NAMIC Wiki - User contributions [en]

UKF Edema

2015-01-09T16:01:03Z

Ruizhi:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
File:1224 wb default single left.png|[Reconstructed Arcuate Fasciculus using Single-tensor UKF tractography]
File:Fig Patient 1 Parameters Left AF.pdf|[Reconstructed Arcuate Fasciculus using UKF tractography with different parameter settings]
File:Figure Seed Regions.pdf|[Reconstructed Arcuate Fasciculus using UKF tractography from different seed regions]
</gallery>

==Key Investigators==
Ruizhi Liao, Lauren O'Donnell

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*Analyze the performance of two-tensor UKF tractography in edema
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*We've done phantom and experiments to analyze the performance of two-tensor model in UKF tractography when tracing peritumoral fibers. We've also done experiments with different parameter settings and from different seed regions to test the sensitivity of UKF tractography.
</div>
</div>

File:Figure Seed Regions.pdf

2015-01-09T16:00:15Z

Ruizhi: uploaded a new version of "File:Figure Seed Regions.pdf"

File:Figure Seed Regions.pdf

2015-01-09T15:59:44Z

Ruizhi:

UKF Edema

2015-01-09T15:58:41Z

Ruizhi: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
File:1224 wb default single left.png|[Reconstructed Arcuate Fasciculus using Single-tensor UKF tractography]
File:Fig Patient 1 Parameters Left AF.pdf|[Reconstructed Arcuate Fasciculus using UKF tractography with different parameter settings]
</gallery>

==Key Investigators==
Ruizhi Liao, Lauren O'Donnell

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*Analyze the performance of two-tensor UKF tractography in edema
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*We've done phantom and experiments to analyze the performance of two-tensor model in UKF tractography when tracing peritumoral fibers. We've also done experiments with different parameter settings and from different seed regions to test the sensitivity of UKF tractography.
</div>
</div>

File:Fig Patient 1 Parameters Left AF.pdf

2015-01-09T15:57:09Z

Ruizhi: uploaded a new version of "File:Fig Patient 1 Parameters Left AF.pdf"

UKF Edema

2015-01-09T15:54:52Z

Ruizhi:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
File:1224 wb default single left.png|[Reconstructed Arcuate Fasciculus using Single-tensor UKF tractography]
File:Fig Patient 1 Parameters Left AF.pdf|[Reconstructed Arcuate Fasciculus using UKF tractography with different parameter settings]
</gallery>

==Key Investigators==
Ruizhi Liao, Lauren O'Donnell

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*Analyze the performance of two-tensor UKF tractography in edema
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*We've done phantom and experiments to analyze the performance of two-tensor model in UKF tractography when tracing peritumoral fibers. We've also done experiments with different parameter settings to test the sensitivity of UKF tractography.
</div>
</div>

UKF Edema

2015-01-09T15:53:57Z

Ruizhi: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
File:1224 wb default single left.png|[Reonstructed Arcuate Fasciculus using Single-tensor UKF tractography]
</gallery>

==Key Investigators==
Ruizhi Liao, Lauren O'Donnell

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*Analyze the performance of two-tensor UKF tractography in edema
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*We've done phantom and experiments to analyze the performance of two-tensor model in UKF tractography when tracing peritumoral fibers. We've also done experiments with different parameter settings to test the sensitivity of UKF tractography.
</div>
</div>

File:Fig Patient 1 Parameters Left AF.pdf

2015-01-09T15:52:21Z

Ruizhi:

UKF Edema

2015-01-09T15:44:59Z

Ruizhi:

File:1224 wb default single left.png

2015-01-09T15:38:58Z

Ruizhi:

New Distance

2015-01-09T14:56:46Z

Ruizhi:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
File:Mean distance output.png|[Output from mean distance]
File:New distance output1.png|[Output from new distance]
File:New distance output2.png|[Output from new distance]
</gallery>

==Key Investigators==
Ruizhi Liao, Lauren O'Donnell

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*Develop a modified distance for measuring the similarity between fiber tracts to improve the performance of clustering fiber tracts, especially to distinct corpus callosum and mistakenly tracked cingulum bundle.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*We've developed and implemented a modified mean distance to incorporate with shape similarity between fiber tracts. The shape similarity model is based on the angle shift among the vectors to direct corresponding sample points along fiber tracts. The modified mean distance can address the challenge of distincting corpus callosum and mistakenly tracked cingulum bundle. The outputs have a relatively smaller intra-Hausdorff-distance of clustered tracts than the outputs from mean distance.
</div>
</div>

File:Mean distance output.png

2015-01-09T14:54:58Z

Ruizhi:

File:New distance output2.png

2015-01-09T14:54:11Z

Ruizhi:

File:New distance output1.png

2015-01-09T14:53:18Z

Ruizhi:

New Distance

2015-01-09T14:46:22Z

Ruizhi: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Ruizhi Liao, Lauren O'Donnell

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*Develop a modified distance for measuring the similarity between fiber tracts to improve the performance of clustering fiber tracts, especially to distinct corpus callosum and mistakenly tracked cingulum bundle.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*We've developed and implemented a modified mean distance to incorporate with shape similarity between fiber tracts. The shape similarity model is based on the angle shift among the vectors to direct corresponding sample points along fiber tracts. The modified mean distance can address the challenge of distincting corpus callosum and mistakenly tracked cingulum bundle. The outputs have a relatively smaller intra-Hausdorff-distance of clustered tracts than the outputs from mean distance.
</div>
</div>

New Distance

2015-01-09T14:42:21Z

Ruizhi: /* Project Description */

New Distance

2015-01-09T14:31:08Z

Ruizhi: /* Project Description */

2015 Winter Project Week

2015-01-09T14:25:45Z

Ruizhi: /* Image-Guided Therapy */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

== Note of Remembrance ==

[[file:ferenc.jpg|right]]
This project week is dedicated to Ferenc Jolesz, leader and mentor to many in the image guided therapy community. There is a [http://ferenc.jolesz.muchloved.com/ tribute page to Ferenc] for people who want to share their thoughts.

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

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

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

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

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| 
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session: CIP]] (Raul San Jose) ''(Amethyst 1)'' 
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) ''(Amethyst 1)'' 
| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]] ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
| Neurosurgical Ultrasound Breakout
|
| [[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:#522200"| [http://ferenc.jolesz.muchloved.com/frame.aspx? A tribute to Ferenc Jolesz] [[2015_Winter_Project_Week|Project Presentations]] ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|
| ''(Olympus B)''
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] ''(Amethyst 1)'' 
| 3:15-4pm: [[2015_Winter_Project_Week_Infrastructure_Breakout|Breakout Session: Infrastructure (JC, Steve, Alex, Hans, Raul)]] ''(Amethyst 1)'' 
|[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[User:Yli|Quantitative Evaluation of Digitally Registered Pre and Post op DTI by 3D ROI Segmentation]] (Li Ye, Sonia Pujol, Steve Pieper, Alireza Mehrtash)
* [[New Distance|A modified distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateNavigation workflow | Workflow for prostate navigation and its components]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)
*[[Valve Replacement | Aortic valve replacement using tracked 3D ultrasound]] (Adam Rankin)
*[[2015_Winter_Project_Week:CommunicationProtocolForOpticalTrackingWithSurfaceScan| Communication Protocol for Optical Tracking with Surface Scan]] (Junichi Tokuda, Sangyong Kim, ByungHyun Cho, Brian Nini, Nobuhiko Hata)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Fissure Enhancement | Supervised fissure enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

==CTE==
* [[Slicer_Tract_Analysis | Measurement and visualization using white matter hierarchies in Slicer]] (Alexander Yarmarkovich, Lauren O'Donnell)

== Lung ==
*[[ Small lung nodule differential diagnosis using 3D Slicer | Small lung nodule differential diagnosis using 3D Slicer]] (Li Ming, Jay Jagadeesan)

==[http://qiicr.org QIICR]==
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* [[2015_Winter_Project_Week:_DICOM_representation_of_QIICR_Iowa_DBP_data|Representation of Iowa QIN data using DICOM]] (Andrey, Christian Bauer, Steve Pieper)
* [[Whole Body PET/CT Reference Region segmentation]] (Christian Bauer)
* [[2015_Winter_Project_Week:Bolus_Arrival_Time_Estimation_in_PK_Modelling|Bolus Arrival Time (BAT) Estimation in PK Modelling]] (Alireza Mehrtash, Andriy Fedorov, Jim Miller)
* [[2015_Winter_Project_Week:DICOM_Module_Improvements|DICOM Module Improvements]] (Alireza Mehrtash, Andriy Fedorov, Ron Kikinis, Steve Pieper)
* [[2015_Winter_Project_Week:Slice_View_Annotations|Slice View Annotations]] (Alireza Mehrtash, Andriy Fedorov, Steve Pieper)

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)
* [[Cortex_Clustering| Experimental tract-based cortical clustering ]] (Lauren O'Donnell, William Wells)

==Slicer4 Extensions==
* [[PET Tumor Segmentation]] (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* [[2015_Winter_Project_Week:SlicerModelGlyphs | Display of point data vectors on Slicer models]] (Francois Budin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)
* [[2015_Winter_Project_Week:RemoveITKv3Compatibility|Remove ITKv3 Compatibility for 64-bit image support]] (Bradley Lowekamp, Hans Johnson?, ?)
* [[2015_Winter_Project_Week:VersorTransforms|ITK Composed Versor Transforms]] (Bradley Lowekamp, Hans Johnson?, ?)

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration.

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

UKF Edema

2015-01-01T15:22:43Z

Ruizhi:

2015 Winter Project Week

2015-01-01T15:20:15Z

Ruizhi: /* Image-Guided Therapy */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

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

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

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

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| 
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) ''(Amethyst 1)'' 
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) ''(Amethyst 1)'' 
| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]] ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''l
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|Project Presentations]] ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2015_SLC_Training_Workshop|Slicer Workshop (Ron Kikinis)]]
| ''(Olympus B)''
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] ''(Amethyst 2)'' 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis(Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[ProstateSegmentation | Prostate segmentation and biopsy]] (Peter Behringer, Andriy Fedorov)
* [[Needle Detection Tutorial | Needle Detection Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

==TBI==

==Stroke==

==Cardiac==

== Lung ==

*Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan, Jim Miller)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Feature Enhancement | Supervised feature enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)

==Head and Neck Cancer / Radiotherapy ==

==[http://qiicr.org QIICR]==
* Mechanism to pull related DICOM series on derived modality load (Andrey, Csaba)
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* Representation of Iowa QIN data using DICOM (Andrey, Christian Bauer)

==Feature Extraction==

==Additional Brain Image Analysis==

==Slicer4 Extensions==
* PET Tumor Segmentation (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter, ?)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration.

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

UKF Edema

2015-01-01T15:18:56Z

Ruizhi: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List </gallery> ==Key Investigators== Ruizhi Liao, Lauren O'Donnell ==Project Descriptio…'

2015 Winter Project Week

2015-01-01T15:16:11Z

Ruizhi: /* Image-Guided Therapy */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

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

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

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

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| 
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) ''(Amethyst 1)'' 
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) ''(Amethyst 1)'' 
| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]] ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''l
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|Project Presentations]] ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2015_SLC_Training_Workshop|Slicer Workshop (Ron Kikinis)]]
| ''(Olympus B)''
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] ''(Amethyst 2)'' 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis(Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[ProstateSegmentation | Prostate segmentation and biopsy]] (Peter Behringer, Andriy Fedorov)
* [[Needle Detection Tutorial | Needle Detection Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
*Performance of UKF tractography in edema (Ruizhi Liao, Lauren O'Donnell)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

==TBI==

==Stroke==

==Cardiac==

== Lung ==

*Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan, Jim Miller)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Feature Enhancement | Supervised feature enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)

==Head and Neck Cancer / Radiotherapy ==

==[http://qiicr.org QIICR]==
* Mechanism to pull related DICOM series on derived modality load (Andrey, Csaba)
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* Representation of Iowa QIN data using DICOM (Andrey, Christian Bauer)

==Feature Extraction==

==Additional Brain Image Analysis==

==Slicer4 Extensions==
* PET Tumor Segmentation (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter, ?)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration.

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

2015 Winter Project Week

2015-01-01T15:15:47Z

Ruizhi: /* Image-Guided Therapy */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

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

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

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

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| 
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) ''(Amethyst 1)'' 
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) ''(Amethyst 1)'' 
| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]] ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''l
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|Project Presentations]] ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2015_SLC_Training_Workshop|Slicer Workshop (Ron Kikinis)]]
| ''(Olympus B)''
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] ''(Amethyst 2)'' 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis(Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[ProstateSegmentation | Prostate segmentation and biopsy]] (Peter Behringer, Andriy Fedorov)
* [[Needle Detection Tutorial | Needle Detection Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
* [[A new modified Frechet distance for measuring the similarity between fiber tracts|New Distance]] (Ruizhi Liao, Lauren O'Donnell)
*Performance of UKF tractography in edema (Ruizhi Liao, Lauren O'Donnell)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

==TBI==

==Stroke==

==Cardiac==

== Lung ==

*Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan, Jim Miller)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Feature Enhancement | Supervised feature enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)

==Head and Neck Cancer / Radiotherapy ==

==[http://qiicr.org QIICR]==
* Mechanism to pull related DICOM series on derived modality load (Andrey, Csaba)
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* Representation of Iowa QIN data using DICOM (Andrey, Christian Bauer)

==Feature Extraction==

==Additional Brain Image Analysis==

==Slicer4 Extensions==
* PET Tumor Segmentation (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter, ?)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration.

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

New Distance

2015-01-01T15:14:59Z

Ruizhi: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List </gallery> ==Key Investigators== Ruizhi Liao, Lauren O'Donnell ==Project Descriptio…'

2015 Winter Project Week

2015-01-01T15:05:33Z

Ruizhi: /* Image-Guided Therapy */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

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

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

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

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| 
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) ''(Amethyst 1)'' 
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) ''(Amethyst 1)'' 
| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]] ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''l
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|Project Presentations]] ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2015_SLC_Training_Workshop|Slicer Workshop (Ron Kikinis)]]
| ''(Olympus B)''
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] ''(Amethyst 2)'' 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis(Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[ProstateSegmentation | Prostate segmentation and biopsy]] (Peter Behringer, Andriy Fedorov)
* [[Needle Detection Tutorial | Needle Detection Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*A new modified Frechet distance for measuring the similarity between fiber tracts (Ruizhi Liao, Lauren O'Donnell)
*Performance of UKF tractography in edema (Ruizhi Liao, Lauren O'Donnell)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

==TBI==

==Stroke==

==Cardiac==

== Lung ==

*Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan, Jim Miller)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Feature Enhancement | Supervised feature enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)

==Head and Neck Cancer / Radiotherapy ==

==[http://qiicr.org QIICR]==
* Mechanism to pull related DICOM series on derived modality load (Andrey, Csaba)
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* Representation of Iowa QIN data using DICOM (Andrey, Christian Bauer)

==Feature Extraction==

==Additional Brain Image Analysis==

==Slicer4 Extensions==
* PET Tumor Segmentation (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter, ?)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration.

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

2015 Winter Project Week

2015-01-01T15:03:54Z

Ruizhi: /* Image-Guided Therapy */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

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

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

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

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| 
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) ''(Amethyst 1)'' 
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) ''(Amethyst 1)'' 
| '''[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]] ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''l
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|Project Presentations]] ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2015_SLC_Training_Workshop|Slicer Workshop (Ron Kikinis)]]
| ''(Olympus B)''
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] ''(Amethyst 2)'' 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis(Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[ProstateSegmentation | Prostate segmentation and biopsy]] (Peter Behringer, Andriy Fedorov)
* [[Needle Detection Tutorial | Needle Detection Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*A modified Frechet distance for measuring the similarity between fiber tracts (Ruizhi Liao, Lauren O'Donnell)
*Performance of UKF tractography in edema (Ruizhi Liao, Lauren O'Donnell)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

==TBI==

==Stroke==

==Cardiac==

== Lung ==

*Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan, Jim Miller)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Feature Enhancement | Supervised feature enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)

==Head and Neck Cancer / Radiotherapy ==

==[http://qiicr.org QIICR]==
* Mechanism to pull related DICOM series on derived modality load (Andrey, Csaba)
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* Representation of Iowa QIN data using DICOM (Andrey, Christian Bauer)

==Feature Extraction==

==Additional Brain Image Analysis==

==Slicer4 Extensions==
* PET Tumor Segmentation (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter, ?)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration.

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital