical applications
***transition from 2.6 to 3
***resource
**IGSTK: overview of architecture, current status, and future plans (Ibanez, Cheng)
*2-3pm: Setting goals for meeting: Each IGT group present what they want to achieve at this meeting.
**2-2:15 - NA-MIC DBP Queens/JHU Gobbi/Csoma/Kazanzides
**2:15-2:30 - NA-MIC Collaborator Georgetown Cleary/Yaniv
**2:30-2:45 - NCIGT BWH Hata
**2:45-3:00 - Kitware
**3:00-3:15pm - NCIGT CIGL Stoll

*3:15-3:30pm: Coffee Break
*3:30pm Adjourn
*4-6pm (optional) demonstration of Slicer for control and display of MRI scanner (prostate module) @Advanced MRI center, 221 Longwood
**LINK
**LINK

==Thursday, December 13==
'''Morning Theme: Where are we?'''
*9:00am breakfast, start work

*9-1030am Discussion over Demos:
**Stoll (laproscopic ultrasound)
**Hata (Tracking at BWH)
**Yaniv (Tracking at Georgetown)
**Pieper (Volume rendering)

*10:30am: coffee break
*11am: continue work
Review of demos
**which function is cool?
**which functionality has to be shared
**what is the common needs?
**who has those missing functions outside of IGT?

*12:30: lunch
*1:30pm: continue work
'''Afternoon Theme: Where are we going?'''
**Resource shring
**priority tasks
**Hypothetical RO1

*3-4pm: Coffee break (and NA-MIC TCON)
*4:00pm: Plan for Hands on IGT Week
*5pm: Review day and plan for Friday (Hata)
*5:30pm: adjourn

==Friday, December 14==
----
*9:00am: breakfast, work
**Focus group discussion ('''What do we do now?''')
**Report to NCIGT
**Action items
*11:15am-noon: Wrapup/Suggestion to NCIGT PIs (Hata)
*noon: adjourn and head out to group lunch

----

==Confirmed Attendees==
#Noby Hata, BWH (NCIGT)
#Steve Pieper, Isomics - (All Days) (NAMIC, NAC)
#Patrick Cheng, Georgetown (NAMIC Collab)
#Ziv Yaniv, Georgetown (NAMIC Collab)
#Kevin Cleary, Georgetown (Wed only) (NAMIC Collab)
#Luis Ibanez, Kitware (NAMIC)
#Sebastien Barre, Kitware (NCIGT)
#Stephen Aylward, Kitware (NCIGT)
#Jeff Stoll (except Thursday), BWH/CIMIT (NCIGT)
#Haiying Liu, BWH (NCIGT)
#Katie Hayes, BWH (NAC)
#Peter Kazanzides (except Friday), JHU (NAMIC Collab)
#Csaba Csoma, JHU (NAMIC/NCIGT Collab)
#David Gobbi, Queens (NAMIC/NCIGT Collab)
#Tina Kapur,BWH (NAMIC/NCIGT)
#Ron Kikinis, BWH (NAMIC/NCIGT)
#Junichi Tokuda, BWH (NCIGT)
#Raul San Jose, BWH (NAC)
#Ferenc Jolesz, BWH (Wed only) (NCIGT/NAC)