NAMIC Wiki - User contributions [en]

2011 Winter Project Week:StenosisDetector

2010-12-27T11:36:51Z

Lantiga: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
Image:step1.png|StensosisDetector Step1
Image:step2.png|StensosisDetector Step2
Image:step3.png|StensosisDetector Step3
Image:step4.png|StensosisDetector Step4
Image:step5.png|StensosisDetector Step5
</gallery>

==Key Investigators==
* University of Heidelberg, Germany: Suares Tamekue
* UPenn: Daniel Haehn
* [http://www.orobix.com Orobix], Italy: Luca Antiga
* SPL: Ron Kikinis

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

<h3>Objective</h3>
We are developing a stenosis detector based on VMTK in Slicer 4. The goal is to be able to visualize stenosis after a vessel segmentation using a wizard-based interface.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the stenosis detector is: first vessel enhancement, level-set segmentation, network extraction and then quantification and visualization of stenosis.

The tool will be evaluated on datasets.

</div>

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

<h3>Progress</h3>
A prototyp of the graphical user interface has been designed and implemented.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable [X]
#Other (Please specify)

==References==
* Antiga L, Piccinelli M, Botti L, Ene-Iordache B, Remuzzi A and Steinman DA. An image-based modeling framework for patient-specific computational hemodynamics. Medical and Biological Engineering and Computing, 46: 1097-1112, Nov 2008.
* D. Hähn. Integration of the vascular modeling toolkit in 3d slicer. SPL, 04 2009. Available online at http://www.spl.harvard.edu/publications/item/view/1728.
* D. Hähn. Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools. Master's Thesis. Department of Medical Informatics, University of Heidelberg, Germany. Feb 2010.
* Piccinelli M, Veneziani A, Steinman DA, Remuzzi A, Antiga L (2009) A framework for geometric analysis of vascular structures: applications to cerebral aneurysms. IEEE Trans Med Imaging. In press.
</div>

2011 Winter Project Week:The Vascular Modeling Toolkit in 3D Slicer

2010-12-27T11:36:16Z

Lantiga: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
Image:Slicervmtk logo.png|VMTK in 3D Slicer
Image:Vesselenhancement.png|Enhancing vasculature structures
Image:Easylevelsetsegmentation.png|Level-Set segmentation
Image:Centerlines.png|Computation of Centerlines
Image:Networkextraction.png|Network extraction of vessel trees
Image:Branchsplitting.png|Branchsplitting
</gallery>

==Key Investigators==
* UPenn: Daniel Haehn, Kilian Pohl
* Rutgers: M. Gokhan Uzunbas
* [http://www.orobix.com Orobix], Italy: Luca Antiga
* SPL: Steve Pieper, Ron Kikinis

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

<h3>Objective</h3>
The Vascular Modeling Toolkit ([http://www.vmtk.org VMTK]) is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

Several 3D Slicer extensions already exist and provide VMTK functionality in Slicer3.

</div>

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

<h3>Approach, Plan</h3>
We want to investigate how to include the VMTK in 3D Slicer functionality in the upcoming Slicer4 application. This should include several enhancements to the existing user interfaces.
</div>

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

<h3>Progress</h3>
..

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable [X]
#Other (Please specify)

==References==
* Antiga L, Piccinelli M, Botti L, Ene-Iordache B, Remuzzi A and Steinman DA. An image-based modeling framework for patient-specific computational hemodynamics. Medical and Biological Engineering and Computing, 46: 1097-1112, Nov 2008.
* D. Hähn. Integration of the vascular modeling toolkit in 3d slicer. SPL, 04 2009. Available online at http://www.spl.harvard.edu/publications/item/view/1728.
* D. Hähn. Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools. Master's Thesis. Department of Medical Informatics, University of Heidelberg, Germany. Feb 2010.
* Piccinelli M, Veneziani A, Steinman DA, Remuzzi A, Antiga L (2009) A framework for geometric analysis of vascular structures: applications to cerebral aneurysms. IEEE Trans Med Imaging. In press.

</div>

2009 Winter Project Week Python

2009-01-09T15:59:36Z

Lantiga: /* Key Investigators */

{|
|[[Image:Python-logo.png |thumb|320px|[http://www.python.org]]
|}

__NOTOC__

===Key Investigators===
* Luca Antiga (Mario Negri Institute)
* Steve Piper (Isomics)
* Demian Wasserman (INRIA)

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

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

<h1>Objective</h1>
To finalize the implementation of the Slicer Python interface and solve packaging problems linked to Scipy.

</div>

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

<h1>Approach, Plan</h1>

The Slicer Python interface now works well for both non-interactive and interactive modules.

Interface has to be stabilized, and it is still lacking setting custom observers to vtkObject.

Documentation has to be improved.

Packaging Scipy is currently a problem.

</div>

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

<h1>Progress</h1>

The Python interface is being adopted by several groups, both for command-line and interactive modules. The Numpy interface works well.

A AddObserver method has been added to the wrapped vtkObject that accepts callbacks written in Python.

The Python breakout session has illustrated the ways Python can be used in Slicer and the ways users can implement their own modules. Slides will be on the wiki in a few days.

A --evalpython option has been added to the Slicer3 executable in order to run Python code in Slicer without starting the GUI (for batch processing)

Packaging problems have been

</div>

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

</div>

AHM 2009

2009-01-08T16:34:37Z

Lantiga: /* Agenda */

__NOTOC__
== Introduction ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"| '''This is the home page for the 2009 NA-MIC all hands meeting (AHM).''' NA-MIC participants meet for a AHM once a year. The purpose of the AHM is to coordinate, discuss plans and report to NIH officers and the external advisory board (EAB). The external advisory board meets with the NA-MIC leadership immediately after the AHM. In parallel, NA-MIC is organizing a project week. These events, with the exception of the EAB meeting, are open to collaborators and potential collaborators.

For more information about the project weeks in general, click [[Engineering:Programming_Events|'''here''']].

For information about the January 2009 project week, see below or click [[2009_Winter_Project_Week|'''here''']].

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"|The 2009 AHM, EAB and Project Week will be held <br>'''January 5-9 2009''', in '''Salt Lake City''', Utah.
|}

== Agenda==

'''wireless connection: capital-ballroom, namic-ballroomB, namic-amethyst'''<br>

{| border="1" cellpadding="5"
|- style="background:#ebeced; color:black" align="left"
| style="width:4%" | '''Time'''
| style="width:12%" | '''Monday, January 5'''
| style="width:12%" | '''Tuesday, January 6'''
| style="width:12%" | '''Wednesday, January 7'''
| style="width:32%" | '''Thursday, January 8 '''
| style="width:12%" | '''Friday, January 9'''
|-
| style="background:#ffffdd; color:black"|
| style="background:#b4d597; color:#522200"| '''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#fff6a6; color:#522200"| '''AHM''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/Capitol A-B], [[2009_EAB|'''EAB''']] in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B]
'''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus A]
| style="background:#b4d597; color:#522200"|'''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
|-
| style="background:#ffffdd; color:black"|'''7:30-8:00'''
| style="background:#ebeced; color:black"|
| style="background:#b4d597; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
| style="background:#fff6a6; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
|-
| style="background:#ffffdd; color:black"|'''8:00-10:00'''
| style="background:#ebeced; color:black"|'''9:30''' Core 1 and 2 PI closed session in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol A]
| style="background:#b4d597; color:black"|Project Work <br> '''8:00-9:00''' [[AHM2009:NITRC and Slicer|How to use NITRC and slicer]] (Steve, Terry)<br>
'''9:00-10:00''' [[AHM2009:Batchmake and XNAT|Using Batchmake and XNAT to process large studies]] (Stephen Aylward and Dan Marcus) in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work <br>'''8:00-9:00''' [[AHM2009:Tutorial Review and Judging|Tutorial Review and Judging]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
'''9:00-10:00''' Particle Correspondence Breakout (Capital Ballroom A)
| style="background:#fff6a6; color:black"|'''8:00''' [[AHM 2009 Introduction|Introduction]], [http://www.spl.harvard.edu/~kikinis Ron Kikinis] <br>
'''8:05''' [[AHM 2009 NA-MIC Highlights|NA-MIC Highlights]] ([http://www.cs.utah.edu/~whitaker/ Ross Whitaker])<br>
'''Roadmap Projects'''<br>
'''8:35''': [[AHM2009:JHU|JHU/Queens]] ([http://research.cs.queensu.ca/~gabor/ Gabor Fichtinger])<br>
'''8:55''': [[AHM2009:UNC|UNC]] ([http://www.med.unc.edu/psych/directories/faculty/hazlett/ Heather Cody])<br>
'''9:15''': [[AHM2009:PNL|PNL]] ([http://pnl.bwh.harvard.edu/people/profiles/kubicki.html Marek Kubicki])<br>
'''9.35''': [[AHM2009:Mind|Mind Institute]] ([http://www.mrn.org/principle-investigators/h.-jeremy-bockholt.html Jeremy Bockolt])<br>
| style="background:#b4d597; color:black"|Project Work <br>
|-
| style="background:#ffffdd; color:black"|'''10:00-10:30'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"| '''10:30-11:30'''[[AHM2009:GUI Testing|Automated GUI Testing for Slicer]] (Sebastien) [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
|-
| style="background:#ffffdd; color:black"|'''10:30-12:00'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"|Project Work
| style="background:#b4d597; color:black"|Project Work <br>

| style="background:#fff6a6; color:black"|
'''Collaborations'''<br>
'''10:30''': [[media:NA-MIC_Mesh_Collaboration_2009.ppt|Iowa collaboration]] ([http://www.engineering.uiowa.edu/faculty-staff/profile-directory/bme/grosland_n.php Nicole Grosland])<br>
'''10:45''': [[AHM2009:ExternalWFU|Wake Forest collaboration]] ([http://www.ece.vt.edu/faculty/wyatt.html Chris Wyatt])<br>
'''11:00''': [[media:NA-MIC_Cleary_RF_Ablation_Georgetown_Jan_2009.ppt|Georgetown U. collaboration]] ([http://www.isis.georgetown.edu/PORTALVBVS/DesktopDefault.aspx?tabindex=2&tabid=8 Kevin Cleary])<br>
'''11:15''': [[media:HAMMER.ppt | UNC collaboration]] ([http://www.med.unc.edu/~dgshen Dinggang Shen])<br>
'''11:30''': [[media:AHM2009_MarioNegriCollaboration.pdf | Mario Negri Collaboration]] ([http://villacamozzi.marionegri.it/~luca/ Luca Antiga])<br>
'''11:45''': Discussion<br>
| style="background:#b4d597; color:black"|Project Work
|-
| style="background:#ffffdd; color:black"|'''12:00-1:00'''
| style="background:#b4d597; color:black"| Lunch
| style="background:#b4d597; color:black"| Lunch <br>
| style="background:#b4d597; color:black"| Lunch<br>
| style="background:#fff6a6; color:black"| Lunch
| style="background:#b4d597; color:black"| Adjourn
|-
| style="background:#ffffdd; color:black"|'''1:00-3:00'''
| style="background:#b4d597; color:black"|[[2009_Winter_Project_Week|Begin Project Activities]]: Introduce Projects and Participants
| style="background:#b4d597; color:black"|[[AHM 2009:DTI Breakout|DTI Discussion]] (Sonia, Randy, Others) [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/Amethyst 1]
| style="background:#b4d597; color:black"|Project Work (Capital Ballroom A) <br> '''1:00-2:00''' [[AHM2009:Python Modules|Python Modules]] (Luca Antiga) <br> '''2:00-3:00''' [[AHM2009:VTKWidgets | VTK Widgets]] (Will Schroeder)
| style="background:#fff6a6; color:black"|
'''Tools and Tutorials''' (coordinator) <br>
'''1:00-1:20''' [[AHM2009:Slicer|Slicer]] ([http://www.spl.harvard.edu/~pieper Steve Pieper])<br>
'''1:20-1:40''' [[AHM2009:Plug-ins|Plug-ins for Slicer]] ([http://wiki.na-mic.org/Wiki/index.php/User:Millerjv Jim Miller])<br>
'''1:40-2:00''' [[AHM2009:Non-interactive-tools|Non-interactive tools]] ([http://www.kitware.com/company/team/aylward.html Stephen Aylward])<br>
'''2:00-3:00''' [[AHM2009:Tutorial-Contest-Winners|Tutorial Contest]]: Presentations by the winners ([http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=64 Randy Gollub])<br>
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:00-3:30'''
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:00-5:00'''
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|'''3:30-4:30''' [[AHM2009:Cell Segmentation|Cell Segmentation]] (Alex G) <br> Project Work <br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work <br>'''3:00-5:00''' Meshing Tutorial (Nicole Grosland, Vincent Magnotta)<br>[[Iowa_Meshing_Tutorial]]<br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#fff6a6; color:black"|[[2008 EAB|EAB]]<br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B]<br>'''3:00-4:00''' Discussion with NA-MIC Leadership<br> '''4:00-5:00''' Closed Session
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''05:00-07:00'''
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|'''05:00-06:00''' [[AHM2009:Meshing Breakout | Meshing Breakout]] (Capital Ballroom A)
| style="background:#fff6a6; color:black"|'''6:00''' Optional: [http://www.skisaltlake.com/murphys.htm Beer at Murphy's] (like last year)
| style="background:#ebeced; color:black"|
|}

Please note that there will be a Core 1&2 Site PI Retreat on the morning of Monday, January 5th. This is a closed session for Core 1&2 Site PIs, with no delegates. The topic is the competitive renewal.

== Dates. Venue. Registration ==
'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 8th'''.
* Project Activities will be held rest of the week between '''Monday, January 5th and Friday, January 9th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. Please either call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) or book online '''by December 4, 2008''' using the code SCISCIA to get rooms at $139/night. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

'''Registration:''' We are charging a registration fee to all participants ($200 for AHM only, and $450 for AHM+). The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click http://www.sci.utah.edu/namic2009/registration.html for online registration. This registration must be completed by December 12, 2008.<br>

'''Connectivity'''
We have three wireless access points at the AHM. Two of them are located in the capital ballroom. One is named capital-ballroom, the other is named capital-ballroom2. If one access point doesn't let you connect it is probably overloaded. In that case, please try connecting to the other one.

== Attendees ==

Please follow http://www.sci.utah.edu/namic2009/registration.html to complete your online registration. The organizers will periodically publish the list of registered attendees in the space below. Attendees should '''NOT''' add their names in this section. This list is a snapshop as of 01:46, 23 December 2008 (UTC)

# Michael Ackerman NA-MIC All Hands Meeting National Library of Medicine at NIH
# Luca Antiga NA-MIC All Hands Meeting and Project Week 2009 Mario Negri Institute
# Kevin Archie NA-MIC All Hands Meeting and Project Week 2009 Washington University
# Nicole Aucoin NA-MIC All Hands Meeting and Project Week 2009 BWH
# Stephen Aylward NA-MIC All Hands Meeting and Project Week 2009 Kitware
# Sebastien Barre NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Morry Blumenfeld NA-MIC All Hands Meeting EAB
# H Jeremy Bockholt NA-MIC All Hands Meeting and Project Week 2009 The Mind Research Network
# Sylvain Bouix NA-MIC All Hands Meeting and Project Week 2009 PNL
# Josh Cates NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# German Cavelier NA-MIC All Hands Meeting NIH-NIMH
# Kiyoyuki Chinzei NA-MIC All Hands Meeting and Project Week 2009 AIST
# Kevin Cleary NA-MIC All Hands Meeting Georgetown University
# Manasi Datar NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Michal Depa NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Harish Doddi NA-MIC All Hands Meeting and Project Week 2009 Stanford University
# Andriy Fedorov NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Gabor Fichtinger NA-MIC All Hands Meeting Queens Univ
# Yi Gao NA-MIC All Hands Meeting and Project Week 2009
# Arnaud Gelas NA-MIC All Hands Meeting and Project Week 2009 Harvard Medical School
# Guido Gerig NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Polina Golland NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Randy L. Gollub NA-MIC All Hands Meeting and Project Week 2009 MGH
# Casey Goodlett NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Alexandre Gouaillard NA-MIC All Hands Meeting and Project Week 2009 Harvard Medical School
# Sylvain Gouttard NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Jeffrey Grethe NA-MIC All Hands Meeting and Project Week 2009 UC San Diego
# Nicole Grosland NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Daniel Haehn NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Nathan Hageman NA-MIC All Hands Meeting and Project Week 2009 UCLA
# Nobuhiko Hata NA-MIC All Hands Meeting and Project Week 2009 Brigham and Womens Hospital
# Kathryn Hayes NA-MIC All Hands Meeting and Project Week 2009 Brigham and Womens Hospital
# Heather Cody Hazlett NA-MIC All Hands Meeting University of North Carolina
# Jaesung Hong NA-MIC All Hands Meeting and Project Week 2009 Kyushu University
# Luis Ibanez NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Chris Johnson NA-MIC All Hands Meeting and Project Week 2009 EAB
# Ron Kikinis NA-MIC All Hands Meeting and Project Week 2009 SPL - BWH
# Ivan Kolesov NA-MIC All Hands Meeting and Project Week 2009 Georgia Tech
# Karthik Krishnan NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Marek Kubicki NA-MIC All Hands Meeting and Project Week 2009 PNL_BWH
# Curtis Lisle NA-MIC All Hands Meeting and Project Week 2009 KnowledgeVis, LLC
# Yanling Liu NA-MIC All Hands Meeting and Project Week 2009 SAIC-Frederick, Inc.
# Zhexing Liu NA-MIC All Hands Meeting and Project Week 2009 NIRAL, UNC
# Terry Lorber NA-MIC All Hands Meeting and Project Week 2009 Isomics, Inc
# Bill Lorensen NA-MIC All Hands Meeting and Project Week 2009 EAB
# Vincent Magnotta NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Daniel Marcus NA-MIC All Hands Meeting and Project Week 2009 Washington University
# Katie Mastrogiacomo NA-MIC All Hands Meeting and Project Week 2009 SPL - BWH
# Cedric Mathieu NA-MIC All Hands Meeting and Project Week 2009 UNC
# Bjoern Menze NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Mikhail Milchenko NA-MIC All Hands Meeting Washington University in St Louis
# James Miller NA-MIC All Hands Meeting and Project Week 2009
# Vandana Mohan NA-MIC All Hands Meeting and Project Week 2009 Georgia Inst of Technology
# kishore mosaliganti NA-MIC All Hands Meeting and Project Week 2009 Harvard Medical School
# Sandy Napel NA-MIC All Hands Meeting EAB
# Marc Niethammer NA-MIC All Hands Meeting and Project Week 2009 UNC Chapel Hill
# Guy Nir NA-MIC All Hands Meeting and Project Week 2009 Technion
# Ipek Oguz NA-MIC All Hands Meeting and Project Week 2009 UNC
# Saikat Pal NA-MIC All Hands Meeting and Project Week 2009 Stanford University
# Steve Pieper NA-MIC All Hands Meeting and Project Week 2009 Isomics, Inc.
# Marcel Prastawa NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Fred Prior NA-MIC All Hands Meeting EAB
# Sonia Pujol NA-MIC All Hands Meeting and Project Week 2009 Surgical Planning Lab, Brigham Womens Hosp
# Vidya Rajagopalan NA-MIC All Hands Meeting and Project Week 2009 Virginia Tech
# Austin Ramme NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Petter Risholm NA-MIC All Hands Meeting and Project Week 2009 Brigham Womens Hospital
# James Ross NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Marco Ruiz NA-MIC All Hands Meeting and Project Week 2009 UCSD
# Raul San Jose NA-MIC All Hands Meeting and Project Week 2009 LMI-BWH
# Peter Savadjiev NA-MIC All Hands Meeting and Project Week 2009 Brigham Womens Hospital
# William Schroeder NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Mark Scully NA-MIC All Hands Meeting and Project Week 2009 The Mind Research Network
# Madeleine Seeland NA-MIC All Hands Meeting and Project Week 2009 LMI
# Gregory Sharp NA-MIC All Hands Meeting and Project Week 2009 MGH
# Dinggang Shen NA-MIC All Hands Meeting UNC-Chapel Hill
# Kiran Shivanna NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Shantanu Singh NA-MIC All Hands Meeting and Project Week 2009 The Ohio State University
# Martin Styner NA-MIC All Hands Meeting and Project Week 2009 University of North Carolina
# Allen Tannenbaum NA-MIC All Hands Meeting and Project Week 2009 Georgia Tech
# Xiaodong Tao NA-MIC All Hands Meeting and Project Week 2009 GE Global Research
# Doug Terry NA-MIC All Hands Meeting and Project Week 2009 Psychiatry Neuroimaging Lab
# Clement Vachet NA-MIC All Hands Meeting and Project Week 2009 UNC
# Koen Van Leemput NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Archana Venkataraman NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Siddharth Vikal NA-MIC All Hands Meeting and Project Week 2009 Queens University
# William Wells NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Carl-Fredrik Westin NA-MIC All Hands Meeting and Project Week 2009 Brigham and Womens Hospital
# Ross Whitaker NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Nathan Wilson NA-MIC All Hands Meeting Cardiovascular Simulation, Inc.
# Chris Wyatt NA-MIC All Hands Meeting
# Alexander Yarmarkovich NA-MIC All Hands Meeting and Project Week 2009 ISOMIC
# Dr. Terry S Yoo NA-MIC All Hands Meeting DHHSNIHNLM

File:AHM2009 MarioNegriCollaboration.pdf

2009-01-08T16:33:42Z

Lantiga:

2008-12-10T19:23:23Z

Lantiga: /* Key Investigators */

{|
|[[Image:Python-logo.png |thumb|320px|[http://www.python.org]]
|}

__NOTOC__

===Key Investigators===
* Luca Antiga (Medical Imaging Unit, Biomedical Engineering Department, Mario Negri Institute)
* Steve Piper (Isomics)

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

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

<h1>Objective</h1>
To finalize the implementation of the Slicer Python interface and solve packaging problems linked to Scipy.

</div>

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

<h1>Approach, Plan</h1>

The Slicer Python interface now works well for both non-interactive and interactive modules. A few improvements are still needed, namely <br>

- calling VTK static methods - e.g. slicer.vtkMath.Norm(v)

- handling modified arguments - e.g. slicer.vtkMath::Normalize(v)

- defining methods with the exact number of arguments (now it's not constrained, so if it's wrong Tcl complains) - this will require a patch on the VTK Tcl wrappers.

- fix a memory leak associated with Python scripted modules.

As for packaging problems, testing will have to be performed on several architectures.

</div>

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

<h1>Progress</h1>

TODO

</div>

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

</div>

2009 Winter Project Week Python

2008-12-10T19:22:44Z

Lantiga: /* Key Investigators */

{|
|[[Image:Python-logo.png |thumb|320px|[http://www.python.org]]
|}

__NOTOC__

===Key Investigators===
* Luca Antiga (Medical Imaging Unit, Biomedical Engineering Department, Mario Negri Institute)
* Steve Piper (Isomics)

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

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

<h1>Objective</h1>
To finalize the implementation of the Slicer Python interface and solve packaging problems linked to Scipy.

</div>

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

<h1>Approach, Plan</h1>

The Slicer Python interface now works well for both non-interactive and interactive modules. A few improvements are still needed, namely <br>
- calling VTK static methods - e.g. slicer.vtkMath.Norm(v)
- handling modified arguments - e.g. slicer.vtkMath::Normalize(v)
- defining methods with the exact number of arguments (now it's not constrained, so if it's wrong Tcl complains) - this will require a patch on the VTK Tcl wrappers.
- fix a memory leak associated with Python scripted modules.

</div>

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

<h1>Progress</h1>

TODO

</div>

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

</div>

2008-06-18T08:15:33Z

Lantiga: /* References */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Python-logo.png |thumb|320px|[http://www.python.org]]]
|}

__NOTOC__

===Key Investigators===
* Luca Antiga
* Dan Blezek
* Mike Halle
* Steve Piper
* Demian Wasserman

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

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

<h1>Objective</h1>
To finalize the use of Python within Slicer for command-line modules, scripted modules and meta-modules (or module chaining). The main rework is needed for scripted modules.

</div>

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

<h1>Approach, Plan</h1>
The plan for the project week is to get the status of Python within Slicer ready for release. This will involve some general code review and some rework on Python Scripted Module infrastructure.
</div>

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

<h1>Progress</h1>

During the January 2008 project week, within [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]], preliminary Python support for Numpy/Scipy, command line modules (executed in the main thread), calling of all registered modules from Python and scripted modules have been added.
</div>

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

</div>

===References===

* [http://www.python.org www.python.org]

2008 Summer Project Week:PythonInSlicer

Lantiga: /* Attendee List */

NA-MIC External Collaborations

2008-03-10T18:53:55Z

Lantiga: /* Additional External Collaborations */

Back to [[NA-MIC_Collaborations|NA-MIC Collaborations]]

=Projects funded by "Collaborations with NCBC PAR"=

This section describes external collaborations with NA-MIC that are funded by NIH under the "Collaboration with NCBC" PAR. (Details for this funding mechanism are provided [[Collaborator:Resources|<big><big>here</big></big>]]).

{|
| style="width:10%" | [[Image:Cli-mesh-quality-small-062607.png|thumb|left|300px|PAR-05-063: R01EB005973 Automated FE Mesh Development]]
| style="width:90%" |

== [[NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development|PAR-05-063: R01EB005973 Automated FE Mesh Development]] ==

This project is funded under an NCBC collaboration grant to PIs Nicole Grosland and Vincent Magnotta at UIowa. The goal of this project is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the [[NA-MIC-Kit|NA-MIC kit]]. [[NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development|More...]]

|-

| | [[Image:NhpATOCPic.jpg|thumb|left|300px]]
| |

==[[NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction|PAR-07-249: R01AA016748 Measuring Alcohol and Stress Interaction with Structural and Perfusion MRI]]==

This project is funded under an NCBC collaboration grant to PIs James Daunais, Robert Kraft, and Chris Wyatt. The goal of this project is to examine the the effects of chronic alcohol self- administration on brain structure and function the monkey brain. MRI image analysis tools from the [[NA-MIC-Kit|NA-MIC kit]] will be adapted for use with the monkey brain datasets. [[NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction|More...]]

|-

| | [[Image:LiverRFAPhantom.png|thumb|left|300px]]
| |

==[[NA-MIC_NCBC_Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors|PAR-05-063: R01CA124377 An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors]]==

This project is funded under an NCBC collaboration grant to PI Kevin Cleary at Georgetown University. The goal of this project 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.[[NA-MIC_NCBC_Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors|More...]]
|-
|}

=Additional External Collaborations=

This section describes external collaborations with NA-MIC that are funded by other mechanisms:

{|
| style="width:10%" | [[Image:BRAINS.gif|thumb|left|300px]]
| style="width:90%" |

==[[NA-MIC Brains Collaboration| PAR-05-057: BRAINS Morphology and Image Analysis]]==

This project is a funded under a Continued Development and Maintenance of Software grant to PIs Vincent Magnotta, Hans Johnson, Jeremy Bockholt, and Nancy Andreasen at the University of Iowa. The goal of this project is to update the '''BRAINS''' image analysis software developed at the University of Iowa. [[NA-MIC Brains Collaboration|More...]]

|-

| | [[Image:LevelSetSegmentGUIModule_alpha.png|thumb|left|300px]]
| |

==[[NA-MIC VMTK Collaboration | Vascular Modeling Toolkit Collaboration]]==

Slicer as a platform for segmentation and geometric analysis of vascular segments and image-based computational fluid dynamics (CFD). [[NA-MIC VMTK Collaboration|More...]]

Collaboration with [http://villacamozzi.marionegri.it/~luca/ Luca Antiga] of the [http://www.marionegri.it Mario Negri Institute].

|-

| | [[Image:27y-leftabdcan-T6SQ-voltage-withheart4.png |thumb|left|300px]]
| |

==[[NA-MIC Childrens Collaboration| Children's Pediatric Cardiology Collaboration with SCI/SPL/Northeastern]]==

Collaboration with John Triedman, Matt Jolley, Dana Brooks, SCI.

|-

| | [[Image:NITRC.png|thumb|left|300px]]
| |
==[[NA-MIC and NITRC| NA-MIC Collaboration with NITRC]]==

The NA-MIC Project is working to make NA-MIC neuroimaging software available through the [http://www.nitrc.org/ NITRC web site]. Supplemental support is helping to create the [[Slicer3:Loadable_Modules | Slicer3 Loadable Modules]] project so that slicer plugins can be hosted on NITRC, allowing greater scalability for developers and users of Slicer.

|-

| | [[Image:Logo_nac.gif|thumb|left|100px|[http://nac.spl.harvard.edu NAC website]]]
| |

==[[Collaboration:NAC| NA-MIC Collaboration with NAC]]==

NAC, the neuroimage analysis center, is a national resource center. NAC is relying on the NA-MIC kit for its general software environment. The mission of NAC is to develop novel concepts for the analysis of images of the brain and develop and disseminate tools based on those concepts.

|-

| | [[Image:Ncigtlogo.gif|thumb|left|100px]]
| |

==[[Collaboration:NCIGT| NA-MIC Collaboration with NCIGT]]==

Here are a couple of sentences to summarize the nature of the NA-MIC Collaboration with NCIGT.

|-
|}

[[Image:AISTlogo.gif|thumb|left|100px]]

==[[Collaboration:AIST| NA-MIC Collaboration with Research and Development Project on Intelligent Surgical Instruments]]==

Intelligent Surgical Instruments Projects uses Open-source software engineering tools developed by NA-MIC, and leverage it to surgical robotics.

File:LevelSetSegmentGUIModule alpha.png

2008-03-10T18:52:56Z

Lantiga:

NA-MIC External Collaborations

2008-03-10T18:35:29Z

Lantiga: /* Vascular Modeling Toolkit */

Back to [[NA-MIC_Collaborations|NA-MIC Collaborations]]

=Projects funded by "Collaborations with NCBC PAR"=

This section describes external collaborations with NA-MIC that are funded by NIH under the "Collaboration with NCBC" PAR. (Details for this funding mechanism are provided [[Collaborator:Resources|<big><big>here</big></big>]]).

{|
| style="width:10%" | [[Image:Cli-mesh-quality-small-062607.png|thumb|left|300px|PAR-05-063: R01EB005973 Automated FE Mesh Development]]
| style="width:90%" |

== [[NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development|PAR-05-063: R01EB005973 Automated FE Mesh Development]] ==

This project is funded under an NCBC collaboration grant to PIs Nicole Grosland and Vincent Magnotta at UIowa. The goal of this project is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the [[NA-MIC-Kit|NA-MIC kit]]. [[NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development|More...]]

|-

| | [[Image:NhpATOCPic.jpg|thumb|left|300px]]
| |

==[[NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction|PAR-07-249: R01AA016748 Measuring Alcohol and Stress Interaction with Structural and Perfusion MRI]]==

This project is funded under an NCBC collaboration grant to PIs James Daunais, Robert Kraft, and Chris Wyatt. The goal of this project is to examine the the effects of chronic alcohol self- administration on brain structure and function the monkey brain. MRI image analysis tools from the [[NA-MIC-Kit|NA-MIC kit]] will be adapted for use with the monkey brain datasets. [[NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction|More...]]

|-

| | [[Image:LiverRFAPhantom.png|thumb|left|300px]]
| |

==[[NA-MIC_NCBC_Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors|PAR-05-063: R01CA124377 An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors]]==

This project is funded under an NCBC collaboration grant to PI Kevin Cleary at Georgetown University. The goal of this project 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.[[NA-MIC_NCBC_Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors|More...]]
|-
|}

=Additional External Collaborations=

This section describes external collaborations with NA-MIC that are funded by other mechanisms:

{|
| style="width:10%" | [[Image:BRAINS.gif|thumb|left|300px]]
| style="width:90%" |

==[[NA-MIC Brains Collaboration| PAR-05-057: BRAINS Morphology and Image Analysis]]==

This project is a funded under a Continued Development and Maintenance of Software grant to PIs Vincent Magnotta, Hans Johnson, Jeremy Bockholt, and Nancy Andreasen at the University of Iowa. The goal of this project is to update the '''BRAINS''' image analysis software developed at the University of Iowa. [[NA-MIC Brains Collaboration|More...]]

|-

| | [[Image:VmtkRefSys1.jpg|thumb|left|300px]]
| |

==[[NA-MIC VMTK Collaboration | Vascular Modeling Toolkit Collaboration]]==

Slicer as a platform for segmentation and geometric analysis of vascular segments and image-based computational fluid dynamics (CFD). [[NA-MIC VMTK Collaboration|More...]]

Collaboration with [http://villacamozzi.marionegri.it/~luca/ Luca Antiga] of the [http://www.marionegri.it Mario Negri Institute].

|-

| | [[Image:27y-leftabdcan-T6SQ-voltage-withheart4.png |thumb|left|300px]]
| |

==[[NA-MIC Childrens Collaboration| Children's Pediatric Cardiology Collaboration with SCI/SPL/Northeastern]]==

Collaboration with John Triedman, Matt Jolley, Dana Brooks, SCI.

|-

| | [[Image:NITRC.png|thumb|left|300px]]
| |
==[[NA-MIC and NITRC| NA-MIC Collaboration with NITRC]]==

The NA-MIC Project is working to make NA-MIC neuroimaging software available through the [http://www.nitrc.org/ NITRC web site]. Supplemental support is helping to create the [[Slicer3:Loadable_Modules | Slicer3 Loadable Modules]] project so that slicer plugins can be hosted on NITRC, allowing greater scalability for developers and users of Slicer.

|-

| | [[Image:Logo_nac.gif|thumb|left|100px|[http://nac.spl.harvard.edu NAC website]]]
| |

==[[Collaboration:NAC| NA-MIC Collaboration with NAC]]==

NAC, the neuroimage analysis center, is a national resource center. NAC is relying on the NA-MIC kit for its general software environment. The mission of NAC is to develop novel concepts for the analysis of images of the brain and develop and disseminate tools based on those concepts.

|-

| | [[Image:Ncigtlogo.gif|thumb|left|100px]]
| |

==[[Collaboration:NCIGT| NA-MIC Collaboration with NCIGT]]==

Here are a couple of sentences to summarize the nature of the NA-MIC Collaboration with NCIGT.

|-
|}

[[Image:AISTlogo.gif|thumb|left|100px]]

==[[Collaboration:AIST| NA-MIC Collaboration with Research and Development Project on Intelligent Surgical Instruments]]==

Intelligent Surgical Instruments Projects uses Open-source software engineering tools developed by NA-MIC, and leverage it to surgical robotics.