NAMIC Wiki - User contributions [en]

2016 Winter Project Week/Projects/ChestImagingPlatformWorkflows

2016-01-08T02:34:25Z

Jcross186: /* Project Description */

==Key Investigators==
* James Ross
* Raúl San José

==Project Description==
The Chest Imaging Platform (CIP) is a collection of C++ libraries, command-line executables, and python modules for segmenting, registering, processing, and quantitatively evaluating medical images of the chest; it is developed with large-scale, batch processing of high-resolution computed tomography (CT) images in mind. Many of the high-level workflows involve executing multiple CIP command-line tools and/or python modules, which imposes a barrier to entry for new users. Nipype is an open-soure, python-based software package that provides the ability to package multiple execution steps into a single workflow. In this project, I will be creating nipype-based workflows of commonly used, high-level tasks in order to make CIP functionality more accessible to new users.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Implement Nipype workflows for commonly used chest image analysis tasks
|

* Focus on automatic lobe segmentation pipeline
|

* Workflows exist for particle deployment and parenchyma phenotype computation
* End-to-end workflow created for automatic lobe segmentation
* A few extra nodes to add
* Include in next CIP release
|}
[[File:jcrProjectWeek2016.jpg|1200px]]

2016 Winter Project Week/Projects/ChestImagingPlatformWorkflows

2016-01-08T02:28:45Z

Jcross186: /* Project Description */

File:JcrProjectWeek2016.jpg

2016-01-08T02:27:30Z

Jcross186:

2016 Winter Project Week/Projects/ChestImagingPlatformWorkflows

2016-01-04T14:58:55Z

Jcross186: /* Project Description */

2016 Winter Project Week/Projects/ChestImagingPlatformWorkflows

2016-01-04T02:15:15Z

Jcross186: /* Project Description */

==Key Investigators==
* James Ross
* Raúl San José

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Implement Nipype workflows for commonly used chest image analysis tasks
|

* Focus on automatic lobe segmentation pipeline
|

* Workflows exist for particle deployment and parenchyma phenotype computation
|}

2016 Winter Project Week/Projects/ChestImagingPlatformWorkflows

2016-01-04T02:10:06Z

Jcross186: /* Key Investigators */

==Key Investigators==
* James Ross
* Raúl San José

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Introduce the new Chest Imaging Platform extension
* Get feedback of interested teams
|

* Present the project in one of the sessions
|
*
|}

2016 Winter Project Week/Projects/ChestImagingPlatformWorkflows

2016-01-04T02:08:59Z

Jcross186: Created page with "==Key Investigators== * James Ross * Raúl San José"

==Key Investigators==
* James Ross
* Raúl San José

2016 Winter Project Week

2016-01-04T02:07:24Z

Jcross186: /* Image Analysis */

__NOTOC__
[[image:PW-MIT2016.png|300px]]

'''Dates:''' January 4-8, 2016

'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)

'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here].
<br>

== 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 [http://www.miccai.org/organization 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].

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]

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 4
!style="width:18%" |Tuesday, January 5
!style="width:18%" |Wednesday, January 6
!style="width:18%" |Thursday, January 7
!style="width:18%" |Friday, January 8
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|'''10:30am-12pm:''' [Tutorial] Diffeomorphic registration and geodesic shooting methods (I). (Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10:00-11:30am:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/NewSlicerExtensions | Slicer Extensions Birds of a Feather]]
|
'''10:00-11:30am:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/SlicerForMedicalRoboticsResearch| Slicer for Medical Robotics Research]]
<br>
|'''8:30-9:30am''' TBD <br>
'''9:30-10:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Image-guided Neurosurgery| Clinical perspective on Image Guided Neurosurgery]] (Alexandra Golby) <br>
'''10:30-11:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Multiparametric MRI| Clinical perspective on Multiparametric MRI]] (Fiona Fennessy)<br>
'''11:30am-12:30pm''' TBD <br>
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''12pm:''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1:00-5:30pm'''
|'''1:00pm-1:05pm: <font color="#503020">Welcome</font>'''<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''2:45-4:00pm:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Ultrasound]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>

'''4:00-5:30pm:''' [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|
|'''1:00-2:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/DiffusionMRI| Diffusion MRI]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br>
'''3:00-4:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/QIICRTools| QIICR Tools]]
|'''1:00-3:00pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20160103%2F20160110
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20160103/20160110
}}

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

='''Projects'''=
*Use this [[2016_Project_Week_Template | Updated Template for project pages]]

== Tractography==
* [[2016_Winter_Project_Week/Projects/Tractography_format_interoperability | Tractography Format Interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/SlicerDMRI_documentation | Slicer Diffusion MR / tractography workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/TractographyModuleDevelop&Test | Tractography Analysis Module Development and Testing]] (Fan Zhang, Pegah Kahaliardabili, Isaiah Norton, Lauren O'Donnell, others)

== IGT ==
* [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/IntegrationCustusX|Integration of CustusX with PLUS on BK System]] (Christian A, Andras Lasso, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*[[2016_Winter_Project_Week/Projects/IntegrationImFusion| Integration of ImFusion MR-US Registration with BWH AMIGO Neurosurgery Setup]] (Sarah Frisken, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso, Christian Askelan)
* [[2016_Winter_Project_Week/Projects/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External Beam Radiotherapy Planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)
* [[2016_Winter_Project_Week/Projects/PLUS | Inter-device messaging for robust support of depth switching]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/PLUSOCR | Exploration of open-source OCR libraries for device meta-data capture without research interface ]] (Adam Rankin)

==Image Analysis==
*[[2016_Winter_Project_Week/Projects/ChestImagingPlatform|Chest Imaging Platform: COPD and Other Pulmonary Diseases]] (Raúl San José, Jorge Onieva, James Ross)
* [[2016_Winter_Project_Week/Projects/ChestImagingPlatformWorkflows|Nipype Workflows for the Chest Imaging Platform]] (James Ross, Raúl San José)
* [[2016 Winter Project Week/Projects/Cluster-Driven Lung Segmentation | Cluster-Driven Segmentation of Lung Nodules]] (Vivek Narayan, Raúl San José, Daniel Blezek, Steve Pieper, Chintan Parmar)
* [[2016_Winter_Project_Week/Projects/BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week/Projects/ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week/Projects/PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Yi Gao, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/SphericalWaveletShapeAnalysis|Spherical Wavelet Shape Analysis]] (Yi Gao, Erich Bremer, Allen Tannenbaum, Ron Kikinis)
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich)
* [[2016_Winter_Project_Week/Projects/SlicerCMFNextSteps | Moving beyond SlicerCMF and Future Projects]] (Beatriz Paniagua, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/ShapeAnalysis | Low-dimensional Principal Geodesic Analysis On the Manifold of Diffeomorphisms]] (Miaomiao Zhang, Polina Golland)
* [[2016_Winter_Project_Week/Projects/DSCAnalysis | Dynamic Susceptibility Contrast (DSC) MRI Analysis]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)

==Infrastructure==
*[[2016_Winter_Project_Week/Projects/UpgradeNAMICSlicerWiki|Upgrade the NAMIC (and Slicer?) Wiki]] (Mike Halle, JC)
* [[2016_Winter_Project_Week/Projects/CommonDataStructure | Common Data Structure for CMF modules in Slicer]] (Jean-Baptiste Vimort, François Budin, Lucia Cevidanes, Beatriz Paniagua, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/StatisticalShapeModeling | Statistical Shape Modeling in Slicer: OA Index]] (Laura Pascal, Beatriz Paniagua, François Budin, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week/Projects/CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab Asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week/Projects/BRAINSFit_in_MeVisLab | Interoperability Tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week/Projects/CLI_Dashboard | Kibana Dashboard for Browsing All Available CLI Modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week/Projects/SegmentationEditorWidget | Editor Widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week/Projects/SlicerTerminologyEditor | Terminology Editor]] (Csaba Pinter, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/DICOMSegObjIntegration | Integration of DICOM Segmentation Image Storage with Segmentations Module]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week/Projects/CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week/Projects/Data Persisting | Mechanism to Persist Clinical User Data from Different Modules Based on SQLite and/or other Database Engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/Workflows | Workflow Module that Enables the Navigation and Data Sharing between Different Modules in a Clinical Workflow ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/AIMInteroperability | AIM for Interoperability]] (Hans Meine, Andrey Fedorov, ??)
* [[2016_Winter_Project_Week/Projects/3DNrrdSequences | Sequences extension support for 3D+t NRRD]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/SlicerEnhancedMR | Developing support for Enhanced MR in Slicer]] (Michael Onken, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/CLIImprovement| Improve CLI robustness and testing]] (Johan Andruejol)

= '''Logistics''' =

*'''Dates:''' January 4-8, 2016
*'''Location:''' MIT, Kiva Conference room; 4th floor of Building 32.
*'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here]. Registration Fee: $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list [[2016_Winter_Project_Week/RoomSharing|here]]

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/namic16 registration site].

#Polina Golland, MIT
#Ron Kikinis, BWH
#Nicole Aucoin, BWH/SPL
#Peter Anderson
#Daniel Blezek, Isomics, Inc.
#Lucia Cevidanes, University of Michigan
#Adrian Dalca, MIT
#Simon Drouin, Montreal Neurological Institute
#Janek Groehl, German Cancer Research Center
#Tina Kapur, BWH/HMS
#Thomas Kirchner, German Cancer Research Center
#Hans Meine, University of Bremen/MEVIS
#Vivek Narayan, Dana Farber Cancer Institute
#Danielle Pace, MIT
#Laura Pascal, University of Michigan
#Steve Pieper, Isomics, Inc.
#Csaba Pinter, Queen's University
#Gregory Sharp, MGH
#James Miller, GE Research
#Kyle Sunderland, Queen's University
#Ethan Ulrich, University of Iowa
#Jean-Baptiste Vimort, University of Michigan
#Miaomiao Zhang, MIT
#Beatrize Paniagua, University of North Carolina at Chapel Hill
#Sonia Pujol, BWH
#Junichi Tokuda, BWH
#Katie Mastrogiacomo, BWH
#Niravkumar Patel, Worcester Polytechnic Institute
#Michael Onken, Open Connections (Germany)
#Erich Bremer, Stony Brook University
#Xiao Da, MGH
#Tobias Frank, Leibniz Universität Hannover
#Kirby Vosburgh, BWH
#P. Jason White, BWH
#Lauren O'Donnell, BWH
#Pegah Kahali, BWH
#Fan Zhang, BWH
#Adam Rankin, Robarts Research Institute
#Simon Leoard, Johns Hopkins University
#David Gering, HealthMyne
#Johan Andruejol, Kitware
#Jean-Christophe Fillion-Robin, Kitware
#Kelly Xu, MIT
#Christian Askeland, SINTEF
#Katharine Carter, BWH
#Nick Todd, BWH
#Ye Cheng, BWH
#Andriy Fedorov, BWH/HMS
#Sudhanshu Semwal, UCCS Professor
#Michael Halle, BWH
#Kallirroi Retzepi, MGH
#Jayender Jagadeesan, BWH
#Nathalie Agar, BWH
#Curtis Lisle, KnowledgeVis, LLC
#Andras Lasso, PerkLab, Queen's University
#Sarah Frisken, BWH
#Yi Gao, Stony Brook University
#Christian Herz, BWH
#Prashin Unadkat, SPL/BWH

2016 Winter Project Week/Projects/ChestImagingPlatform

2016-01-03T23:38:31Z

Jcross186: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* Raúl San José
* Jorge Onieva
* James Ross
* Alex Yarmarkovich

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Introduce the new Chest Imaging Platform extension
* Get feedback of interested teams
|

* Present the project in one of the sessions
|
*
|}

==Background and References==
http://www.chestimagingplatform.org

2016 Winter Project Week

2016-01-03T23:35:39Z

Jcross186: /* Image Analysis */

__NOTOC__
[[image:PW-MIT2016.png|300px]]

'''Dates:''' January 4-8, 2016

'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)

'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here].
<br>

== 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 [http://www.miccai.org/organization 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].

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]

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 4
!style="width:18%" |Tuesday, January 5
!style="width:18%" |Wednesday, January 6
!style="width:18%" |Thursday, January 7
!style="width:18%" |Friday, January 8
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|'''10:30am-12pm:''' [Tutorial] Diffeomorphic registration and geodesic shooting methods (I). (Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10:00-11:30am:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/NewSlicerExtensions | Slicer Extensions Birds of a Feather]]
|
'''10:00-11:30am:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/SlicerForMedicalRoboticsResearch| Slicer for Medical Robotics Research]]
<br>
|'''8:30-9:30am''' TBD <br>
'''9:30-10:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Image-guided Neurosurgery| Clinical perspective on Image Guided Neurosurgery]] (Alexandra Golby) <br>
'''10:30-11:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Multiparametric MRI| Clinical perspective on Multiparametric MRI]] (Fiona Fennessy)<br>
'''11:30am-12:30pm''' TBD <br>
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''12pm:''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1:00-5:30pm'''
|'''1:00pm-1:05pm: <font color="#503020">Welcome</font>'''<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''2:45-4:00pm:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Ultrasound]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>

'''4:00-5:30pm:''' [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|
|'''1:00-2:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/DiffusionMRI| Diffusion MRI]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br>
'''3:00-4:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/QIICRTools| QIICR Tools]]
|'''1:00-3:00pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20160103%2F20160110
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20160103/20160110
}}

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

='''Projects'''=
*Use this [[2016_Project_Week_Template | Updated Template for project pages]]

== Tractography==
* [[2016_Winter_Project_Week/Projects/Tractography_format_interoperability | Tractography Format Interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/SlicerDMRI_documentation | Slicer Diffusion MR / tractography workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/TractographyModuleDevelop&Test | Tractography Analysis Module Development and Testing]] (Fan Zhang, Pegah Kahaliardabili, Isaiah Norton, Lauren O'Donnell, others)

== IGT ==
* [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/IntegrationCustusX|Integration of CustusX with PLUS on BK System]] (Christian A, Andras Lasso, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*[[2016_Winter_Project_Week/Projects/IntegrationImFusion| Integration of ImFusion MR-US Registration with BWH AMIGO Neurosurgery Setup]] (Sarah Frisken, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso, Christian Askelan)
* [[2016_Winter_Project_Week/Projects/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External Beam Radiotherapy Planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)
* [[2016_Winter_Project_Week/Projects/PLUS | Inter-device messaging for robust support of depth switching]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/PLUSOCR | Exploration of open-source OCR libraries for device meta-data capture without research interface ]] (Adam Rankin)

==Image Analysis==
*[[2016_Winter_Project_Week/Projects/ChestImagingPlatform|Chest Imaging Platform: COPD and Other Pulmonary Diseases]] (Raúl San José, Jorge Onieva, James Ross)
* [[2016 Winter Project Week/Projects/Cluster-Driven Lung Segmentation | Cluster-Driven Segmentation of Lung Nodules]] (Vivek Narayan, Raúl San José, Daniel Blezek, Steve Pieper, Chintan Parmar)
* [[2016_Winter_Project_Week/Projects/BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week/Projects/ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week/Projects/PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Yi Gao, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/SphericalWaveletShapeAnalysis|Spherical Wavelet Shape Analysis]] (Yi Gao, Erich Bremer, Allen Tannenbaum, Ron Kikinis)
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich)
* [[2016_Winter_Project_Week/Projects/SlicerCMFNextSteps | Moving beyond SlicerCMF and Future Projects]] (Beatriz Paniagua, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/ShapeAnalysis | Low-dimensional Principal Geodesic Analysis On the Manifold of Diffeomorphisms]] (Miaomiao Zhang, Polina Golland)
* [[2016_Winter_Project_Week/Projects/DSCAnalysis | Dynamic Susceptibility Contrast (DSC) MRI Analysis]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)

==Infrastructure==
*[[2016_Winter_Project_Week/Projects/UpgradeNAMICSlicerWiki|Upgrade the NAMIC (and Slicer?) Wiki]] (Mike Halle, JC)
* [[2016_Winter_Project_Week/Projects/CommonDataStructure | Common Data Structure for CMF modules in Slicer]] (Jean-Baptiste Vimort, François Budin, Lucia Cevidanes, Beatriz Paniagua, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/StatisticalShapeModeling | Statistical Shape Modeling in Slicer: OA Index]] (Laura Pascal, Beatriz Paniagua, François Budin, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week/Projects/CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab Asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week/Projects/BRAINSFit_in_MeVisLab | Interoperability Tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week/Projects/CLI_Dashboard | Kibana Dashboard for Browsing All Available CLI Modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week/Projects/SegmentationEditorWidget | Editor Widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week/Projects/SlicerTerminologyEditor | Terminology Editor]] (Csaba Pinter, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/DICOMSegObjIntegration | Integration of DICOM Segmentation Image Storage with Segmentations Module]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week/Projects/CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week/Projects/Data Persisting | Mechanism to Persist Clinical User Data from Different Modules Based on SQLite and/or other Database Engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/Workflows | Workflow Module that Enables the Navigation and Data Sharing between Different Modules in a Clinical Workflow ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/AIMInteroperability | AIM for Interoperability]] (Hans Meine, Andrey Fedorov, ??)
* [[2016_Winter_Project_Week/Projects/3DNrrdSequences | Sequences extension support for 3D+t NRRD]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/SlicerEnhancedMR | Developing support for Enhanced MR in Slicer]] (Michael Onken, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/CLIImprovement| Improve CLI robustness and testing]] (Johan Andruejol)

= '''Logistics''' =

*'''Dates:''' January 4-8, 2016
*'''Location:''' MIT, Kiva Conference room; 4th floor of Building 32.
*'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here]. Registration Fee: $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list [[2016_Winter_Project_Week/RoomSharing|here]]

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/namic16 registration site].

#Polina Golland, MIT
#Ron Kikinis, BWH
#Nicole Aucoin, BWH/SPL
#Peter Anderson
#Daniel Blezek, Isomics, Inc.
#Lucia Cevidanes, University of Michigan
#Adrian Dalca, MIT
#Simon Drouin, Montreal Neurological Institute
#Janek Groehl, German Cancer Research Center
#Tina Kapur, BWH/HMS
#Thomas Kirchner, German Cancer Research Center
#Hans Meine, University of Bremen/MEVIS
#Vivek Narayan, Dana Farber Cancer Institute
#Danielle Pace, MIT
#Laura Pascal, University of Michigan
#Steve Pieper, Isomics, Inc.
#Csaba Pinter, Queen's University
#Gregory Sharp, MGH
#James Miller, GE Research
#Kyle Sunderland, Queen's University
#Ethan Ulrich, University of Iowa
#Jean-Baptiste Vimort, University of Michigan
#Miaomiao Zhang, MIT
#Beatrize Paniagua, University of North Carolina at Chapel Hill
#Sonia Pujol, BWH
#Junichi Tokuda, BWH
#Katie Mastrogiacomo, BWH
#Niravkumar Patel, Worcester Polytechnic Institute
#Michael Onken, Open Connections (Germany)
#Erich Bremer, Stony Brook University
#Xiao Da, MGH
#Tobias Frank, Leibniz Universität Hannover
#Kirby Vosburgh, BWH
#P. Jason White, BWH
#Lauren O'Donnell, BWH
#Pegah Kahali, BWH
#Fan Zhang, BWH
#Adam Rankin, Robarts Research Institute
#Simon Leoard, Johns Hopkins University
#David Gering, HealthMyne
#Johan Andruejol, Kitware
#Jean-Christophe Fillion-Robin, Kitware
#Kelly Xu, MIT
#Christian Askeland, SINTEF
#Katharine Carter, BWH
#Nick Todd, BWH
#Ye Cheng, BWH
#Andriy Fedorov, BWH/HMS
#Sudhanshu Semwal, UCCS Professor
#Michael Halle, BWH
#Kallirroi Retzepi, MGH
#Jayender Jagadeesan, BWH
#Nathalie Agar, BWH
#Curtis Lisle, KnowledgeVis, LLC
#Andras Lasso, PerkLab, Queen's University
#Sarah Frisken, BWH
#Yi Gao, Stony Brook University
#Christian Herz, BWH
#Prashin Unadkat, SPL/BWH

Supervised Fissure Enhancement

2015-01-08T22:16:52Z

Jcross186: /* Project Description */

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

==Key Investigators==
* James Ross (Brigham and Women's Hospital, Boston)

* German Gonzalez (Brigham and Women's Hospital, Boston)

* Rola Harmouche (Brigham and Women's Hospital, Boston)

==Project Description==
[[File:Namic2015_supervisedFissureEnhancement.jpg|550px]]
[[File:Jcr_namic_2015_results.jpg|500px]]

The Chest Imaging Platform provides automatic tools for lung lobe segmentation. These rely in part on detecting pulmonary fissures, which can be difficult due to poor signal-to-noise ratios and/or lung pathologies.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Use positive and negative examples of fissures to train a classifier that can be used to detect/enhance fissures
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Guided by approach described in van Rikxoort et al: 'Supervised enhancement filters: application to fissure detection in chest CT scans'

* Use itkDiscreteHessianGaussianImageFunction and itkDiscreteGaussianDerivativeImageFunction for point-wise computation of Hessian and gradient features

* Use logistic regression as classifier. Investigate different feature subsets for best classification results.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Early experiments are promising. Would like to speed up gradient and Hessian computations.
* Results: Increased itkDiscreteHessianGaussianImageFunction and itkDiscreteGaussianDerivativeImageFunction max error parameter from 0.01 to 0.5. Noticed a factor of ten speed-up with negligible impact on logistic regression classifier
</div>
</div>

File:Jcr namic 2015 results.jpg

2015-01-08T22:11:02Z

Jcross186:

2015 Winter Project Week COPD Breakout

2015-01-06T16:25:53Z

Jcross186: /* Code Structure */

== Introduction==
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in [https://www.copdgene.org COPDGene].
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===

=== Team ===
* Raul San Jose
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

Collaborators
* George Washko
* Alejandro Diaz

== Architecture ==
[[File:CIPArchitecture.png]]

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components [http://www.na-mic.org/Wiki/images/0/0b/CipTools.pptx slides]
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Modules Categories ===

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

File:CipTools.pptx

2015-01-06T16:24:59Z

Jcross186:

Supervised Fissure Enhancement

2015-01-04T17:59:43Z

Jcross186: /* Project Description */

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

==Key Investigators==
* James Ross (Brigham and Women's Hospital, Boston)

* German Gonzalez (Brigham and Women's Hospital, Boston)

* Rola Harmouche (Brigham and Women's Hospital, Boston)

==Project Description==
[[File:Namic2015_supervisedFissureEnhancement.jpg|550px]]

The Chest Imaging Platform provides automatic tools for lung lobe segmentation. These rely in part on detecting pulmonary fissures, which can be difficult due to poor signal-to-noise ratios and/or lung pathologies.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Use positive and negative examples of fissures to train a classifier that can be used to detect/enhance fissures
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Guided by approach described in van Rikxoort et al: 'Supervised enhancement filters: application to fissure detection in chest CT scans'

* Use itkDiscreteHessianGaussianImageFunction and itkDiscreteGaussianDerivativeImageFunction for point-wise computation of Hessian and gradient features

* Use logistic regression as classifier. Investigate different feature subsets for best classification results.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Early experiments are promising. Would like to speed up gradient and Hessian computations.
</div>
</div>

Supervised Fissure Enhancement

2015-01-04T17:58:25Z

Jcross186: /* Project Description */

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

==Key Investigators==
* James Ross (Brigham and Women's Hospital, Boston)

* German Gonzalez (Brigham and Women's Hospital, Boston)

* Rola Harmouche (Brigham and Women's Hospital, Boston)

==Project Description==
[[File:Namic2015_supervisedFissureEnhancement.jpg|700px]]

The Chest Imaging Platform provides automatic tools for lung lobe segmentation. These rely in part on detecting pulmonary fissures, which can be difficult due to poor signal-to-noise ratios and/or lung pathologies.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Use positive and negative examples of fissures to train a classifier that can be used to detect/enhance fissures
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Guided by approach described in van Rikxoort et al: 'Supervised enhancement filters: application to fissure detection in chest CT scans'

* Use itkDiscreteHessianGaussianImageFunction and itkDiscreteGaussianDerivativeImageFunction for point-wise computation of Hessian and gradient features

* Use logistic regression as classifier. Investigate different feature subsets for best classification results.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Early experiments are promising. Would like to speed up gradient and Hessian computations.
</div>
</div>

Supervised Fissure Enhancement

2015-01-04T17:58:07Z

Jcross186: /* Project Description */

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

==Key Investigators==
* James Ross (Brigham and Women's Hospital, Boston)

* German Gonzalez (Brigham and Women's Hospital, Boston)

* Rola Harmouche (Brigham and Women's Hospital, Boston)

==Project Description==
[[File:Namic2015_supervisedFissureEnhancement.jpg|400px]]

The Chest Imaging Platform provides automatic tools for lung lobe segmentation. These rely in part on detecting pulmonary fissures, which can be difficult due to poor signal-to-noise ratios and/or lung pathologies.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Use positive and negative examples of fissures to train a classifier that can be used to detect/enhance fissures
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Guided by approach described in van Rikxoort et al: 'Supervised enhancement filters: application to fissure detection in chest CT scans'

* Use itkDiscreteHessianGaussianImageFunction and itkDiscreteGaussianDerivativeImageFunction for point-wise computation of Hessian and gradient features

* Use logistic regression as classifier. Investigate different feature subsets for best classification results.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Early experiments are promising. Would like to speed up gradient and Hessian computations.
</div>
</div>

Supervised Fissure Enhancement

2015-01-04T17:57:52Z

Jcross186: /* Project Description */

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

==Key Investigators==
* James Ross (Brigham and Women's Hospital, Boston)

* German Gonzalez (Brigham and Women's Hospital, Boston)

* Rola Harmouche (Brigham and Women's Hospital, Boston)

==Project Description==
[[File:Namic2015_supervisedFissureEnhancement.jpg|200px]]

The Chest Imaging Platform provides automatic tools for lung lobe segmentation. These rely in part on detecting pulmonary fissures, which can be difficult due to poor signal-to-noise ratios and/or lung pathologies.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Use positive and negative examples of fissures to train a classifier that can be used to detect/enhance fissures
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Guided by approach described in van Rikxoort et al: 'Supervised enhancement filters: application to fissure detection in chest CT scans'

* Use itkDiscreteHessianGaussianImageFunction and itkDiscreteGaussianDerivativeImageFunction for point-wise computation of Hessian and gradient features

* Use logistic regression as classifier. Investigate different feature subsets for best classification results.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Early experiments are promising. Would like to speed up gradient and Hessian computations.
</div>
</div>

File:Namic2015 supervisedFissureEnhancement.jpg

2015-01-04T17:56:15Z

Jcross186:

Supervised Fissure Enhancement

2015-01-04T17:50:55Z

Jcross186: /* Project Description */

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

==Key Investigators==
* James Ross (Brigham and Women's Hospital, Boston)

* German Gonzalez (Brigham and Women's Hospital, Boston)

* Rola Harmouche (Brigham and Women's Hospital, Boston)

==Project Description==
The Chest Imaging Platform provides automatic tools for lung lobe segmentation. These rely in part on detecting pulmonary fissures, which can be difficult due to poor signal-to-noise ratios and/or lung pathologies.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Use positive and negative examples of fissures to train a classifier that can be used to detect/enhance fissures
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Guided by approach described in van Rikxoort et al: 'Supervised enhancement filters: application to fissure detection in chest CT scans'

* Use itkDiscreteHessianGaussianImageFunction and itkDiscreteGaussianDerivativeImageFunction for point-wise computation of Hessian and gradient features

* Use logistic regression as classifier. Investigate different feature subsets for best classification results.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Early experiments are promising. Would like to speed up gradient and Hessian computations.
</div>
</div>

Supervised Fissure Enhancement

2015-01-04T17:40:30Z

Jcross186: /* Key Investigators */

Supervised Fissure Enhancement

2015-01-04T17:40:04Z

Jcross186: /* Key Investigators */

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

==Key Investigators==
James Ross (Brigham and Women's Hospital, Boston)
German Gonzalez (Brigham and Women's Hospital, Boston)
Rola Harmouche (Brigham and Women's Hospital, Boston)

==Project Description==
Here
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</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>
*
</div>
</div>

Supervised Fissure Enhancement

2015-01-04T17:09:26Z

Jcross186: /* Project Description */

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

==Key Investigators==

==Project Description==
Here
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</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>
*
</div>
</div>

Supervised Fissure Enhancement

2015-01-04T17:09:06Z

Jcross186: /* Project Description */

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

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
Here
<h3>Objective</h3>
*
</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>
*
</div>
</div>

Supervised Fissure Enhancement

2015-01-04T17:08:23Z

Jcross186: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List </gallery> ==Key Investigators== ==Project Description== <div style="margin: 20px;…'

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

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</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>
*
</div>
</div>

2015 Winter Project Week

2015-01-04T17:08:07Z

Jcross186: /* COPD */

__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]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''l
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_SLC_Training_Workshop|Slicer Workshop (Ron Kikinis)]]
| <font color="#44AA88">''(Olympus B)''</font>
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(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]] <br><font color="#44AA88">''(Amethyst 2)'' <br> 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| 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 Finder Tutorial | Needle Finder 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 Fissure Enhancement | Supervised fissure 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]==
* [[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, William Wells)

==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

2015-01-04T17:07:40Z

Jcross186: /* COPD */

__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]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''l
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_SLC_Training_Workshop|Slicer Workshop (Ron Kikinis)]]
| <font color="#44AA88">''(Olympus B)''</font>
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(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]] <br><font color="#44AA88">''(Amethyst 2)'' <br> 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| 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 Finder Tutorial | Needle Finder 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 Fissure 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]==
* [[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, William Wells)

==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

2014 Winter Project Week:CIP Infrastructure Testing and SuperBuild

2014-01-10T05:20:45Z

Jcross186: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
James Ross, Raul San Jose

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a library of tools (Chest Imaging Platform) for the processing and the analysis of chest images. The main objective is to make the tools available to the public by providing a common infrastructure that in turn can be incorporated into Slicer by means of the Slicer CIP library. The goals for this week are twofold: 1) set up a software testing framework to improve code quality control, and 2) create a simplified mechanism for downloading and building the CIP and the packages on which it depends.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use CTest to orchestrate CIP testing
* Set up infrastructure / directory structure within CIP to execute one or two initial tests
* Explore the use of CDash to display testing results
* The CIP depends on several software packages: ITK, VTK, FLTK, Teem, and boost. We will mimic the Super-Build approach taken with Slicer4 to automatically retrieve and build these packages as part of the overall CIP build process
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Successfully created testing infrastructure; ran an submitted an initial test to newly created CDash dashboard
* We were able to use superbuild to download and build ITK, VTK, teem, and boost. We also got components of the CIP to build, although there are a few remaining issues to iron out.
</div>
</div>
[[File:CIP_CDash.jpg]]

File:CIP CDash.jpg

2014-01-10T05:18:40Z

Jcross186:

2014 Winter Project Week:CIP Infrastructure Testing and SuperBuild

2014-01-10T05:13:03Z

Jcross186: /* Project Description */

2014 Winter Project Week:CIP Infrastructure Testing and SuperBuild

2014-01-05T15:45:48Z

Jcross186: /* Project Description */

2014 Winter Project Week:CIP Infrastructure Testing and SuperBuild

2014-01-05T15:41:26Z

Jcross186: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
James Ross, Raul San Jose

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a library of tools (Chest Imaging Platform) for the processing and the analysis of chest images. The main objective is to make the tools available to the public by providing a common infrastructure that in turn can be incorporated into Slicer by means of the Slicer CIP library. The goals for this week are twofold: 1) set up a software testing framework to improve code quality control, and 2) create a simplified mechanism for downloading and building the CIP and the packages on which it depends.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use CTest to orchestrate CIP testing
* Set up infrastructure / directory structure within CIP to execute one or two initial tests
* Explore the use of CDash to display testing results
* The CIP depends on several software packages: (ITK, VTK, FLTK, Teem, and boost. We will mimic the Super-Build approach taken with Slicer4 to automatically retrieve and build these packages as part of the overall CIP build process
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Winter Project Week:CIP Infrastructure Testing and SuperBuild

2014-01-05T15:40:58Z

Jcross186: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
James Ross, Raul San Jose

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a library of tools (Chest Imaging Platform) for the processing and the analysis of chest images. The main objective is to make the tools available to the public by providing a common infrastructure that in turn can be incorporated into Slicer by means of the Slicer CIP library. The goals for this week are twofold: 1) set up a software testing framework to improve code quality control, and 2) create a simplified mechanism for downloading and building the CIP and the packages on which it depends.
</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>
* Use CTest to orchestrate CIP testing
* Set up infrastructure / directory structure within CIP to execute one or two initial tests
* Explore the use of CDash to display testing results
* The CIP depends on several software packages: (ITK, VTK, FLTK, Teem, and boost. We will mimic the Super-Build approach taken with Slicer4 to automatically retrieve and build these packages as part of the overall CIP build process
</div>
</div>

2014 Winter Project Week:CIP Infrastructure Testing and SuperBuild

2014-01-05T15:34:29Z

Jcross186: /* Key Investigators */

2009 Winter Project Week LungImagingPlatform

2009-01-04T19:33:46Z

Jcross186:

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

__NOTOC__

===Key Investigators===
* James Ross
* Raul San Jose

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

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

<h1>Objective</h1>
Our goal is to develop a lung imaging platform for the clinical understanding of multiple lung diseases such as Chronic Obstructive Pulmonary Disease (COPD), Asthma, and Interstitial Lung Disease (ILD) among others. Quantitative lung imaging is a key component of on-going genetic and molecular biology studies that are being carried out at BWH and other centers across USA. A significant example of these new efforts is [[http://www.copdgene.org/|COPD Genetics Epidemiology]] multicenter study. The NAMIC Kit and Slicer 3 are ideal candidates for the implementation of such efforts.

Our goals for this week are threefold:
* Design the main platform components.
* Dynamic programming approaches for the extraction of 3D airways.
* Porting our current imaging platform, [[http://www.airwayinspector.org| Airway Inspector]] based on 3D Slicer to Slicer 3.

</div>

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

<h1>Approach, Plan</h1>
Our approach is to develop a module in Slicer 3 that has the following components:
* A unique library that can be linked against and shared by other Slicer modules or external applications.
* Command Line Modules that encapsulate the individual algorithmic components of the platform without strings attached to a particular solution. The idea is to enable rapid prototyping and deployment of the solutions before they are fully integrated.
* Custom solutions for disease-oriented applications: our plan is to discuss how an explication can customize the Slicer 3 layout.

We will focus on the following design aspects:
* MRML data structures for tubular-type anatomical structures.
* Support for quantitative imaging: handling data tables in Slicer 3 from MRML to Command Line Modules.
* ITK filter hierarchies for the main image analysis components: extraction of lung lobes, airways and vessels.
* Customizable GUI layout.

</div>

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

<h1>Progress</h1>
* A semiautomatic lobe segmentation has been successfully implemented in Slicer 3 as a Command Line Module.
* Initial design needs have been discussed.

</div>

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

</div>

=== Related projects ===
Other projects that share some common goals are:
* [http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_SlicerLayouts | User Interface Flexible Layouts]
* [http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Slicer_VMTK | Vessel Segmentation in Slicer using VMTK ]
* [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week:GT_TubularSurfaceSeg | ubular volumetric segmentation framework ]

=== References ===

File:SagittalLungLobes.jpg

2009-01-04T19:31:34Z

Jcross186:

Slicer3:VisualBlog

2007-08-15T21:13:15Z

Jcross186:

__NOTOC__
=== Image from James and Jim on Wednesday, August 15, 2007===

[[Image:LightBox.png| | thumb | 300px]]

"LightBox" functionality has been added which allows a user to display mutliple slices of a 3D dataset in a single viewport.

=== Image from Dirk, Matthew, Jim, and Steve on Monday, August 13, 2007===

[[Image:Livers.png| | thumb | 300px]]

A new label map smoothing tool has been added to help with our [[NA-MIC_Collaborations#Children.27s_Pediatric_Cardiology_Collaboration_with_SCI.2FSPL.2FNortheastern | collaboration with Children's Hospital Boston, SCI at University of Utah and Northeastern University]]. The unfiltered labelmap is shown in blue, and the filtered results are shown in peach. The filtering algorithm was developed at University of Utah by Josh Cates and Ross Whitaker, and implemented in ITK by GE Research. It is integrated in slicer3 as a command line module using the execution model. The models are shown unsmoothed in order to better visualize the underlying labelmaps.

=== Image from Steve and Wendy on Monday, August 6, 2007===

[[Image:Editbox.png| thumb | 300px]]

New Editor functionality, with EditBox which is invoked using the F1 key (will soon be moved to the space bar).

=== Image from Brad and Kilian on Wednesday, June, 21, 2007===
[[Image:EMSegment31Structures.png| thumb | 300px]] Example of [[Projects/Structural/2007_Project_Week_EMSegmentation_Validation | EMSegmenter in Slicer3]]

=== Image from pieper on Friday, June, 9, 2007===
[[Image:ConnectivityMap.png| thumb | 300px]]
Slicer3 Module for [[Algorithm:MIT:DTI_StochasticTractography | Stochastic Tractography]] from MIT (Ngo, Golland) and BWH (Westin, Kubicki).

=== Image from ipek on Wednesday, June, 6, 2007===
[[Image:kwmeshvisu-slicer-logo.png| thumb | 300px]]
UNC Logo in Slicer3 for KWMeshVisu (Ipek Oguz, Martin Styner).

=== Image from wjp on Wednesday, May, 30, 2007===
[[Image:CineDisplayDesigns.png| thumb | 300px]]
Design mockups for Slicer3's Cine Display interface (William Leue, Wendy Plesniak).

=== Image from pieper on Tuesday, May, 30, 2007===
[[Image:Atlas-2007-05-16.png| thumb | 200px]]
The SPL-PNL brain atlas loaded in Slicer3. Demonstrates model hierarchy and clipping.

=== Image from davisb on Monday, April, 27, 2007===
[[Image:EMSegmentation_Results_Screenshot.png| thumb | 200px]]
EMSegment screenshot---segmentation results and work-flow GUI

=== Image from magnotta on Monday, April, 16, 2007===
[[image:Mimx.png| thumb | 200px]]
Mimx Logo in Slicer3 for VoxelMeshingModule

=== Image from blezek on Tuesday, April, 10, 2007 at 8:00AM ===

[[Image:PythonMenu.png | thumb | 200px]]
Python incorporated into [[Slicer3:Python | Slicer]].

[[Image:PythonConsole.png | thumb | 200px]]
Bringing up the Python console

Now, do something interesting with it!

>>> # import MatPlotLib via pylab functions so we can refer to them directly
>>> from pylab import *
>>> imshow ( data[128,:,:] )
>>> # Instruct pylab to show our plots... hit return to continue entering commands.
>>> show()

[[Image:Pythonimshow.png | thumb | 200px]]
Voila!

=== Image from wjp on Thursday, March 22, 2007 at 10:00AM ===
[[image:ZoomWindow.png | thumb | 200px]]
New GUI elements: Shows a magnified view in the GUI panel of an area around the mouse in any Slice Window.

=== Image from wjp on Thursday, March 22, 2007 at 10:00AM ===
[[image:NavigationWindow.png | thumb | 200px]]
New GUI elements: Shows birds-eye-view of the scene relative to the outline of the 3D Viewer's window in the 'Manipulate 3D View' GUI panel.

=== Image from pieper on Tuesday, January 16, 2007 at 7:58PM ===
[[image:Slicer3FirstTractography.png | thumb | 200px]]
From Lauren, shows fiber tracts loaded from a file and with display properties controlled by the GUI.

=== Image from wjp on Friday, December 29, 2006 at 3:23PM ===

[[Image:S3GUI-12-29-06.png|200px]] Module choose and navigation functionality integrated into the application toolbar to create more space for module GUIs on the side panel. Slice Controller widgets also updated to have more functionality available, a button to link and unlink their control, and an improved visual design.

=== Image from wjp on Monday, November 28, 2006 at 6:40M ===

[[Image:S3GUIWithLogo.png|200px]] New 3D Slicer logo integrated with slicer GUI.

=== Image from pieper on Thursday, October 26, 2006 at 1:54M ===

[[Image:QueryAtlas-fBIRN-Slicer3-2006-10-23.png|200px]] FreeSurfer structural data (cortical and subcortical segmentation) with fBIRN functional overlay, shown as part of Slicer3-based BIRN Query Atlas project.

=== Image from pieper on Thursday, October 05, 2006 at 1:08PM ===

[[Image:Clipping.png|200px]] Clipping with the slice plane is now supported, along with thresholded image display.

=== Image from naucoin on Friday, September 08, 2006 at 12:14pm ===

[[Image:FreeSurfer-Curvature-2006-09-08.png|200px]]

The FreeSurfer colour lookup table has been added to the Slicer3 FreeSurfer Library. A curvature overlay file was loaded and displayed on bert/surf/lh.pial as loaded in via the Models module.

=== Image from naucoin on Friday, September 08, 2006 at 11:24am ===

[[Image:FreeSurfer-Annotation-2006-09-08-B.png|200px]]

The FreeSurfer scalar reader has been integrated as a Slicer 3 Library, and surfaces can be read via the Models module. Shot shows standard bert/surf/lh.pial plus a test script to load the annotation labels file.

=== Image from pieper on Tuesday, August 08, 2006 at 4:26PM ===

[[Image:Editor-module-prototype.png|200px]] A number of things have come together to allow the new prototype editor module:
* the label map layers are enabled
* lookup table support in the layer logic
* a new set of 2D UI widgets
* generalized painting infrastructure, which is based on requests and feedback from NA-MIC Core 3 users and other users of Slicer2
** paint brush has a 'threshold' option in which the label map only gets painted if the background intensity is in a specified range
** paint brush optionally won't overpaint existing voxels
** 'eye dropper' mode allows you to start painting with the label value where you first clicked (so you don't need to go to the UI to change the label color as often).
** all painting operations can happen on arbitrarily transformed volumes. This allows the painting plane to be aligned with the major axis of a structure like the hippocampus
** background layers are interpolated to current screen resolution (not limited to nearest neighbor sampling as in slicer2's draw mode)
** painting is performed using a circular brush with a diameter selected by the user. this makes it easier to follow the contours of curved biological structures.
** the cursor is turned off on mouse down and reappears on mouse up so you can see the exact pixels you are drawing (a circle around the cursor location indicates the mouse location)

A few limitations make this still a 'prototype' including:

* there's no convenient way to save your label maps volumes (except as dicom)
* the color map is currently random
* only label numbers 0-255 will show as distinct colors
* no hot keys for frequently used operations
* brush radius is in screen space units rather than RAS (means that the brush is effectively getting bigger and smaller as you zoom in and out)
* the paint algorithm is implemented inefficiently and can be slow when painting large numbers of pixels
* much of the code is written in tcl - new vtk classes are needed to implement the functionality more efficiently.

=== Image from pieper on Friday, July 28, 2006 at 9:04AM ===

[[Image:Oblique-slice-test.png|200px]] Test of making a non-orthogonal slice plane. This was created by manually setting the SliceToRAS matrix in the vtkMRMLSliceNode. GUI is not yet hooked up for oblique slices.

=== Image from pieper on Thursday, July 27, 2006 at 5:21PM ===

[[Image:Single-pixel.png|200px]] Shows that a single pixel voxel in black is exactly bounded by a unit cube in RAS space. Also the blinking eye buttons for slice visiblility are hooked up and there is now a red-yellow-green color coding for the slice windows (carried over from slicer2).

=== Image from pieper on Thursday, July 13, 2006 at 4:49PM ===

[[Image:Textured-slice-planes.png|200px]] Test of interactive slice textured plane control. Not yet eneabled through GUI, but driven by a [http://www.na-mic.org:8000/websvn/filedetails.php?repname=Slicer3&path=%2Ftrunk%2FBase%2FGUI%2FTesting%2FTestSliceModels.tcl&rev=0&sc=1 test script] that you can source into the console.
Type Control-T to bring up interactor, then

source Base/GUI/Testing/TestSliceModels.tcl
SliceModelsAdd

This test does things the right way in that it creates model nodes for the slices and the updates of the planes is triggered by observers on the Slice Logic. But it does things the wrong way in that it creates the texture in an ''ad hoc'' way for now since we don't yet have a clean way to specify textures in the model display nodes. Also, the Viewer renders on every changes to the slice view, so as you pan/zoom/scroll the slices the redraws are jerky. Next step is to figure out how best to get this functionality integrated into the C++. Probably there should be a vtkSlicerSliceModelsLogic class that's managed by the vtkSlicerSliceGUI.

=== Image from pieper on Tuesday, July 11, 2006 at 3:39PM ===

[[Image:Slicer3-lung.png|200px]] Example model read from vtk file and loaded in slicer3

=== Image from pieper on Monday, July 03, 2006 at 3:35PM ===

[[Image:Logo-widget.png|200px]] Test of the new logo widget for adding module-specific watermark logos directly in the 3d view. Uses a vtkLogoWidget from VTK cvs head. Kitware is working on cmake support to notify developers when a VTK cvs update is needed. Once that is done, the logo code will be added to slicer3 svn.

=== Image from pieper on Monday, June 26, 2006 at 10:38AM ===

[[Image:Slicer3-pan-zoom-anno-2006-06-26.png|200px]] New annotations and key bindings. Middle mouse to pan, right mouse to zoom.

=== Image by pieper on Wednesday, June 21, 2006 at 1:01PM ===

[[Image:Slicer3_command-line-median-filter-2006-06-21.png|200px]] results of the command line median filter module

=== Image by millerjv on Tuesday, June 20, 2006 at 4:37PM ===

[[Image:SlicerScreenShot7.png|200px]] {First command line module to export data, execute, and import data back into Slicer}

=== Image by millerjv on Friday, June 16, 2006 at 11:15AM ===

[[Image:SlicerScreenShot5.png|200px]] {Command line module with an enumerated parameter as a radio button}

=== Image by millerjv on Wednesday, June 14, 2006 at 10:20AM ===

[[Image:Slicer3ApplicationSettings.png|200px]] {Slicer applications settings panel showing the module search path}

=== Image from pieper on Tuesday, June 13, 2006 at 8:23PM ===

[[Image:SlicerScreenShot2.png|200px]] Another command line module example from Jim

=== Image from pieper on Tuesday, June 13, 2006 at 8:20PM ===

[[Image:SlicerScreenShot1.png|200px]] Example from Jim Miller showing the automatic GUI generation from XML collected from execution module commands

=== Image from pieper on Tuesday, June 13, 2006 at 8:18PM ===

[[Image:Slicer-sample-2006-06-13.png|200px]] Example screen shot showing that there is a basic interface in place.

== About the VisualBlog ==

The VisualBlog is meant to be an easy place to upload screenshot so that both developers and outside observes can track the progress of the project.

=== Upload Script ===

To simplify the process of uploading images and blog entries, you can use a helper script called [http://www.na-mic.org:8000/svn/NAMICSandBox/trunk/wikimage/wikimage.tcl wikimage] which uploads the image and caption to this page. You must have a [http://www.tcl.tk Tcl/Tk] and [http://curl.haxx.se curl] installed on your machine to use wikimage.

''NOTE:'' tested and working on Windows with Cygwin, needs debugging on Linux.

Example usage
./wikimage.tcl screenshot-of-my-new-feature-2006-06-14.png This shows my neat new slicer feature that I added in just minutes of pleasureable coding...

You will need to have a wiki account in order to do the upload. If you're wiki account isn't the same name as your local machine login, use the --user command line option to specify it.

Full usage:

usage: wikimage [options] (image_filename) (caption)
(image_filename) is the file to upload
(caption) is the rest of the command line
[options] is one of the following:
--gallery : wiki page where image link should be added
--thumb-size : size of gallery thumbnail (default 200px)
-u --user : wiki user name (default is env USER)
-p --password : wiki login password
--url : url of the wiki (default wiki.na-mic.org)
-c --cookie-jar : file to save your cookies (default 'mycookies')
--help : prints this message and exits

Of course after you've uploaded you can use regular wiki tools to edit and augment your caption.

=== Plans ===

We're looking into adding the wikimage command as menu item in slicer to further simplify, but for now it can be run on the command line.

Every month or so we can copy the contents of the page to an archive location so this page doesn't get too long.

Projects/Slicer3/2007 Project Week Lightbox

2007-08-15T21:03:56Z

Jcross186:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:SlicerLightboxStoryboard.png|thumb|320px|Storyboard for multiple view.]]
|[[Image:LightBox.png|thumb|320px|As implemented in Slicer3.]]
|}

__NOTOC__
===Key Investigators===
* GE: James Ross, Jim Miller
* BWH: Wendy Plesniak
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
Provide a multiview layout facility for 2D image viewers.

</div>

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

<h1>Approach, Plan</h1>

* Use multiple renderers in a single render window
* Modify reslice and compositing pipeline to generate N slices instead of one
* Modify SWidgets to handle the additional renderer->render window coordinate frame
* Modify SliceNode to store a layout (plus serialization)
* Modify SliceControllerWidget to provide controls to set the layout

</div>

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

<h1>Progress</h1>

Great progress!

Still working on
* Coordinate and image value readouts [done]
* Slice spacing for tiles verses sliders/scrollwheel
* Fiducials
* Active pane selector
* Performance (could optimize for scrolling)

Will need to coordinate with:
* Geometry layers

</div>

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

</div>

===References===

File:LightBox.png

2007-08-15T21:02:31Z

Jcross186: