NAMIC Wiki - User contributions [en]

File:Example data.zip

2017-05-22T18:44:39Z

Fan:

2017 Winter Project Week/WhiteMatterAnalysis

2017-01-13T15:53:38Z

Fan:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
Image:Left CB.png|Left-view Cerebellum
Image:Post CB.png|Posterior-view Cerebellum
Image:Left ParsOp.png|Left-view Pars Opercularis
Image:Sup ParsOp.png|Superior-view Pars Opercularis


</gallery>

==Key Investigators==

* Fan Zhang, BWH
* Shun Gong, BWH
* Isaiah Norton, BWH
* Ye Wu, BWH
* Lauren J. O'Donnell, BWH

==Project Description==
This project is part of the whitematteranalysis software that provides an automated whole brain tractgoraphy registration and segmentation framework. The aim of this project is to integrate a new Slicer module FiberEndpointAnalysis into the whitematteranalysis pipeline.

{| 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;"
|

Calculate the overlap of fiber tract (endpoint regions) with anatomical parcellation (e.g. freesurfer) or functional region (e.g. fMRI).
|

* Release the FiberEndPointFromLabelMap module as part of SandBox in SlicerDMRI.
* Integrate the module into the whitematteranalysis software.
* Testing and documentation about the new functionality.
|

* Done: Module released in SandBox: https://github.com/SlicerDMRI/Sandbox
* Done: Integrate EndpointAnalysis into whitematteranalysis: https://github.com/SlicerDMRI/whitematteranalysis
* Done: Documentation: https://github.com/SlicerDMRI/whitematteranalysis/wiki/Running-the-Clustering-Pipeline#commands-to-do-endpoint-analysis
* Done: Testing finished.
|}

==Background and References==

*SlicerDMRI: http://slicerdmri.github.io
*WhiteMatterAnalysis: https://github.com/SlicerDMRI/whitematteranalysis

2017 Winter Project Week/SlicerDMRIDocumentationAndTesting

2017-01-13T15:43:51Z

Fan: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Shun Gong, BWH
* Ye Wu, BWH
* Isaiah Norton, BWH
* Fan Zhang, BWH
* Lauren J. O'Donnell, BWH

==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;"
|

The aim is to provide improved documentations and tutorials about the modules and functions in SlicerDMRI.
|

* Update online documentations to latest version
* Improve testing coverage
* Improve website
* Update sandbox extensions and release with tutorials and testing cases
* Make a SlicerDMRI logo
|

*Improved the documentations and tutorials about SlicerDMRI: https://github.com/SlicerDMRI/slicerdmri.github.io/tree/master/docs/tutorials
*Improved the documentations about white matter analysis: https://github.com/SlicerDMRI/whitematteranalysis/wiki/Running-the-Clustering-Pipeline
*Built a new tutorial:http://www.na-mic.org/Wiki/images/5/57/Fiber_Bundle_Volume_Measurement.pptx
*Made sandbox online available: https://github.com/SlicerDMRI/Sandbox
*Made a SlicerDMRI logo
|}

==Background and References==

*SlicerDMRI: http://slicerdmri.github.io
* SlicerDMRISandbox issues: https://github.com/SlicerDMRI/Sandbox/issues

2017 Winter Project Week/WhiteMatterAnalysis

2017-01-13T14:52:48Z

Fan:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
Image:Left CB.png|Left-view Cerebellum
Image:Post CB.png|Posterior-view Cerebellum
Image:Left ParsOp.png|Left-view Pars Ppercularis
Image:Sup ParsOp.png|Superior-view Pars Ppercularis


</gallery>

==Key Investigators==

* Fan Zhang, BWH
* Shun Gong, BWH
* Isaiah Norton, BWH
* Ye Wu, BWH
* Lauren J. O'Donnell, BWH

==Project Description==
This project is part of the whitematteranalysis software that provides an automated whole brain tractgoraphy registration and segmentation framework. The aim of this project is to integrate a new Slicer module FiberEndpointAnalysis into the whitematteranalysis pipeline.

{| 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;"
|

Calculate the overlap of fiber tract (endpoint regions) with anatomical parcellation (e.g. freesurfer) or functional region (e.g. fMRI).
|

* Release the FiberEndPointFromLabelMap module as part of SandBox in SlicerDMRI.
* Integrate the module into the whitematteranalysis software.
* Testing and documentation about the new functionality.
|

* Done: Module released in SandBox: https://github.com/SlicerDMRI/Sandbox
* Done: Integrate EndpointAnalysis into whitematteranalysis: https://github.com/SlicerDMRI/whitematteranalysis
* Done: Documentation: https://github.com/SlicerDMRI/whitematteranalysis/wiki/Running-the-Clustering-Pipeline#commands-to-do-endpoint-analysis
* Done: Testing finished.
|}

==Background and References==

*SlicerDMRI: http://slicerdmri.github.io
*WhiteMatterAnalysis: https://github.com/SlicerDMRI/whitematteranalysis

2017 Winter Project Week/WhiteMatterAnalysis

2017-01-13T14:24:07Z

Fan:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
Image:Left CB.png|Left-view Cerebellum
Image:Post CB.png|Posterior-view Cerebellum
Image:Left ParsOp.png|Left-view Pars Ppercularis
Image:Sup ParsOp.png|Superior-view Pars Ppercularis


</gallery>

==Key Investigators==

* Fan Zhang, BWH
* Shun Gong, BWH
* Isaiah Norton, BWH
* Ye Wu, BWH
* Lauren J. O'Donnell, BWH

==Project Description==
This project is part of the whitematteranalysis software that provides an automated whole brain tractgoraphy registration and segmentation framework. The aim of this project is to integrate a new Slicer module FiberEndpointAnalysis into the whitematteranalysis pipeline.

{| 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;"
|

Calculate the overlap of fiber tract (endpoint regions) with anatomical parcellation (e.g. freesurfer) or functional region (e.g. fMRI).
|

* Release the FiberEndPointFromLabelMap module as part of SandBox in SlicerDMRI.
* Integrate the module into the whitematteranalysis software.
* Design testing cases about the new functionality.
|

* Done: Module released in SandBox: https://github.com/SlicerDMRI/Sandbox
* Done: Integrate EndpointAnalysis into whitematteranalysis: https://github.com/SlicerDMRI/whitematteranalysis
* Done: Testing finished.
|}

==Background and References==

*SlicerDMRI: http://slicerdmri.github.io
*WhiteMatterAnalysis: https://github.com/SlicerDMRI/whitematteranalysis

2017 Winter Project Week/SlicerDMRIDocumentationAndTesting

2017-01-13T14:18:18Z

Fan: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Shun Gong, BWH
* Ye Wu, BWH
* Isaiah Norton, BWH
* Fan Zhang, BWH
* Lauren J. O'Donnell, BWH

==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;"
|

The aim is to provide improved documentations and tutorials about the modules and functions in SlicerDMRI.
|

* Update online documentations to latest version
* Improve testing coverage
* Improve website
* Update sandbox extensions and release with tutorials and testing cases
* Make a SlicerDMRI logo
|

*Improved the documentations and tutorials about SlicerDMRI: https://github.com/SlicerDMRI/slicerdmri.github.io/tree/master/docs/tutorials
*Built a new tutorial:http://www.na-mic.org/Wiki/images/5/57/Fiber_Bundle_Volume_Measurement.pptx
*Made sandbox online available: https://github.com/SlicerDMRI/Sandbox
*Made a SlicerDMRI logo
|}

==Background and References==

*SlicerDMRI: http://slicerdmri.github.io
* SlicerDMRISandbox issues: https://github.com/SlicerDMRI/Sandbox/issues

2017 Winter Project Week/WhiteMatterAnalysis

2017-01-13T05:25:12Z

Fan:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
Image:Left CB.png|Left-view Cerebellum
Image:Post CB.png|Posterior-view Cerebellum
Image:Left ParsOp.png|Left-view Pars Ppercularis
Image:Sup ParsOp.png|Superior-view Pars Ppercularis


</gallery>

==Key Investigators==

* Fan Zhang, BWH
* Shun Gong, BWH
* Isaiah Norton, BWH
* Ye Wu, BWH
* Lauren J. O'Donnell, BWH

==Project Description==
This project is part of the whitematteranalysis software that provides an automated whole brain tractgoraphy registration and segmentation framework. The aim of this project is to integrate a new Slicer module FiberEndpointAnalysis into the whitematteranalysis pipeline.

{| 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;"
|

Calculate the overlap of fiber tract (endpoint regions) with anatomical parcellation (e.g. freesurfer) or functional region (e.g. fMRI).
|

* Release the FiberEndPointFromLabelMap module as part of SandBox in SlicerDMRI.
* Integrate the module into the whitematteranalysis software.
* Design testing cases about the new functionality.
|

* Done: SandBox Release: https://github.com/SlicerDMRI/Sandbox
* Done: Integrate EndpointAnalysis into whitematteranalysis: https://github.com/SlicerDMRI/whitematteranalysis
* Done: Testing finished.
|}

==Background and References==

*SlicerDMRI: http://slicerdmri.github.io
*WhiteMatterAnalysis: https://github.com/SlicerDMRI/whitematteranalysis

File:Sup ParsOp.png

2017-01-13T05:18:38Z

Fan:

File:Post CB.png

2017-01-13T05:18:04Z

Fan:

File:Left ParsOp.png

2017-01-13T05:17:35Z

Fan:

File:Left CB.png

2017-01-13T05:16:51Z

Fan:

File:Fiber Bundle Volume Measurement.pptx

2017-01-12T17:43:00Z

Fan: Fan uploaded a new version of File:Fiber Bundle Volume Measurement.pptx

2017 Winter Project Week/WhiteMatterAnalysis

2017-01-12T16:14:43Z

Fan:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Fan Zhang, BWH
* Shun Gong, BWH
* Isaiah Norton, BWH
* Ye Wu, BWH
* Lauren J. O'Donnell, BWH

==Project Description==
This project is part of the whitematteranalysis software that provides an automated whole brain tractgoraphy registration and segmentation framework. The aim of this project is to integrate a new Slicer module FiberEndpointAnalysis into the whitematteranalysis pipeline.

{| 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;"
|

Calculate the overlap of fiber tract (endpoint regions) with anatomical parcellation (e.g. freesurfer) or functional region (e.g. fMRI).
|

* Release the FiberEndPointFromLabelMap module as part of SandBox in SlicerDMRI.
* Integrate the module into the whitematteranalysis software.
* Testing and documentation about the new functionality.
|

* SandBox Release: https://github.com/SlicerDMRI/Sandbox
*
|}

==Background and References==

*SlicerDMRI: http://slicerdmri.github.io
*WhiteMatterAnalysis: https://github.com/SlicerDMRI/whitematteranalysis

2017 Tutorial Contest

2017-01-12T16:06:02Z

Fan:

[[2017_Winter_Project_Week#Agenda|Back to Winter project week Agenda]]
==Introduction==
[http://www.slicer.org Slicer4.6] is used to perform meaningful research tasks. As part of the 3D Slicer Training activities we are building a curated portfolio of tutorials for the basic functions and specialized functionality available in Slicer.

The primary purpose of the Winter 2017 tutorial contest is to enrich the training materials that are available to end-users and developers using 3D Slicer. The contest provides members of the medical image computing and radiology research community a methodology and a framework for developing step-by-step tutorials on advanced image analysis methods. We believe participants will be motivated to join this event to enhance the dissemination of their own algorithms that they have incorporated into the Slicer4 platform, and to enhance training of Slicer4 functionality for their own laboratory groups.

==Organizer==
Sonia Pujol, Ph.D., Director of Training, Neuroimage Analysis Center, Brigham and Women's Hospital, Harvard Medical School

==Categories==
*Category 1 (*new*): '''DEMONSTRATION'''. This category allows new comers to the Slicer community to provide short demos based on slides and/or videos of their application.
*Category 2: '''ALGORITHM TUTORIAL'''. In this category the tutorial will teach a user how to make an algorithm work on their data.
*Category 3: '''EXTENSION TUTORIAL'''. In this category, the tutorial will teach a user how to use an Extension of Slicer.
*Category 4: '''END TO END SOLUTION TUTORIAL'''. In this category, the tutorial will teach a user how to solve a particular clinical problem using a workflow implemented in Slicer.
*Category 5: '''TUTORIAL UPGRADE/UPDATE"'. This category allows teams who participated in the past tutorial contest editions to submit an update/upgrade of their previous submission.

Entries in each category require the following material:
* scientific background and application motivation
* step-by-step instructions
* anonymized sample dataset

=Rules=
The evaluation criteria for the 2017 tutorial contest are below:
*Tutorial must be based on the Slicer 4.6 release version of the software.
*To enter the contest, you must provide 'a version of the tutorial that works on all supported platforms (Mac,Windows,Linux)
*Tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]
*Tutorial data must be anonymized
*Tutorial must include contact information of the primary author (e-mail and phone number)
*Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template_2016.ppt‎ | Winter 2017 contest tutorial template]].
*If applicable, the tutorial must provide clear directions for downloading and installing additional modules 

=Submission Process=
''' Submission dead-line: Wednesday January 11, 2017'''
* To enter the contest, please follow the 5 steps below:
**1. Create a wiki page for your tutorial on the NA-MIC wiki.
**2. Upload your slides/demos and tutorial dataset. Your tutorial and data must be named as 'TutorialName_TutorialContestWinter2017.pdf' and 'TutorialData_TutorialContestWinter2017.zip'
**3. Add a link to the uploaded tutorial and datasets on your tutorial page.
**4. Copy the template of the [http://wiki.na-mic.org/Wiki/index.php/Training:Winter_2017_Contest_Table Winter 2017 test table ] on your tutorial page, and document the status of your cross-platform testing (Mac, Windows, Linux).
**5. Once you have completed step 1-4, add a link to your tutorial page in the list below and send a notification email to Sonia Pujol (spujol at bwh.harvard.edu) to receive a confirmation of your submission.

=Tutorials=
*Simple Python Tool for Quality Control of DWI data (Laurent Chauvin)
*SHARPM-PDM (Beatriz Paniagua)
*Segmentation Module (Csaba Pinter)
*[[Media:ROSIGTLTutorial_Tokuda_Jan2017.pptx| Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink (Junichi Tokuda)]]
*Slicer Pathology (Erich Bremer)
*[[Media:Fiber_Bundle_Volume_Measurement.pptx|Fiber Bundle Volume Measurement]], [[Media:FiberVolume_data.zip| tutorial data]] (Shun Gong)

= Review Session=
The review session of the 2017 Tutorial Contest will take place on Thursday January 12 at the Massachusetts Institute of Technology, Cambrigde, MA as part of the Winter 2017 Slicer Project Week.
All contestants will be invited to present brief highlights of their tutorials. Each presentation should be 5-minute summary of the submission.

=Results=
The winner of the 2017 tutorial contest will be announced on Friday January 13 during the closing session of the Slicer Project Week.

2017 Tutorial Contest

2017-01-12T16:04:01Z

Fan:

[[2017_Winter_Project_Week#Agenda|Back to Winter project week Agenda]]
==Introduction==
[http://www.slicer.org Slicer4.6] is used to perform meaningful research tasks. As part of the 3D Slicer Training activities we are building a curated portfolio of tutorials for the basic functions and specialized functionality available in Slicer.

The primary purpose of the Winter 2017 tutorial contest is to enrich the training materials that are available to end-users and developers using 3D Slicer. The contest provides members of the medical image computing and radiology research community a methodology and a framework for developing step-by-step tutorials on advanced image analysis methods. We believe participants will be motivated to join this event to enhance the dissemination of their own algorithms that they have incorporated into the Slicer4 platform, and to enhance training of Slicer4 functionality for their own laboratory groups.

==Organizer==
Sonia Pujol, Ph.D., Director of Training, Neuroimage Analysis Center, Brigham and Women's Hospital, Harvard Medical School

==Categories==
*Category 1 (*new*): '''DEMONSTRATION'''. This category allows new comers to the Slicer community to provide short demos based on slides and/or videos of their application.
*Category 2: '''ALGORITHM TUTORIAL'''. In this category the tutorial will teach a user how to make an algorithm work on their data.
*Category 3: '''EXTENSION TUTORIAL'''. In this category, the tutorial will teach a user how to use an Extension of Slicer.
*Category 4: '''END TO END SOLUTION TUTORIAL'''. In this category, the tutorial will teach a user how to solve a particular clinical problem using a workflow implemented in Slicer.
*Category 5: '''TUTORIAL UPGRADE/UPDATE"'. This category allows teams who participated in the past tutorial contest editions to submit an update/upgrade of their previous submission.

Entries in each category require the following material:
* scientific background and application motivation
* step-by-step instructions
* anonymized sample dataset

=Rules=
The evaluation criteria for the 2017 tutorial contest are below:
*Tutorial must be based on the Slicer 4.6 release version of the software.
*To enter the contest, you must provide 'a version of the tutorial that works on all supported platforms (Mac,Windows,Linux)
*Tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]
*Tutorial data must be anonymized
*Tutorial must include contact information of the primary author (e-mail and phone number)
*Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template_2016.ppt‎ | Winter 2017 contest tutorial template]].
*If applicable, the tutorial must provide clear directions for downloading and installing additional modules 

=Submission Process=
''' Submission dead-line: Wednesday January 11, 2017'''
* To enter the contest, please follow the 5 steps below:
**1. Create a wiki page for your tutorial on the NA-MIC wiki.
**2. Upload your slides/demos and tutorial dataset. Your tutorial and data must be named as 'TutorialName_TutorialContestWinter2017.pdf' and 'TutorialData_TutorialContestWinter2017.zip'
**3. Add a link to the uploaded tutorial and datasets on your tutorial page.
**4. Copy the template of the [http://wiki.na-mic.org/Wiki/index.php/Training:Winter_2017_Contest_Table Winter 2017 test table ] on your tutorial page, and document the status of your cross-platform testing (Mac, Windows, Linux).
**5. Once you have completed step 1-4, add a link to your tutorial page in the list below and send a notification email to Sonia Pujol (spujol at bwh.harvard.edu) to receive a confirmation of your submission.

=Tutorials=
*Simple Python Tool for Quality Control of DWI data (Laurent Chauvin)
*SHARPM-PDM (Beatriz Paniagua)
*Segmentation Module (Csaba Pinter)
*[[File:ROSIGTLTutorial_Tokuda_Jan2017.pptx| Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink (Junichi Tokuda)]]
*Slicer Pathology (Erich Bremer)
*[[File:Fiber_Bundle_Volume_Measurement.pptx|Fiber Bundle Volume Measurement (Shun Gong)]], [[File:FiberVolume_data.zip| data]]

= Review Session=
The review session of the 2017 Tutorial Contest will take place on Thursday January 12 at the Massachusetts Institute of Technology, Cambrigde, MA as part of the Winter 2017 Slicer Project Week.
All contestants will be invited to present brief highlights of their tutorials. Each presentation should be 5-minute summary of the submission.

=Results=
The winner of the 2017 tutorial contest will be announced on Friday January 13 during the closing session of the Slicer Project Week.

File:Fiber Bundle Volume Measurement.pptx

2017-01-12T16:00:38Z

Fan:

File:FiberVolume data.zip

2017-01-12T15:56:37Z

Fan:

2017 Winter Project Week/SlicerDMRIDocumentationAndTesting

2017-01-09T18:16:14Z

Fan:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Shun Gong, BWH
* Ye Wu, BWH
* Isaiah Norton, BWH
* Fan Zhang, BWH
* Lauren J. O'Donnell, BWH

==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;"
|

The aim is to provide improved documentations and tutorials about the modules and functions in SlicerDMRI.
|

* Update online documentations to latest version
* Improve testing coverage
* Improve website
* Update sandbox extensions and release with tutorials and testing cases
* Make a SlicerDMRI logo
|

*
|}

==Background and References==

*SlicerDMRI: http://slicerdmri.github.io
* SlicerDMRISandbox issues: https://github.com/SlicerDMRI/Sandbox/issues

2017 Winter Project Week/SlicerDMRIDocumentationAndTesting

2017-01-09T16:48:48Z

Fan:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Shun Gong, BWH
* Ye Wu, BWH
* Isaiah Norton, BWH
* Fan Zhang, BWH
* Lauren J. O'Donnell, BWH

==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;"
|

The aim is to provide improved documentations and tutorials about the modules and functions in SlicerDMRI.
|

* Update online documentations to latest version
* Improve testing coverage
* Improve website
* Update sandbox extensions and release with tutorials and testing cases
* Make a SlicerDRMI logo
|

*
|}

==Background and References==

*SlicerDMRI: http://slicerdmri.github.io
* SlicerDMRISandbox issues: https://github.com/SlicerDMRI/Sandbox/issues

2017 Winter Project Week/SlicerDMRIDocumentationAndTesting

2017-01-09T14:22:59Z

Fan:

2017 Winter Project Week

2017-01-09T14:22:31Z

Fan:

__NOTOC__
[[image:PW-Winter2017.png|300px]]

=Welcome to the web page for the 24th Project Week!=

The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

==Logistics==

*'''Dates:''' January 9-13, 2017.
*'''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)
*'''Transportation:''' Public transportation is highly encouraged, as no parking permits will be issued by MIT. For a list of local garages, please see [http://web.mit.edu/facilities/transportation/parking/visitors/public_parking.html here]
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and 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], enhancements to the underlying building blocks [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 open source hackathon event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 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_Project_Weeks|here]].

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

==Conference Calls for Preparation==

Conference call phone number and notes are available [[TCONS:2017_Winter_Project_Week|here]].

==Calendar==

'''''The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.''''' 

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20170108/20170114
}}

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

='''Projects'''=

*Use this [[2017_Project_Week_Template | Updated Template for project pages]]

== Learning and GPUs ==
#[[2017 Winter Project Week/Deep Learning for Medical Image Computation| Deep Learning for Medical Image Computing]] (Tina Kapur)
#[[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Tina Kapur, Ziyang Wang, Guillaume Pernelle, Paolo Zaffino)
#[[2017 Winter Project Week/DeepInfer| DeepInfer: Open-source Deep Learning Deployment Toolkit]] (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)
#[[2017 Winter Project Week/Diffusely abnormal white matter segmentation with 3d U-net| Diffusely abnormal white matter segmentation with 3d U-net]] (Mohsen Ghafoorrian, Bram Platel, Sandy Wells, Tina Kapur)
# [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)
#[[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)
#[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)
#[[2017 Winter Project Week/Convolutional neural nets for lung cancer survival prediction | Convolutional neural nets for lung cancer survival prediction]] (Ahmed Hosny, Chintan Parmar, Roman Zeleznik, Hugo Aerts)

== Web Technologies ==
#[[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)
#[[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
#[[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
#[[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)
#[[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)
#[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper, Teodora Szasz)
#[[2017 Winter Project Week/Electron App to add, navigate and visualize DICOM images | Electron App to add, navigate and visualize DICOM images]] (Smruti Padhy, Satrajit Ghosh, Mathias Goncalves)
#[[2017 Winter Project Week/AMI: A 3D Medical Imaging Javascript Library | AMI: A 3D Medical Imaging Javascript Library]] (Rudolph Pienaar, Teodora Szasz)
#[[2017_Winter_Project_Week/MedicalVisualizerUsingParaViewWeb | Medical Visualizer using ParaViewWeb]] (Teodora Szasz)
#[[2017 Winter Project Week/SimplePowerfulBeautifulMedicalVisualizerWithAMI | Simple, Powerful and Beautiful Medical Visualizer with AMI]] (Jorge Luis Bernal Rusiel, Nicolas Rannou, Rudolph Pienaar)

== IGT: Navigation, Robotics, Surgical Planning ==
#[[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
#[[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)
#[[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)
#[[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
#[[2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction| 3D surgical planning solution for autologous breast reconstruction]] (Michael Chae, Andras Lasso, Julian Smith, Warren Rozen, David Hunter-Smith)

==dMRI==
#[[2017 Winter Project Week/WhiteMatterAnalysis | Fiber endpoint analysis for neurosurgical planning]] (Fan Zhang, Shun Gong, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)
#[[2017 Winter Project Week/LORDWI | Density-based DMRI registration ]] (Henrik Groenholt Jensen, Lauren J. O'Donnell, Tina Kapur, Fan Zhang, Carl-Fredrik Westin)
#[[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Shun Gong, Ye Wu, Isaiah Norton, Fan Zhang, Lauren J. O'Donnell)
#[[2017 Winter Project Week/DiPy_in_Slicer | DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)
#[[2017 Winter Project Week/DWI_Similarity_Metrics | Identification of information-rich patches in Diffusion-Weighted Images]] (Laurent Chauvin, Fan Zhang, Lauren J. O'Donnell, Matthew Toews)

==Quantitative Imaging Informatics==
#[[2017 Winter Project Week/dcmqi | dcmqi library]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
#[[2017 Winter Project Week/QuantitativeReporting | DICOM QuantitativeReporting]] (Christian Herz, Andrey Fedorov)
#[[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)
#[[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)
#[[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)

== Shape Analysis, Segmentation, and Visualization ==
#[[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
#[[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)
#[[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)
#[[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
#[[2017 Winter Project Week/GeodesicSegmentationandLungtumorAnalysis| Geodesic Segmentation and Lung tumor Analysis]] (Patmaa S, Sarthak Pati, Ratheesh k, Mark B, Yong F, Despina K, Ragini V, Christos D)
#[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)
#[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)
#[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)
#[[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)

== Infrastructure ==
#[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)
#[[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
#[[2017 Winter Project Week/UpdatingCommunityForums | Updating Community Forums (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)
#[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
#[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)
#[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)

==Training and Dissemination==
#[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)

= '''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/2017projectweek registration site].

# Aman Shboul, Zaina :: Old Dominion University
# Aerts, Hugo :: DFCI-Harvard
# Alam, Mahbubul :: Old Dominion University
# Anderson, Peter :: Retired
# Andruejol, Johan :: Kitware, Inc.
# Bakeng, Janne Beate :: SINTEF
# Beers, Andrew :: Massachusetts General Hospital
# Bernal Rusiel, Jorge Luis :: Boston Children's Hospital
# Bremer, Erich :: Stony Brook University
# Burke, Brice :: American University of Antigua College of Medicine
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital
# Chae, Michael :: Monash University
# Chauvin, Laurent :: ETS
# Dalca, Adrian :: Massachusetts Institute of Technology
# DiPrima, Tammy :: Stony Brook University
# Drouin, Simon :: Montreal Neurological Institute
# Fan, Zhipeng :: Brigham and Women's Hospital
# Fedorov, Andriy :: Brigham and Women's Hospital
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.
# Fishbaugh, James :: New York University
# Frank, Tobias :: Leibniz Universität Hannover
# Frisken, Sarah :: Brigham and Women's Hospital
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid
# Ghafoorian, Mohsen :: Brigham and Women's Hospital
# Ghosh, Satrajit :: Massachusetts Institute of Technology
# Girault, Alexis :: Kitware, Inc.
# Golland, Polina :: Massachusetts Institute of Technology
# Gollub, Randy :: Massachusetts General Hospital
# Goncalves, Mathias :: Massachusetts Institute of Technology
# Gong, Shun :: Brigham and Women's Hospital
# Guerrier de Dumast, Priscille :: University of Michigan
# Harris, Gordon :: Massachusetts General Hospital
# Helba, Brian :: Kitware, Inc.
# Herz, Christian :: Brigham and Women's Hospital
# Hong, Sungmin :: New York University
# Hosny, Ahmed :: Dana-Farber
# Jagadeesan, Jayender :: Brigham and Women's Hospital
# Jarecka, Dorota :: Massachusetts Institute of Technology
# Jensen, Henrik G. :: University of Copenhagen
# Kaczmarzyk, Jakub :: Massachusetts Institute of Technology
# Kapur, Tina :: Brigham and Women's Hospital
# Kennedy, David :: UMass Medical School
# Kikinis, Ron :: Brigham and Women's Hospital
# Lasso, Andras :: PerkLab, Queen's University
# Lauer, Rebekka :: Humboldt University Berlin
# Lisle, Curtis :: KnowledgeVis, LLC
# Mastrogiacomo, Katie :: Brigham and Women's Hospital
# Mateus, D. :: TUM
# Mehrtash, Alireza :: Brigham and Women's Hospital
# Meine, Hans :: University of Bremen
# Meyer, Anneke :: University of Magdeburg
# Miller, James :: GE Research
# Mirabel, Clement :: University of Michigan
# Nitsch, Jennifer :: University of Bremen
# Norton, Isaiah :: Brigham and Women's Hospital
# O'Donnell, Lauren :: Brigham and Women's Hospital
# Oram, Louise :: The Intervention Centre-Oslo University Hospital
# Padhy, Smruti :: Massachusetts Institute of Technology
# Paniagua, Beatriz :: Kitware, Inc.
# Parmar, Chintan :: DFCI-Harvard Medical School
# Peled, Sharon :: Brigham and Women's Hospital
# Pieper, Steve :: Isomics, Inc.
# Pinter, Csaba :: Queen's University
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School
# Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School
# Rankin, Adam :: Robarts Research Institute
# Rheault, Francois :: Université de Sherbrooke
# Roethe, Anna :: Humboldt University / Charité University Hospital Berlin
# Sharp, Gregory :: Massachusetts General Hospital
# Sridharan, Patmaa :: University of Pennsylvania-CBICA
# Szasz, Teodora :: University of Chicago
# Unadkat, Prashin :: Brigham and Women's Hospital
# Van Griethuysen , Joost :: Netherlands Cancer Institute
# Vidyaratne, Lasitha :: Old Dominion University
# Wang, Yaofei :: Brigham and Women's Hospital
# Wang, Ziyang :: Brigham and Women's Hospital
# Wei, Dawei :: Brigham and Women's Hospital
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School
# Xu, Wanxin :: Brigham and Women's Hospital
# Yang, Yixin :: Brigham and Women's Hospital
# Ye, Wu :: Brigham and Women's Hospital
# Zaffino, Paolo :: Magna Graecia University of Catanzaro, Italy
# Zeleznik, Roman :: DFCI
# Zhang, Fan :: Brigham and Women's Hospital
# Zhang, Miaomiao :: Massachusetts Institute of Technology
# Zhang, Yuqian :: Brigham and Women's Hospital
# Zhou, Haoyin :: Brigham and Women's Hospital
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital

2017 Winter Project Week/WhiteMatterAnalysis

2017-01-09T14:18:10Z

Fan:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Fan Zhang, BWH
* Shun Gong, BWH
* Isaiah Norton, BWH
* Ye Wu, BWH
* Lauren J. O'Donnell, BWH

==Project Description==
This project is part of the whitematteranalysis software that provides an automated whole brain tractgoraphy registration and segmentation framework. The aim of this project is to integrate a new Slicer module FiberEndpointAnalysis into the whitematteranalysis pipeline.

{| 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;"
|

Calculate the overlap of fiber tract (endpoint regions) with anatomical parcellation (e.g. freesurfer) or functional region (e.g. fMRI).
|

* Release the FiberEndPointFromLabelMap module as part of SandBox in SlicerDMRI.
* Integrate the module into the whitematteranalysis software.
* Testing and documentation about the new functionality.
|


|}

==Background and References==

*SlicerDMRI: http://slicerdmri.github.io
*WhiteMatterAnalysis: https://github.com/SlicerDMRI/whitematteranalysis

2017 Winter Project Week

2017-01-07T19:38:01Z

Fan:

__NOTOC__
[[image:PW-Winter2017.png|300px]]

=Welcome to the web page for the 24th Project Week!=

The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

==Logistics==

*'''Dates:''' January 9-13, 2017.
*'''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)
*'''Transportation:''' Public transportation is highly encouraged, as no parking permits will be issued by MIT. For a list of local garages, please see [http://web.mit.edu/facilities/transportation/parking/visitors/public_parking.html here]
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and 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], enhancements to the underlying building blocks [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 open source hackathon event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 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_Project_Weeks|here]].

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

==Conference Calls for Preparation==

Conference call phone number and notes are available [[TCONS:2017_Winter_Project_Week|here]].

==Calendar==

'''''The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.''''' 

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20170108/20170114
}}

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

='''Projects'''=

*Use this [[2017_Project_Week_Template | Updated Template for project pages]]

== Learning and GPUs ==
#[[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Ziyang Wang, Guillaume Pernelle, Paolo Zaffino, Tina Kapur)
# [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)
#[[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)
#[[2017 Winter Project Week/DeepInfer| DeepInfer: Open-source Deep Learning Deployment Toolkit]] (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)
#[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)
#[[2017 Winter Project Week/Diffusely abnormal white matter segmentation with 3d U-net| Diffusely abnormal white matter segmentation with 3d U-net]] (Mohsen Ghafoorrian, Bram Platel, Sandy Wells, Tina Kapur)

== Web Technologies ==
#[[2017_Winter_Project_Week/MedicalVisualizerUsingParaViewWeb | Medical Visualizer using ParaViewWeb]] (Teodora Szasz)
#[[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)
#[[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
#[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper, Teodora Szasz)
#[[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)
#[[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
#[[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)
#[[2017 Winter Project Week/Electron App to add, navigate and visualize DICOM images | Electron App to add, navigate and visualize DICOM images]] (Smruti Padhy, Satrajit Ghosh, Mathias Goncalves)
#[[2017 Winter Project Week/AMI: A 3D Medical Imaging Javascript Library | AMI: A 3D Medical Imaging Javascript Library]] (Rudolph Pienaar, Teodora Szasz)

== IGT: Navigation, Robotics, Surgical Planning ==
#[[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
#[[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)
#[[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)
#[[2017 Winter Project Week/OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab | OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab ]] (Scheherazade Kraß (Shery), Junichi Tokuda, Longquan Chen, )
#[[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
#[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)
#[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)
#[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)
#[[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)

==dMRI==
#[[2017 Winter Project Week/WhiteMatterAnalysis | Fiber endpoint analysis for neurosurgical planning]] (Fan Zhang, Shun Gong, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)
#[[2017 Winter Project Week/LORDWI | Density-based DMRI registration ]] (Henrik Groenholt Jensen, Lauren J. O'Donnell, Tina Kapur, Fan Zhang, Carl-Fredrik Westin)
#[[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)
#[[2017 Winter Project Week/DiPy_in_Slicer | DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)
#[[2017 Winter Project Week/DWI_Similarity_Metrics | Identification of information-rich patches in Diffusion-Weighted Images]] (Laurent Chauvin, Fan Zhang, Lauren J. O'Donnell, Matthew Toews)

==Quantitative Imaging Informatics==
#[[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
#[[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)
#[[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)
#[[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)

== Visualization ==
#[[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)

== Infrastructure ==
#[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)
#[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
#[[2017 Winter Project Week/UpdatingCommunityForums | Updating Community Forums (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)
#[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Piper)
#[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)
#[[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)

==Shape Analysis==
#[[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
#[[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)

==To be Categorized==
#[[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
#[[2017 Winter Project Week/GeodesicSegmentationandLungtumorAnalysis| Geodesic Segmentation and Lung tumor Analysis]] (Patmaa S, Sarthak Pati, Ratheesh k, Mark B, Yong F, Despina K, Ragini V, Christos D)
#[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)
#[[2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction| 3D surgical planning solution for autologous breast reconstruction]] (Michael Chae, Andras Lasso, Julian Smith, Warren Rozen, David Hunter-Smith)

= '''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/2017projectweek registration site].

# Aman Shboul, Zaina :: Old Dominion University
# Aerts, Hugo :: DFCI-Harvard
# Alam, Mahbubul :: Old Dominion University
# Anderson, Peter :: Retired
# Andruejol, Johan :: Kitware, Inc.
# Bakeng, Janne Beate :: SINTEF
# Beers, Andrew :: Massachusetts General Hospital
# Bernal Rusiel, Jorge Luis :: Boston Children's Hospital
# Bremer, Erich :: Stony Brook University
# Burke, Brice :: American University of Antigua College of Medicine
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital
# Chae, Michael :: Monash University
# Chauvin, Laurent :: ETS
# Dalca, Adrian :: Massachusetts Institute of Technology
# DiPrima, Tammy :: Stony Brook University
# Drouin, Simon :: Montreal Neurological Institute
# Fan, Zhipeng :: Brigham and Women's Hospital
# Fedorov, Andriy :: Brigham and Women's Hospital
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.
# Fishbaugh, James :: New York University
# Frank, Tobias :: Leibniz Universität Hannover
# Frisken, Sarah :: Brigham and Women's Hospital
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid
# Ghafoorian, Mohsen :: Brigham and Women's Hospital
# Ghosh, Satrajit :: Massachusetts Institute of Technology
# Girault, Alexis :: Kitware, Inc.
# Golland, Polina :: Massachusetts Institute of Technology
# Gollub, Randy :: Massachusetts General Hospital
# Goncalves, Mathias :: Massachusetts Institute of Technology
# Gong, Shun :: Brigham and Women's Hospital
# Guerrier de Dumast, Priscille :: University of Michigan
# Harris, Gordon :: Massachusetts General Hospital
# Helba, Brian :: Kitware, Inc.
# Herz, Christian :: Brigham and Women's Hospital
# Hong, Sungmin :: New York University
# Hosny, Ahmed :: Dana-Farber
# Jagadeesan, Jayender :: Brigham and Women's Hospital
# Jarecka, Dorota :: Massachusetts Institute of Technology
# Jensen, Henrik G. :: University of Copenhagen
# Kaczmarzyk, Jakub :: Massachusetts Institute of Technology
# Kapur, Tina :: Brigham and Women's Hospital
# Kennedy, David :: UMass Medical School
# Kikinis, Ron :: Brigham and Women's Hospital
# Lasso, Andras :: PerkLab, Queen's University
# Lauer, Rebekka :: Humboldt University Berlin
# Lisle, Curtis :: KnowledgeVis, LLC
# Mastrogiacomo, Katie :: Brigham and Women's Hospital
# Mateus, D. :: TUM
# Mehrtash, Alireza :: Brigham and Women's Hospital
# Meine, Hans :: University of Bremen
# Meyer, Anneke :: University of Magdeburg
# Miller, James :: GE Research
# Mirabel, Clement :: University of Michigan
# Nitsch, Jennifer :: University of Bremen
# Norton, Isaiah :: Brigham and Women's Hospital
# O'Donnell, Lauren :: Brigham and Women's Hospital
# Oram, Louise :: The Intervention Centre-Oslo University Hospital
# Padhy, Smruti :: Massachusetts Institute of Technology
# Paniagua, Beatriz :: Kitware, Inc.
# Parmar, Chintan :: DFCI-Harvard Medical School
# Peled, Sharon :: Brigham and Women's Hospital
# Pieper, Steve :: Isomics, Inc.
# Pinter, Csaba :: Queen's University
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School
# Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School
# Rankin, Adam :: Robarts Research Institute
# Rheault, Francois :: Université de Sherbrooke
# Roethe, Anna :: Humboldt University / Charité University Hospital Berlin
# Sharp, Gregory :: Massachusetts General Hospital
# Sridharan, Patmaa :: University of Pennsylvania-CBICA
# Szasz, Teodora :: University of Chicago
# Unadkat, Prashin :: Brigham and Women's Hospital
# Van Griethuysen , Joost :: Netherlands Cancer Institute
# Vidyaratne, Lasitha :: Old Dominion University
# Wang, Yaofei :: Brigham and Women's Hospital
# Wang, Ziyang :: Brigham and Women's Hospital
# Wei, Dawei :: Brigham and Women's Hospital
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School
# Xu, Wanxin :: Brigham and Women's Hospital
# Yang, Yixin :: Brigham and Women's Hospital
# Ye, Wu :: Brigham and Women's Hospital
# Zaffino, Paolo :: Magna Graecia University of Catanzaro, Italy
# Zeleznik, Roman :: DFCI
# Zhang, Fan :: Brigham and Women's Hospital
# Zhang, Miaomiao :: Massachusetts Institute of Technology
# Zhang, Yuqian :: Brigham and Women's Hospital
# Zhou, Haoyin :: Brigham and Women's Hospital
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital

2017 Winter Project Week

2016-12-27T18:16:13Z

Fan:

2017 Winter Project Week/WhiteMatterAnalysis

2016-12-27T18:15:43Z

Fan:

2017 Winter Project Week/WhiteMatterAnalysis

2016-12-27T18:15:23Z

Fan:

2017 Winter Project Week/SlicerDMRIDocumentationAndTesting

2016-12-07T14:44:43Z

Fan: /* Background and References */

2017 Winter Project Week/WhiteMatterAnalysis

2016-12-07T14:44:09Z

Fan: /* Project Description */

2017 Winter Project Week/SlicerDMRIDocumentationAndTesting

2016-12-07T14:43:43Z

Fan: Created page with "__NOTOC__ <gallery> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the l..."

2017 Winter Project Week

2016-12-07T14:42:12Z

Fan: /* Infrastructure */

__NOTOC__
[[image:PW-Winter2017.png|300px]]

'''Welcome to the web page for the 24th Project Week!'''
The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

=='''Logistics''' ==

*'''Dates:''' January 9-13, 2017.
*'''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/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and 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], enhancements to the underlying building blocks [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 open source hackathon event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 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]

==Conference Calls for Preparation==

Domestic conference call number: 800-501-8979 
Access code: 7327389 

[[media:TollFree.png|International conference call numbers]] 
Access code: 7327389 

Weekly, Tuesdays 10am, Boston time from Nov 22, 2016 to Jan 3rd, 2017

===Tcon #4: December 6 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials

Participants
* Tina Kapur (MIT) - organizer
* Steve Pieper (Isomics/BWH)
* Beatriz, JC (Kitware)

===Tcon #3: November 29 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials
Participants
* Tina Kapur (MIT) - organizer; planning Nvidia webinars. Proposal to use Monday as a schedule for the deep learning workshop before workshop begins.
*Steve Pieper (Isomics/BWH) - NVidia update; met with Abdul at NVidia (Medical applications of deep learning). Positive meeting and Slicer might be a reference platform. NVIdia will host a Monday Afternoon session at Project Week and hold outside webinars for basic deep learning information. Considering two or three days of a few hours each for webinar. Discussion of a prize board awarded for demonstrations that Nvidia could use.
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Beatriz, Alexis, and JC (Kitware) - Slicer support and 3 other projects (1) customized childrern's medical, (1) Alex submitted volumetric meshing project in Slicer idea to the NA-MIC email list; have a discussion on Meshing; the goal is for Finite Element analsis and light imaging (2), better MATLAB integration (use Python-like interface). (3) Beatrix - shape analysis algorithms to be added to Slicer based on recently-funded grant.
*JC (Kitware) - integration of iPython and Slicer; Tina Suggested also Deep Infer framework to integrate with Slicer
*Louise Oram (Stockholm) - Specialization of Slicer for Liver surgery, possibly using SliceLet approach or other way to tailor the Slicer UI. Currently customizations need to be in the Extension catalog. Also interested in Liver vessel segmentation project and other Liver segmentation tasks. This might complement with MeVIS lab capability focused on liver. Separate modules for liver surgery that might be integrated together later.
*Frank Pricework (BWH) - General GPU programming; experiment with rehosting algorithms has has previously developed to GPU.
*Paolo, Italy - (Summer Project Week Host)
*Naboo (Old Dominion) - two possible projects, not certain yet - (1) smaller training datasets for medical images, (2) braining atlas segmentation integration with Slicer.
*Curt Lisle (KnowledgeVis) - (1) web-based transition of subset of Slicer capability, (2) Iowa Meshing Module move from 3.6 to 4.7 (with Alex from Kitware); (3) possible integration of web-based volume rendering;
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Eric Seigler - OHIS Cornerstone Lesion Tracker author; Integrating interactive segmentation into the web-based framework

Discussions
*Training deep learning networks with smaller datasets.
*Integrating of projects with Slicer & architecture will be a discussion topic during the week.
*Everybody, be sure to register on the Wiki for the workshop; come up with a title and short description of the project(s) you will work on.
*OK to send info to the NA-MIC email list

===Tcon #2: November 22 ===
*10am Boston time
*Topics: continue Deep Learning, Web-based software
*Participants (interests)
# Tina Kapur, BWH (needle detection)
# Steve Pieper, Isomics (web-based software, GPU computing)
#Mahbub, Old Dominion University (creating architectures for deep learning networks in matlab, bridge to Slicer, MICCAI challenge code into Slicer, make learning faster and with less training)
#Siddiqi, Old Dominion
#Nicole Aucoin, BWH
#Abdul, NVIDIA Business Development (potential deep learning tutorials by web conference before the event, then at the event)
#Able Brown, NVIDIA
#JC, Kitware
#Krisztina Fischer, BWH
#Andrew Beard, MGH (deep learning, parameter estimation from MRI)
#Gordon Harris, MGH
#Laurent Chauvin, ETS Montreal (CNN, GPUs)
#John Toeber, Bremen U
#Lauren O'Donnell, BWH
#Fan Zhang, BWH
#Isaiah Norton, BWH
#Wu Ye, BWH
#Erik Siegler, MGH (Slicer / ePad connection with LesionTracker; more web-based technologies; discussion of ePad custom widget that will send out connections to remote jobs., PET/CT Lymphoma workshop as extension to lesion tracker.)
#Pete Anderson (Open source tracker)
#Guillaume Pernelle, Imperial College (CNNs, LSTMs, Deep Learning, GPUs)
#Mike Halle, BWH (slicer cross-platform architecture to work for hardware-specific; proxy running cloud that can support interface, Atlas browser is an active project for web-based interface. Slicer success is primarily application-level tools. The community could benefit with architectural study.)
#Louise, Oslo, Norway (high-speed pipelining of image processing for liver resections. )
#Paolo, Catanzaro, Italy (Multiple GPU system architecture)
#Salvatore, Catanzaro, Italy
#Daniel Rubin, Stanford
#Curt Lisle, Knowledgevis (has image web-based workflow systems; Deeply interested in web transition of imaging technologies. Also interested (but not experienced) in deep learning application; particularly feature recognition; small animal imaging applications)
#Charles Guttman, BWH (has MS data, wants to use Docker-based repository. (Boutique looks like a good repository)

===Tcon #1: November 15 ===
*10am Boston time
*Emergent interest in the application of Deep Learning techniques to medical image analysis.

Participants and interests
*#Tina Kapur, BWH -- needle detection
*#Steve Pieper, Isomics - GPUs
*#Andras Lasso, Queens - Slicer expert
*#Frankie Preiswerk, BWH -- hybrid ultrasound and MRI, interested in NVIDIA workshop
*#JC, Kitware -- Slicer expert
*#Mike Halle, BWH -- image feature search using deep learning (w/ Sandy Wells)
*#Peter Neher, DKFZ (filling in for Marco Nolden) -- experience with deep learning with face recognition
*#Nicole Aucoin, BWH -- Slicer expert
*#Alireza Mehrtash, UBC, BWH -- deep learning for prostate interventions, extension server for deep learning for Slicer
*#Daniel Rubin deep learning
*#Krisztina Fischer -- teaching

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 9
!style="width:18%" |Tuesday, January 10
!style="width:18%" |Wednesday, January 11
!style="width:18%" |Thursday, January 12
!style="width:18%" |Friday, January 13
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#faedb6"| '''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|rowspan="2"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-10:30am'''
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|-
|bgcolor="#ffffdd"|'''10:30am-12pm:'''
|'''Talk (Sebastian Ourselin, PhD, UCL)'''
|
|
|
|Project Reporting
|-
|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-2:30pm:''' Project Presentations
|
|
|
|'''1:30-2:30pm:''' [[AMIGO_TourPW2017Winter|AMIGO Tour]]
|-
|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 (Optional) [[2017_Winter_Project_Week/Dinner|Dinner on Thursday Night]]
|
|}

==Calendar==

'''''The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.''''' 

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20170108/20170114
}}

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

='''Projects'''=

*Use this [[2017_Project_Week_Template | Updated Template for project pages]]

== Learning and GPUs ==

== Web Technologies ==

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin)

== IGT ==
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)

== Infrastructure ==
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)

== DICOM ==

= '''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/2017projectweek registration site].

2017 Winter Project Week

2016-12-07T14:41:22Z

Fan: /* Infrastructure */

__NOTOC__
[[image:PW-Winter2017.png|300px]]

'''Welcome to the web page for the 24th Project Week!'''
The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

=='''Logistics''' ==

*'''Dates:''' January 9-13, 2017.
*'''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/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and 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], enhancements to the underlying building blocks [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 open source hackathon event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 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]

==Conference Calls for Preparation==

Domestic conference call number: 800-501-8979 
Access code: 7327389 

[[media:TollFree.png|International conference call numbers]] 
Access code: 7327389 

Weekly, Tuesdays 10am, Boston time from Nov 22, 2016 to Jan 3rd, 2017

===Tcon #4: December 6 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials

Participants
* Tina Kapur (MIT) - organizer
* Steve Pieper (Isomics/BWH)
* Beatriz, JC (Kitware)

===Tcon #3: November 29 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials
Participants
* Tina Kapur (MIT) - organizer; planning Nvidia webinars. Proposal to use Monday as a schedule for the deep learning workshop before workshop begins.
*Steve Pieper (Isomics/BWH) - NVidia update; met with Abdul at NVidia (Medical applications of deep learning). Positive meeting and Slicer might be a reference platform. NVIdia will host a Monday Afternoon session at Project Week and hold outside webinars for basic deep learning information. Considering two or three days of a few hours each for webinar. Discussion of a prize board awarded for demonstrations that Nvidia could use.
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Beatriz, Alexis, and JC (Kitware) - Slicer support and 3 other projects (1) customized childrern's medical, (1) Alex submitted volumetric meshing project in Slicer idea to the NA-MIC email list; have a discussion on Meshing; the goal is for Finite Element analsis and light imaging (2), better MATLAB integration (use Python-like interface). (3) Beatrix - shape analysis algorithms to be added to Slicer based on recently-funded grant.
*JC (Kitware) - integration of iPython and Slicer; Tina Suggested also Deep Infer framework to integrate with Slicer
*Louise Oram (Stockholm) - Specialization of Slicer for Liver surgery, possibly using SliceLet approach or other way to tailor the Slicer UI. Currently customizations need to be in the Extension catalog. Also interested in Liver vessel segmentation project and other Liver segmentation tasks. This might complement with MeVIS lab capability focused on liver. Separate modules for liver surgery that might be integrated together later.
*Frank Pricework (BWH) - General GPU programming; experiment with rehosting algorithms has has previously developed to GPU.
*Paolo, Italy - (Summer Project Week Host)
*Naboo (Old Dominion) - two possible projects, not certain yet - (1) smaller training datasets for medical images, (2) braining atlas segmentation integration with Slicer.
*Curt Lisle (KnowledgeVis) - (1) web-based transition of subset of Slicer capability, (2) Iowa Meshing Module move from 3.6 to 4.7 (with Alex from Kitware); (3) possible integration of web-based volume rendering;
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Eric Seigler - OHIS Cornerstone Lesion Tracker author; Integrating interactive segmentation into the web-based framework

Discussions
*Training deep learning networks with smaller datasets.
*Integrating of projects with Slicer & architecture will be a discussion topic during the week.
*Everybody, be sure to register on the Wiki for the workshop; come up with a title and short description of the project(s) you will work on.
*OK to send info to the NA-MIC email list

===Tcon #2: November 22 ===
*10am Boston time
*Topics: continue Deep Learning, Web-based software
*Participants (interests)
# Tina Kapur, BWH (needle detection)
# Steve Pieper, Isomics (web-based software, GPU computing)
#Mahbub, Old Dominion University (creating architectures for deep learning networks in matlab, bridge to Slicer, MICCAI challenge code into Slicer, make learning faster and with less training)
#Siddiqi, Old Dominion
#Nicole Aucoin, BWH
#Abdul, NVIDIA Business Development (potential deep learning tutorials by web conference before the event, then at the event)
#Able Brown, NVIDIA
#JC, Kitware
#Krisztina Fischer, BWH
#Andrew Beard, MGH (deep learning, parameter estimation from MRI)
#Gordon Harris, MGH
#Laurent Chauvin, ETS Montreal (CNN, GPUs)
#John Toeber, Bremen U
#Lauren O'Donnell, BWH
#Fan Zhang, BWH
#Isaiah Norton, BWH
#Wu Ye, BWH
#Erik Siegler, MGH (Slicer / ePad connection with LesionTracker; more web-based technologies; discussion of ePad custom widget that will send out connections to remote jobs., PET/CT Lymphoma workshop as extension to lesion tracker.)
#Pete Anderson (Open source tracker)
#Guillaume Pernelle, Imperial College (CNNs, LSTMs, Deep Learning, GPUs)
#Mike Halle, BWH (slicer cross-platform architecture to work for hardware-specific; proxy running cloud that can support interface, Atlas browser is an active project for web-based interface. Slicer success is primarily application-level tools. The community could benefit with architectural study.)
#Louise, Oslo, Norway (high-speed pipelining of image processing for liver resections. )
#Paolo, Catanzaro, Italy (Multiple GPU system architecture)
#Salvatore, Catanzaro, Italy
#Daniel Rubin, Stanford
#Curt Lisle, Knowledgevis (has image web-based workflow systems; Deeply interested in web transition of imaging technologies. Also interested (but not experienced) in deep learning application; particularly feature recognition; small animal imaging applications)
#Charles Guttman, BWH (has MS data, wants to use Docker-based repository. (Boutique looks like a good repository)

===Tcon #1: November 15 ===
*10am Boston time
*Emergent interest in the application of Deep Learning techniques to medical image analysis.

Participants and interests
*#Tina Kapur, BWH -- needle detection
*#Steve Pieper, Isomics - GPUs
*#Andras Lasso, Queens - Slicer expert
*#Frankie Preiswerk, BWH -- hybrid ultrasound and MRI, interested in NVIDIA workshop
*#JC, Kitware -- Slicer expert
*#Mike Halle, BWH -- image feature search using deep learning (w/ Sandy Wells)
*#Peter Neher, DKFZ (filling in for Marco Nolden) -- experience with deep learning with face recognition
*#Nicole Aucoin, BWH -- Slicer expert
*#Alireza Mehrtash, UBC, BWH -- deep learning for prostate interventions, extension server for deep learning for Slicer
*#Daniel Rubin deep learning
*#Krisztina Fischer -- teaching

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 9
!style="width:18%" |Tuesday, January 10
!style="width:18%" |Wednesday, January 11
!style="width:18%" |Thursday, January 12
!style="width:18%" |Friday, January 13
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#faedb6"| '''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|rowspan="2"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-10:30am'''
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|-
|bgcolor="#ffffdd"|'''10:30am-12pm:'''
|'''Talk (Sebastian Ourselin, PhD, UCL)'''
|
|
|
|Project Reporting
|-
|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-2:30pm:''' Project Presentations
|
|
|
|'''1:30-2:30pm:''' [[AMIGO_TourPW2017Winter|AMIGO Tour]]
|-
|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 (Optional) [[2017_Winter_Project_Week/Dinner|Dinner on Thursday Night]]
|
|}

==Calendar==

'''''The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.''''' 

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20170108/20170114
}}

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

='''Projects'''=

*Use this [[2017_Project_Week_Template | Updated Template for project pages]]

== Learning and GPUs ==

== Web Technologies ==

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin)

== IGT ==
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)

== Infrastructure ==
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Documentation and Testing]] ( Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)

== DICOM ==

= '''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/2017projectweek registration site].

2017 Winter Project Week/WhiteMatterAnalysis

2016-12-07T14:40:21Z

Fan: /* Background and References */

2017 Winter Project Week/WhiteMatterAnalysis

2016-12-07T14:40:05Z

Fan: /* Background and References */

2017 Winter Project Week/WhiteMatterAnalysis

2016-12-07T14:39:28Z

Fan: /* Key Investigators */

2017 Winter Project Week/WhiteMatterAnalysis

2016-12-07T14:38:46Z

Fan: Created page with "__NOTOC__ <gallery> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the l..."

2017 Winter Project Week

2016-12-07T14:32:01Z

Fan: /* Infrastructure */

__NOTOC__
[[image:PW-Winter2017.png|300px]]

'''Welcome to the web page for the 24th Project Week!'''
The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

=='''Logistics''' ==

*'''Dates:''' January 9-13, 2017.
*'''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/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and 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], enhancements to the underlying building blocks [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 open source hackathon event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 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]

==Conference Calls for Preparation==

Domestic conference call number: 800-501-8979 
Access code: 7327389 

[[media:TollFree.png|International conference call numbers]] 
Access code: 7327389 

Weekly, Tuesdays 10am, Boston time from Nov 22, 2016 to Jan 3rd, 2017

===Tcon #4: December 6 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials

Participants
* Tina Kapur (MIT) - organizer
* Steve Pieper (Isomics/BWH)
* Beatriz, JC (Kitware)

===Tcon #3: November 29 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials
Participants
* Tina Kapur (MIT) - organizer; planning Nvidia webinars. Proposal to use Monday as a schedule for the deep learning workshop before workshop begins.
*Steve Pieper (Isomics/BWH) - NVidia update; met with Abdul at NVidia (Medical applications of deep learning). Positive meeting and Slicer might be a reference platform. NVIdia will host a Monday Afternoon session at Project Week and hold outside webinars for basic deep learning information. Considering two or three days of a few hours each for webinar. Discussion of a prize board awarded for demonstrations that Nvidia could use.
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Beatriz, Alexis, and JC (Kitware) - Slicer support and 3 other projects (1) customized childrern's medical, (1) Alex submitted volumetric meshing project in Slicer idea to the NA-MIC email list; have a discussion on Meshing; the goal is for Finite Element analsis and light imaging (2), better MATLAB integration (use Python-like interface). (3) Beatrix - shape analysis algorithms to be added to Slicer based on recently-funded grant.
*JC (Kitware) - integration of iPython and Slicer; Tina Suggested also Deep Infer framework to integrate with Slicer
*Louise Oram (Stockholm) - Specialization of Slicer for Liver surgery, possibly using SliceLet approach or other way to tailor the Slicer UI. Currently customizations need to be in the Extension catalog. Also interested in Liver vessel segmentation project and other Liver segmentation tasks. This might complement with MeVIS lab capability focused on liver. Separate modules for liver surgery that might be integrated together later.
*Frank Pricework (BWH) - General GPU programming; experiment with rehosting algorithms has has previously developed to GPU.
*Paolo, Italy - (Summer Project Week Host)
*Naboo (Old Dominion) - two possible projects, not certain yet - (1) smaller training datasets for medical images, (2) braining atlas segmentation integration with Slicer.
*Curt Lisle (KnowledgeVis) - (1) web-based transition of subset of Slicer capability, (2) Iowa Meshing Module move from 3.6 to 4.7 (with Alex from Kitware); (3) possible integration of web-based volume rendering;
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Eric Seigler - OHIS Cornerstone Lesion Tracker author; Integrating interactive segmentation into the web-based framework

Discussions
*Training deep learning networks with smaller datasets.
*Integrating of projects with Slicer & architecture will be a discussion topic during the week.
*Everybody, be sure to register on the Wiki for the workshop; come up with a title and short description of the project(s) you will work on.
*OK to send info to the NA-MIC email list

===Tcon #2: November 22 ===
*10am Boston time
*Topics: continue Deep Learning, Web-based software
*Participants (interests)
# Tina Kapur, BWH (needle detection)
# Steve Pieper, Isomics (web-based software, GPU computing)
#Mahbub, Old Dominion University (creating architectures for deep learning networks in matlab, bridge to Slicer, MICCAI challenge code into Slicer, make learning faster and with less training)
#Siddiqi, Old Dominion
#Nicole Aucoin, BWH
#Abdul, NVIDIA Business Development (potential deep learning tutorials by web conference before the event, then at the event)
#Able Brown, NVIDIA
#JC, Kitware
#Krisztina Fischer, BWH
#Andrew Beard, MGH (deep learning, parameter estimation from MRI)
#Gordon Harris, MGH
#Laurent Chauvin, ETS Montreal (CNN, GPUs)
#John Toeber, Bremen U
#Lauren O'Donnell, BWH
#Fan Zhang, BWH
#Isaiah Norton, BWH
#Wu Ye, BWH
#Erik Siegler, MGH (Slicer / ePad connection with LesionTracker; more web-based technologies; discussion of ePad custom widget that will send out connections to remote jobs., PET/CT Lymphoma workshop as extension to lesion tracker.)
#Pete Anderson (Open source tracker)
#Guillaume Pernelle, Imperial College (CNNs, LSTMs, Deep Learning, GPUs)
#Mike Halle, BWH (slicer cross-platform architecture to work for hardware-specific; proxy running cloud that can support interface, Atlas browser is an active project for web-based interface. Slicer success is primarily application-level tools. The community could benefit with architectural study.)
#Louise, Oslo, Norway (high-speed pipelining of image processing for liver resections. )
#Paolo, Catanzaro, Italy (Multiple GPU system architecture)
#Salvatore, Catanzaro, Italy
#Daniel Rubin, Stanford
#Curt Lisle, Knowledgevis (has image web-based workflow systems; Deeply interested in web transition of imaging technologies. Also interested (but not experienced) in deep learning application; particularly feature recognition; small animal imaging applications)
#Charles Guttman, BWH (has MS data, wants to use Docker-based repository. (Boutique looks like a good repository)

===Tcon #1: November 15 ===
*10am Boston time
*Emergent interest in the application of Deep Learning techniques to medical image analysis.

Participants and interests
*#Tina Kapur, BWH -- needle detection
*#Steve Pieper, Isomics - GPUs
*#Andras Lasso, Queens - Slicer expert
*#Frankie Preiswerk, BWH -- hybrid ultrasound and MRI, interested in NVIDIA workshop
*#JC, Kitware -- Slicer expert
*#Mike Halle, BWH -- image feature search using deep learning (w/ Sandy Wells)
*#Peter Neher, DKFZ (filling in for Marco Nolden) -- experience with deep learning with face recognition
*#Nicole Aucoin, BWH -- Slicer expert
*#Alireza Mehrtash, UBC, BWH -- deep learning for prostate interventions, extension server for deep learning for Slicer
*#Daniel Rubin deep learning
*#Krisztina Fischer -- teaching

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 9
!style="width:18%" |Tuesday, January 10
!style="width:18%" |Wednesday, January 11
!style="width:18%" |Thursday, January 12
!style="width:18%" |Friday, January 13
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#faedb6"| '''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|rowspan="2"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-10:30am'''
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|-
|bgcolor="#ffffdd"|'''10:30am-12pm:'''
|'''Talk (Sebastian Ourselin, PhD, UCL)'''
|
|
|
|Project Reporting
|-
|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-2:30pm:''' Project Presentations
|
|
|
|'''1:30-2:30pm:''' [[AMIGO_TourPW2017Winter|AMIGO Tour]]
|-
|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 (Optional) [[2017_Winter_Project_Week/Dinner|Dinner on Thursday Night]]
|
|}

==Calendar==

'''''The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.''''' 

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20170108/20170114
}}

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

='''Projects'''=

*Use this [[2017_Project_Week_Template | Updated Template for project pages]]

== Learning and GPUs ==

== Web Technologies ==

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin)

== IGT ==
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)

== Infrastructure ==
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Documentation and Testing]] (Fan Zhang, Shun Gong, Ye Wu, Isaiah Norton, Lauren J. O'Donnell)

== DICOM ==

= '''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/2017projectweek registration site].

2017 Winter Project Week

2016-12-07T14:31:17Z

Fan: /* IGT */

__NOTOC__
[[image:PW-Winter2017.png|300px]]

'''Welcome to the web page for the 24th Project Week!'''
The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

=='''Logistics''' ==

*'''Dates:''' January 9-13, 2017.
*'''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/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and 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], enhancements to the underlying building blocks [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 open source hackathon event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 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]

==Conference Calls for Preparation==

Domestic conference call number: 800-501-8979 
Access code: 7327389 

[[media:TollFree.png|International conference call numbers]] 
Access code: 7327389 

Weekly, Tuesdays 10am, Boston time from Nov 22, 2016 to Jan 3rd, 2017

===Tcon #4: December 6 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials

Participants
* Tina Kapur (MIT) - organizer
* Steve Pieper (Isomics/BWH)
* Beatriz, JC (Kitware)

===Tcon #3: November 29 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials
Participants
* Tina Kapur (MIT) - organizer; planning Nvidia webinars. Proposal to use Monday as a schedule for the deep learning workshop before workshop begins.
*Steve Pieper (Isomics/BWH) - NVidia update; met with Abdul at NVidia (Medical applications of deep learning). Positive meeting and Slicer might be a reference platform. NVIdia will host a Monday Afternoon session at Project Week and hold outside webinars for basic deep learning information. Considering two or three days of a few hours each for webinar. Discussion of a prize board awarded for demonstrations that Nvidia could use.
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Beatriz, Alexis, and JC (Kitware) - Slicer support and 3 other projects (1) customized childrern's medical, (1) Alex submitted volumetric meshing project in Slicer idea to the NA-MIC email list; have a discussion on Meshing; the goal is for Finite Element analsis and light imaging (2), better MATLAB integration (use Python-like interface). (3) Beatrix - shape analysis algorithms to be added to Slicer based on recently-funded grant.
*JC (Kitware) - integration of iPython and Slicer; Tina Suggested also Deep Infer framework to integrate with Slicer
*Louise Oram (Stockholm) - Specialization of Slicer for Liver surgery, possibly using SliceLet approach or other way to tailor the Slicer UI. Currently customizations need to be in the Extension catalog. Also interested in Liver vessel segmentation project and other Liver segmentation tasks. This might complement with MeVIS lab capability focused on liver. Separate modules for liver surgery that might be integrated together later.
*Frank Pricework (BWH) - General GPU programming; experiment with rehosting algorithms has has previously developed to GPU.
*Paolo, Italy - (Summer Project Week Host)
*Naboo (Old Dominion) - two possible projects, not certain yet - (1) smaller training datasets for medical images, (2) braining atlas segmentation integration with Slicer.
*Curt Lisle (KnowledgeVis) - (1) web-based transition of subset of Slicer capability, (2) Iowa Meshing Module move from 3.6 to 4.7 (with Alex from Kitware); (3) possible integration of web-based volume rendering;
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Eric Seigler - OHIS Cornerstone Lesion Tracker author; Integrating interactive segmentation into the web-based framework

Discussions
*Training deep learning networks with smaller datasets.
*Integrating of projects with Slicer & architecture will be a discussion topic during the week.
*Everybody, be sure to register on the Wiki for the workshop; come up with a title and short description of the project(s) you will work on.
*OK to send info to the NA-MIC email list

===Tcon #2: November 22 ===
*10am Boston time
*Topics: continue Deep Learning, Web-based software
*Participants (interests)
# Tina Kapur, BWH (needle detection)
# Steve Pieper, Isomics (web-based software, GPU computing)
#Mahbub, Old Dominion University (creating architectures for deep learning networks in matlab, bridge to Slicer, MICCAI challenge code into Slicer, make learning faster and with less training)
#Siddiqi, Old Dominion
#Nicole Aucoin, BWH
#Abdul, NVIDIA Business Development (potential deep learning tutorials by web conference before the event, then at the event)
#Able Brown, NVIDIA
#JC, Kitware
#Krisztina Fischer, BWH
#Andrew Beard, MGH (deep learning, parameter estimation from MRI)
#Gordon Harris, MGH
#Laurent Chauvin, ETS Montreal (CNN, GPUs)
#John Toeber, Bremen U
#Lauren O'Donnell, BWH
#Fan Zhang, BWH
#Isaiah Norton, BWH
#Wu Ye, BWH
#Erik Siegler, MGH (Slicer / ePad connection with LesionTracker; more web-based technologies; discussion of ePad custom widget that will send out connections to remote jobs., PET/CT Lymphoma workshop as extension to lesion tracker.)
#Pete Anderson (Open source tracker)
#Guillaume Pernelle, Imperial College (CNNs, LSTMs, Deep Learning, GPUs)
#Mike Halle, BWH (slicer cross-platform architecture to work for hardware-specific; proxy running cloud that can support interface, Atlas browser is an active project for web-based interface. Slicer success is primarily application-level tools. The community could benefit with architectural study.)
#Louise, Oslo, Norway (high-speed pipelining of image processing for liver resections. )
#Paolo, Catanzaro, Italy (Multiple GPU system architecture)
#Salvatore, Catanzaro, Italy
#Daniel Rubin, Stanford
#Curt Lisle, Knowledgevis (has image web-based workflow systems; Deeply interested in web transition of imaging technologies. Also interested (but not experienced) in deep learning application; particularly feature recognition; small animal imaging applications)
#Charles Guttman, BWH (has MS data, wants to use Docker-based repository. (Boutique looks like a good repository)

===Tcon #1: November 15 ===
*10am Boston time
*Emergent interest in the application of Deep Learning techniques to medical image analysis.

Participants and interests
*#Tina Kapur, BWH -- needle detection
*#Steve Pieper, Isomics - GPUs
*#Andras Lasso, Queens - Slicer expert
*#Frankie Preiswerk, BWH -- hybrid ultrasound and MRI, interested in NVIDIA workshop
*#JC, Kitware -- Slicer expert
*#Mike Halle, BWH -- image feature search using deep learning (w/ Sandy Wells)
*#Peter Neher, DKFZ (filling in for Marco Nolden) -- experience with deep learning with face recognition
*#Nicole Aucoin, BWH -- Slicer expert
*#Alireza Mehrtash, UBC, BWH -- deep learning for prostate interventions, extension server for deep learning for Slicer
*#Daniel Rubin deep learning
*#Krisztina Fischer -- teaching

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 9
!style="width:18%" |Tuesday, January 10
!style="width:18%" |Wednesday, January 11
!style="width:18%" |Thursday, January 12
!style="width:18%" |Friday, January 13
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#faedb6"| '''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|rowspan="2"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-10:30am'''
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|-
|bgcolor="#ffffdd"|'''10:30am-12pm:'''
|'''Talk (Sebastian Ourselin, PhD, UCL)'''
|
|
|
|Project Reporting
|-
|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-2:30pm:''' Project Presentations
|
|
|
|'''1:30-2:30pm:''' [[AMIGO_TourPW2017Winter|AMIGO Tour]]
|-
|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 (Optional) [[2017_Winter_Project_Week/Dinner|Dinner on Thursday Night]]
|
|}

==Calendar==

'''''The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.''''' 

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20170108/20170114
}}

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

='''Projects'''=

*Use this [[2017_Project_Week_Template | Updated Template for project pages]]

== Learning and GPUs ==

== Web Technologies ==

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin)

== IGT ==
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)

== Infrastructure ==
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Documentation and Testing]] (Fan Zhang, Isaiah Norton, Shun Gong, Ye Wu, Lauren J. O'Donnell)

== DICOM ==

= '''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/2017projectweek registration site].

2017 Winter Project Week

2016-12-07T14:28:26Z

Fan: /* Infrastructure */

__NOTOC__
[[image:PW-Winter2017.png|300px]]

'''Welcome to the web page for the 24th Project Week!'''
The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

=='''Logistics''' ==

*'''Dates:''' January 9-13, 2017.
*'''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/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and 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], enhancements to the underlying building blocks [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 open source hackathon event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 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]

==Conference Calls for Preparation==

Domestic conference call number: 800-501-8979 
Access code: 7327389 

[[media:TollFree.png|International conference call numbers]] 
Access code: 7327389 

Weekly, Tuesdays 10am, Boston time from Nov 22, 2016 to Jan 3rd, 2017

===Tcon #4: December 6 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials

Participants
* Tina Kapur (MIT) - organizer
* Steve Pieper (Isomics/BWH)
* Beatriz, JC (Kitware)

===Tcon #3: November 29 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials
Participants
* Tina Kapur (MIT) - organizer; planning Nvidia webinars. Proposal to use Monday as a schedule for the deep learning workshop before workshop begins.
*Steve Pieper (Isomics/BWH) - NVidia update; met with Abdul at NVidia (Medical applications of deep learning). Positive meeting and Slicer might be a reference platform. NVIdia will host a Monday Afternoon session at Project Week and hold outside webinars for basic deep learning information. Considering two or three days of a few hours each for webinar. Discussion of a prize board awarded for demonstrations that Nvidia could use.
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Beatriz, Alexis, and JC (Kitware) - Slicer support and 3 other projects (1) customized childrern's medical, (1) Alex submitted volumetric meshing project in Slicer idea to the NA-MIC email list; have a discussion on Meshing; the goal is for Finite Element analsis and light imaging (2), better MATLAB integration (use Python-like interface). (3) Beatrix - shape analysis algorithms to be added to Slicer based on recently-funded grant.
*JC (Kitware) - integration of iPython and Slicer; Tina Suggested also Deep Infer framework to integrate with Slicer
*Louise Oram (Stockholm) - Specialization of Slicer for Liver surgery, possibly using SliceLet approach or other way to tailor the Slicer UI. Currently customizations need to be in the Extension catalog. Also interested in Liver vessel segmentation project and other Liver segmentation tasks. This might complement with MeVIS lab capability focused on liver. Separate modules for liver surgery that might be integrated together later.
*Frank Pricework (BWH) - General GPU programming; experiment with rehosting algorithms has has previously developed to GPU.
*Paolo, Italy - (Summer Project Week Host)
*Naboo (Old Dominion) - two possible projects, not certain yet - (1) smaller training datasets for medical images, (2) braining atlas segmentation integration with Slicer.
*Curt Lisle (KnowledgeVis) - (1) web-based transition of subset of Slicer capability, (2) Iowa Meshing Module move from 3.6 to 4.7 (with Alex from Kitware); (3) possible integration of web-based volume rendering;
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Eric Seigler - OHIS Cornerstone Lesion Tracker author; Integrating interactive segmentation into the web-based framework

Discussions
*Training deep learning networks with smaller datasets.
*Integrating of projects with Slicer & architecture will be a discussion topic during the week.
*Everybody, be sure to register on the Wiki for the workshop; come up with a title and short description of the project(s) you will work on.
*OK to send info to the NA-MIC email list

===Tcon #2: November 22 ===
*10am Boston time
*Topics: continue Deep Learning, Web-based software
*Participants (interests)
# Tina Kapur, BWH (needle detection)
# Steve Pieper, Isomics (web-based software, GPU computing)
#Mahbub, Old Dominion University (creating architectures for deep learning networks in matlab, bridge to Slicer, MICCAI challenge code into Slicer, make learning faster and with less training)
#Siddiqi, Old Dominion
#Nicole Aucoin, BWH
#Abdul, NVIDIA Business Development (potential deep learning tutorials by web conference before the event, then at the event)
#Able Brown, NVIDIA
#JC, Kitware
#Krisztina Fischer, BWH
#Andrew Beard, MGH (deep learning, parameter estimation from MRI)
#Gordon Harris, MGH
#Laurent Chauvin, ETS Montreal (CNN, GPUs)
#John Toeber, Bremen U
#Lauren O'Donnell, BWH
#Fan Zhang, BWH
#Isaiah Norton, BWH
#Wu Ye, BWH
#Erik Siegler, MGH (Slicer / ePad connection with LesionTracker; more web-based technologies; discussion of ePad custom widget that will send out connections to remote jobs., PET/CT Lymphoma workshop as extension to lesion tracker.)
#Pete Anderson (Open source tracker)
#Guillaume Pernelle, Imperial College (CNNs, LSTMs, Deep Learning, GPUs)
#Mike Halle, BWH (slicer cross-platform architecture to work for hardware-specific; proxy running cloud that can support interface, Atlas browser is an active project for web-based interface. Slicer success is primarily application-level tools. The community could benefit with architectural study.)
#Louise, Oslo, Norway (high-speed pipelining of image processing for liver resections. )
#Paolo, Catanzaro, Italy (Multiple GPU system architecture)
#Salvatore, Catanzaro, Italy
#Daniel Rubin, Stanford
#Curt Lisle, Knowledgevis (has image web-based workflow systems; Deeply interested in web transition of imaging technologies. Also interested (but not experienced) in deep learning application; particularly feature recognition; small animal imaging applications)
#Charles Guttman, BWH (has MS data, wants to use Docker-based repository. (Boutique looks like a good repository)

===Tcon #1: November 15 ===
*10am Boston time
*Emergent interest in the application of Deep Learning techniques to medical image analysis.

Participants and interests
*#Tina Kapur, BWH -- needle detection
*#Steve Pieper, Isomics - GPUs
*#Andras Lasso, Queens - Slicer expert
*#Frankie Preiswerk, BWH -- hybrid ultrasound and MRI, interested in NVIDIA workshop
*#JC, Kitware -- Slicer expert
*#Mike Halle, BWH -- image feature search using deep learning (w/ Sandy Wells)
*#Peter Neher, DKFZ (filling in for Marco Nolden) -- experience with deep learning with face recognition
*#Nicole Aucoin, BWH -- Slicer expert
*#Alireza Mehrtash, UBC, BWH -- deep learning for prostate interventions, extension server for deep learning for Slicer
*#Daniel Rubin deep learning
*#Krisztina Fischer -- teaching

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 9
!style="width:18%" |Tuesday, January 10
!style="width:18%" |Wednesday, January 11
!style="width:18%" |Thursday, January 12
!style="width:18%" |Friday, January 13
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#faedb6"| '''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|rowspan="2"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-10:30am'''
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|-
|bgcolor="#ffffdd"|'''10:30am-12pm:'''
|'''Talk (Sebastian Ourselin, PhD, UCL)'''
|
|
|
|Project Reporting
|-
|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-2:30pm:''' Project Presentations
|
|
|
|'''1:30-2:30pm:''' [[AMIGO_TourPW2017Winter|AMIGO Tour]]
|-
|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 (Optional) [[2017_Winter_Project_Week/Dinner|Dinner on Thursday Night]]
|
|}

==Calendar==

'''''The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.''''' 

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20170108/20170114
}}

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

='''Projects'''=

*Use this [[2017_Project_Week_Template | Updated Template for project pages]]

== Learning and GPUs ==

== Web Technologies ==

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin)

== IGT ==
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)

== Infrastructure ==
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Documentation and Testing]] (Fan Zhang, Isaiah Norton, Shun Gong, Ye Wu, Lauren J. O'Donnell)

== DICOM ==

= '''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/2017projectweek registration site].

2016 Summer Project Week/SlicerDMRIDocumentation

2016-06-14T16:32:48Z

Fan: Created page with "__NOTOC__ <gallery> Image:PW-Summer2016.png|Projects List </gallery> ==Key Investigators== * Lauren J. O'Donnell * Fan Zhang * Isaiah No..."

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

==Key Investigators==
* Lauren J. O'Donnell
* Fan Zhang
* Isaiah Norton

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Tutorials and documentations that explain how to use the modules in SlicerDMRI: https://github.com/SlicerDMRI/SlicerDMRI
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* N/A
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* N/A
</div>
</div>

2016 Summer Project Week

2016-06-14T16:29:01Z

Fan:

__NOTOC__

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

='''Logistics'''=
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
*'''Location:''' Heidelberg, Germany.
**'''Getting to Heidelberg:''' Most will fly into Frankfurt Main International (FRA). At the airport look for "long distance trains". There you can buy a ticket from the machine to Heidelberg Hauptbahnhof (main station), around EUR 25. It usually takes less than an hour, with a change in Mannheim to a regional train. https://www.bahn.de . If you arrive on Sunday you can take a bus from the station to the Old Town or where your hotel is. Heidelberg is pretty small, look for directions on Google Maps. If you arrive on Monday see below on how to get to DKFZ directly.
**'''Monday''' at German Cancer Research Center - DKFZ
*** Enter through the main lobby ( just north of https://goo.gl/maps/e3ZbcsM5KC82, you can't miss it, it's the tallest building on campus with a big "dkfz." on top). The meeting room is on the 8th floor (H824, "Glaskasten", "glass box"). We will leave some instructions how to get there at the reception. The meeting time in the lobby will be 8:45am
*** To get to DKFZ in the morning you can use the Google Maps link above, public transport information is available there. For people staying in the Old Town, near Bismarckplatz or coming from the station it will be most likely Bus #32, exit at stop "Chirurgische Klinik", which is the second one after crossing the Neckar river. More detailed timetables at [http://fahrplanauskunft.vrn.de/vrn/XSLT_TRIP_REQUEST2?language=en the local transportation services VRN]. If you are up early there is also a nice [https://goo.gl/maps/SRRG6x7KDNU2 walk along the river].
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
*Preparatory Conference Calls:
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

='''Agenda'''=
Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:7%" |Time
!style="width:15%" |Monday, June 20 [https://goo.gl/maps/e3ZbcsM5KC82 DKFZ]
!style="width:3%" |Tuesday, June 21 IPCAI
!style="width:15%" |Wednesday, June 22 Congress Hall of CARS
!style="width:15%" |Thursday, June 23 Congress Hall of CARS
!style="width:15%" |Friday, June 24 Congress Hall of CARS
!style="width:15%" |Saturday, June 25 Congress Hall of CARS
|-
|bgcolor="#ffffdd"|'''9am-10am'''
|bgcolor="#ffffff"| What does a Neurosurgeon need from technologists? (Alexandra Golby, MD)
|bgcolor="#ffffff"; rowspan="8"|
|bgcolor="#ffffff"|[[Breakout Session/Shared Software Platform for Ultrasound-Guided Medical Interventions]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''10:00am-10:30am'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''10:30-12pm'''
|bgcolor="#ffffff"| TBD
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="4"|
|-
|bgcolor="#ffffdd"|'''3:00pm-3:30pm'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''3:30pm-5:00pm'''
|bgcolor="#ffffff"| [[Breakout Session/Slicer Extensions]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|}

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

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

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

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

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

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

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

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

='''Projects'''=
* Use this [[2016_Summer_Project_Week_Template | template]] for project pages

=== IGT ===
* [[2016 Summer Project Week/Integrating/Using OpenIGTLink for the communications of Robotics devices | Integrating/Using OpenIGTLink for the Communications of Robotics Devices]] (Scheherazade Kraß, Longquan Chen)
* [[2016 Summer Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Guillaume Pernelle, Andre Mastmeyer, Tina Kapur, Paolo Zaffino)
* [[2016 Summer Project Week/Guided Ultrasound Calibration | Guided Ultrasound Calibration]] (Elvis Chen, Inês Prata, Tamas Ungi)
* [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Thomas Kirchner, Janne Beate Bakeng)
* [[2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink | Integrating PLUS in Applications using OpenIGTLink]] (Christian Askeland, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland, Longquan Chen, Simon Drouin)
* [[2016 Summer Project Week/SliceTracker | SliceTracker for Data Collection and Prostate Biopsy Support ]] (Christian Herz, Peter Behringer, Andrey Fedorov)
* [[2016 Summer Project Week/Sacral Neuromodulation | Sacral Neuromodulation ]] (Javier Pascau, Rocío López, Tamas Ungi)
* [[2016 Summer Project Week/Intra-procedural prostate motion characterization | Prostate Motion Characterization ]] (Peter Behringer, Christian Herz, Andrey Fedorov)
* [[2016 Summer Project Week/Structural-functional measurements | Structural - Functional Relationship Measurements of Tractography Data with fMRI ]] (Lauren J. O'Donnell, Yannick Suter)
* [[2016 Summer Project Week/Uncertainty-aware Information Fusion | Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation]] (Bojan Kocev, Sarah Frisken, William Wells)
* [[2016 Summer Project Week/Slicelet For Ultrasound Acquisition | Slicelet for Ultrasound Acquisition]] (Sarah Frisken, Prashin Unadkat, Steve Pieper)

=== Infrastructure ===
* [[2016 Summer Project Week/3D Lasso Selection | Implementation and Testing Performance of 3-D Lasso Selection within the Segmentation Editor Infrastructure ]] (Davide Punzo, Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2016 Summer Project Week/Segmentations Integration | Integration of Segmentations Infrastructure and Related Modules to Slicer Core]] (Csaba Pinter, Andras Lasso)
* [[2016 Summer Project Week/DICOM Tractography Results | Finalizing DICOM Tractography Results Implementation in DCMTK for BWH Project]] (Michael Onken)

=== Augmented Reality ===
* [[2016 Summer Project Week/VRPN Integration | VRPN Integration]] (Dženan Zukić)
* [[2016 Summer Project Week/OpenVR_integration | OpenVR Integration]] (Adam Rankin)
* [[2016 Summer Project Week/AR with a tablet device in the surgical room | AR with a Tablet Device in the Surgical Room]] (Javier Pascau, David García)

=== Cloud ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)

=== Atlas construction ===
* [[2016 Summer Project Week/Histological Brain Atlas | Tool for the construction of an integrated brain atlas based on histology and MRI]] (Fernando Pérez García)

=== Informatics ===
* [[2016 Summer Project Week/DICOM Parametric Maps | Finalizing DICOM Parametric Map Implementation in DCMTK for QIICR project]] (Michael Onken, Jan Schlamelcher, Andrey Fedorov, Christian Herz)
* [[2016 Summer Project Week/dcmqi | DICOM for Quantitative Imaging (dcmqi) Library]] (Andrey Fedorov, Christian Herz, Marco Nolden, Hans Meine, Csaba Pinter, Steve Pieper, et al)
* [[2016 Summer Project Week/MeVisLab SEG Colors | Support Reading and Writing DICOM Tags for SEG Colors]] (Hans Meine)
* [[2016 Summer Project Week/Segmentation Editor and Terminology | Segmentation Editor and Terminology]] (Nicole Aucoin, Andrey Fedorov, Csaba Pinter)

=== Tutorial===
* [[2016 Summer Project Week/CameraTutorial | How to use Basler Cameras for Medical Applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)
* [[2016 Summer Project Week/SlicerDMRIDocumentation | Tutorials and Documentations in SlicerDMRI]] (Lauren J. O'Donnell, Fan Zhang, Isaiah Norton)

= '''Registrants''' =

'''REGISTRATION:''' Please add your name to this list if you are definitely planning to attend. If you are not already on it, please add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]. We need to know the number of people at DKFZ, so if you are there on Monday, please add "(Mon)" next to your name. Official registration for the event is through the CARS conference at http://www.cars-int.org/cars_2016/registration.html -- which you can do now or onsite.

# Tina Kapur, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA (Mon)
# Ron Kikinis, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA and University of Bremen / Fraunhofer MEVIS, Germany (Mon)
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal. (Mon)
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School (Mon)
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Steve Pieper, Isomics, Inc., USA (Mon)
# Nicole Aucoin, Brigham and Women's Hospital (Mon)
# Simon Drouin, Montreal Neurological Institute (Mon)
# Thomas Kirchner, German Cancer Research Center (Mon)
# Elvis Chen, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Adam Rankin, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Christian Askeland, SINTEF, Norway (Mon)
# Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany
# Longquan Chen, BWH/HMS, Boston, USA (Mon)
# Davide Punzo, Kapteyn Astronomical Institute, Netherlands (Mon)
# Lauren O'Donnell, BWH/HMS
# Yannick Suter, BWH/HMS (Mon)
# Junichi Tokuda, BWH/HMS (Mon)
# Sarah Frisken, BWH/HMS (Mon)
# Prashin Unadkat, BWH/HMS
# Anna Roethe, Charite, Berlin
# Michael Onken, Open Connections, Germany (Mon)
#Jan Schlamelcher, Open Connections/OFFIS, Germany
# Janne Beate Bakeng, SINTEF, Norway
# Ole Vegard Solberg, SINTEF, Norway
# Jon Eiesland, SINTEF, Norway
# Tamas Ungi, Queen's University, Canada (Mon)
# Andras Lasso, Queen's University, Canada (Mon)
# Csaba Pinter, Queen's University, Canada (Mon)
# Thomas Vaughan, Queen's University, Canada (Mon)
#Gabor Fichtinger, Queen's University, Canada
# Javier Pascau, Universidad Carlos III de Madrid, Spain (Mon)
# Verónica García-Vazquez, Universidad Carlos III de Madrid, Spain (Mon)
# Mónica García-Sevilla, Universidad Carlos III de Madrid, Spain (Mon)
# David García-Mato, Universidad Carlos III de Madrid, Spain (Mon)
# Rocío López-Velazco, Universidad Carlos III de Madrid, Spain (Mon)
# Raúl San José, BWH/HMS, Boston
# Pietro Nardeli, BWH/HMS, Boston
# Andrey Fedorov, BWH/HMS, Boston (Mon, Wed, Thu)
# Christian Herz, BWH/HMS, Boston (Mon)
# Frank Lindseth, NTNU/SINTEF, Norway
# Peter Behringer, Basler AG, Germany
# Santhirarajah Mathimugan, Basler AG, Germany
# Koji Kobayashi, Vocsis Corporation, Japan
# David Black, University of Bremen / Fraunhofer MEVIS, Germany (Mon)
#William Wells, BWH/HMS (Mon)
# Attila Nagy, University of Szeged, Hungary (Mon)
# Bojan Kocev, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Sara Fernández Vidal, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Fernando Pérez García, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Marco Nolden, [http://mbi.dkfz-heidelberg.de Medical and Biological Informatics, German Cancer Research Center] (Mon)
# Christian Hansen, [http://isgwww.cs.uni-magdeburg.de/cas/ University of Magdeburg], Germany (Mon)

'''Please don't forget to add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].'''

File:Cli data.zip

2016-03-07T04:20:48Z

Fan: Dataset for CLI application tutorial

Dataset for CLI application tutorial

File:FiberBundleSelectionAndScalarMeasurement TutorialContestWinter2016.zip

2016-02-04T15:57:25Z

Fan: Fan uploaded a new version of File:FiberBundleSelectionAndScalarMeasurement TutorialContestWinter2016.zip

File:FiberBundleSelectionAndScalarMeasurement TutorialContestWinter2016 Snapshot.png

2016-02-04T15:51:13Z

Fan:

File:FiberBundleSelectionAndScalarMeasurement TutorialContestWinter2016.pdf

2016-02-04T15:49:35Z

Fan: Fan uploaded a new version of File:FiberBundleSelectionAndScalarMeasurement TutorialContestWinter2016.pdf

File:FiberBundleSelectionAndScalarMeasurement TutorialContestWinter2016.pdf

2016-02-04T15:44:37Z

Fan: Fan uploaded a new version of File:FiberBundleSelectionAndScalarMeasurement TutorialContestWinter2016.pdf

File:FiberBundleSelectionAndScalarMeasurement TutorialContestWinter2016.pdf

2016-02-04T15:43:57Z

Fan: Fan uploaded a new version of File:FiberBundleSelectionAndScalarMeasurement TutorialContestWinter2016.pdf

2016 Winter Project Week/Projects/TractographyModuleDevelop&Test

2016-01-08T15:39:36Z

Fan: /* Project Description */

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

</gallery>

==Key Investigators==

* Fan Zhang, BWH
* Pegah Kahaliardabili, BWH
* Isaiah Norton, BWH
* Lauren O'Donnell, BWH
* others

==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;"
|
* Update the existing modules in Tractography category of 3D Slicer, and add testing cases .
* Develop new modules for tractography processing.
|
* FiberTractMeasurements (in Slicer now): Compute a set of different scalar measurements (such as FA and trace) from fiber tracts.
* FiberTractClean: Using an input whole brain mask, remove spurious fibers that are very parallel to the surface of the mask (e.g. in skull or CSF). Also remove very short fibers (by default those with fewer than 2 points, which are just an artifact of unsuccessful seeding).
* FiberEndPointFromLabelMap: Allow a user to calculate the number of fiber endpoints touching certain regions according to a label map. The label map is provided by users, which can be generated from, e.g., Freesurfer.
|
* Coding - Finished
* Testing - Finished
* Integration - Ongoing
|}

==Background and References==

2016 Winter Project Week

2016-01-08T15:27:44Z

Fan: /* Tractography */

__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].
 

== 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"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|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) 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]]
 
|'''8:30-9:30am''' MR, US, Mass Spect guided Breast Surgery (Melissa Mallory, Nathalie Agar, Gabrielle Gauvin, Andras Lasso) 
'''9:30-10:30am''' Clinical perspective on Image Guided Neurosurgery (Alexandra Golby) 
'''10:30-11:30am''' Clinical perspective on Multiparametric MRI (Fiona Fennessy) 
'''11:30am-12pm''' Drug Delivery to Brain (Jason White) 
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ----------------- 
'''12pm:''' [[Winter2016TutorialContest|Tutorial Contest Winner Announcement]] 
[[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: Welcome''' 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ----------------- 
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads) 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ----------------- 
'''2:45-4:00pm:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Ultrasound]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ----------------- 

'''4:00-5:30pm:''' [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) 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]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]] 
'''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]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]] 
'''3:30-5:00pm:''' Breakout Session: [[Events:TutorialContestJanuary2016 |2016 Tutorial Contest Review (Kiva)]]
| [[AMIGO Tours#Project Week 22|AMIGO Tour]]
|-
|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 (Optional) [[2016_Winter_Project_Week/Dinner|Dinner on Thursday Night]]
|
|}

==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]]

== IGT ==
* [[2016_Winter_Project_Week/Projects/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External Beam Radiotherapy Planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
* [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin, Thomas Kirchner, Janek Groehl)
*[[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/PLUS | Improvement of PLUS communication with Slicer (skip, see US standardization)]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/SliceTracker | Prostate motion tracking and navigation in Slicer ]] (Christian Herz, Andrey Fedorov, Andras Lasso)
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)
* [[2016_Winter_Project_Week/Projects/GABA_Delivery |Localized GABA delivery via BBB disruption]] (Nick Todd)
* [[2016_Winter_Project_Week/Projects/3DNrrdSequences | Sequences extension support for 3D+t NRRD]] (Adam Rankin)

== 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)

==Image Analysis==
* [[2016_Winter_Project_Week/Projects/CongenitalHeart | Interactive patch-based segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)
* [[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/SphericalWaveletShapeAnalysis|Spherical Wavelet Shape Analysis]] (Yi Gao, Erich Bremer, Allen Tannenbaum, Ron Kikinis)
* [[2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Yi Gao, Nicole Aucoin, Andrey Fedorov)
* [[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/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]] (Sandy Wells, Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Randy Gollub)
* [[2016_Winter_Project_Week/Projects/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich, Andrey Fedorov, Andras Lasso)
* [[2016_Winter_Project_Week/Projects/DSCAnalysis | Dynamic Susceptibility Contrast (DSC) MRI Analysis]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)

* [[2016_Winter_Project_Week/Projects/ShapeAnalysis | Low-dimensional Principal Geodesic Analysis On the Manifold of Diffeomorphisms]] (Miaomiao Zhang, Polina Golland)

==Infrastructure==
*[[2016_Winter_Project_Week/Projects/UpgradeNAMICSlicerWiki|Upgrade the NAMIC + Slicer Web Infrastructure]] (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]] (Nicole Aucoin, Csaba Pinter, 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/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/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)
* [[2016_Winter_Project_Week/Projects/ExploringCollaborationVisualization| Exploring a collaboration in visualization]] (SK Semwal)

= '''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
#Beatriz 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
#Kelli 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
#Jorge Onieva, BWH
#James Ross, BWH
#Raul SanJose, BWH
#Jayashree Kalpathy-Cramer, MGH/HMS
#Daniel Glazer, BWH
#Valentin Demeusy, SPL Intern
#Ameet Jain, Phillips Research
#Utsav Soni, BWH
#Matthew Toews, Ecole de Technologie Superieure
#Isaiah Norton, BWH
#Sean Doyle, MGH
#Stuart Pomerantz, MGH
#Randy Gollub, MGH
#Melissa Mallory, BWH
#Axel Krieger, Children's National Medical Center
#Nobuhiko Hata, BWH
#Carl-Fredrik Westin, BWH/HMS
#Terry Yoo, NLM-NIH/Harvard IACS

2016 Winter Project Week

2016-01-08T15:26:45Z

Fan: /* Tractography */

__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].
 

== 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"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|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) 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]]
 
|'''8:30-9:30am''' MR, US, Mass Spect guided Breast Surgery (Melissa Mallory, Nathalie Agar, Gabrielle Gauvin, Andras Lasso) 
'''9:30-10:30am''' Clinical perspective on Image Guided Neurosurgery (Alexandra Golby) 
'''10:30-11:30am''' Clinical perspective on Multiparametric MRI (Fiona Fennessy) 
'''11:30am-12pm''' Drug Delivery to Brain (Jason White) 
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ----------------- 
'''12pm:''' [[Winter2016TutorialContest|Tutorial Contest Winner Announcement]] 
[[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: Welcome''' 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ----------------- 
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads) 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ----------------- 
'''2:45-4:00pm:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Ultrasound]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ----------------- 

'''4:00-5:30pm:''' [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) 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]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]] 
'''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]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]] 
'''3:30-5:00pm:''' Breakout Session: [[Events:TutorialContestJanuary2016 |2016 Tutorial Contest Review (Kiva)]]
| [[AMIGO Tours#Project Week 22|AMIGO Tour]]
|-
|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 (Optional) [[2016_Winter_Project_Week/Dinner|Dinner on Thursday Night]]
|
|}

==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]]

== IGT ==
* [[2016_Winter_Project_Week/Projects/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External Beam Radiotherapy Planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
* [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin, Thomas Kirchner, Janek Groehl)
*[[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/PLUS | Improvement of PLUS communication with Slicer (skip, see US standardization)]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/SliceTracker | Prostate motion tracking and navigation in Slicer ]] (Christian Herz, Andrey Fedorov, Andras Lasso)
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)
* [[2016_Winter_Project_Week/Projects/GABA_Delivery |Localized GABA delivery via BBB disruption]] (Nick Todd)
* [[2016_Winter_Project_Week/Projects/3DNrrdSequences | Sequences extension support for 3D+t NRRD]] (Adam Rankin)

== 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/TractographyModuleDevelop&Test | Tractography Analysis Module Development and Testing]] (Fan Zhang, Pegah Kahaliardabili, Isaiah Norton, Lauren O'Donnell, others)

==Image Analysis==
* [[2016_Winter_Project_Week/Projects/CongenitalHeart | Interactive patch-based segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)
* [[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/SphericalWaveletShapeAnalysis|Spherical Wavelet Shape Analysis]] (Yi Gao, Erich Bremer, Allen Tannenbaum, Ron Kikinis)
* [[2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Yi Gao, Nicole Aucoin, Andrey Fedorov)
* [[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/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]] (Sandy Wells, Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Randy Gollub)
* [[2016_Winter_Project_Week/Projects/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich, Andrey Fedorov, Andras Lasso)
* [[2016_Winter_Project_Week/Projects/DSCAnalysis | Dynamic Susceptibility Contrast (DSC) MRI Analysis]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)

* [[2016_Winter_Project_Week/Projects/ShapeAnalysis | Low-dimensional Principal Geodesic Analysis On the Manifold of Diffeomorphisms]] (Miaomiao Zhang, Polina Golland)

==Infrastructure==
*[[2016_Winter_Project_Week/Projects/UpgradeNAMICSlicerWiki|Upgrade the NAMIC + Slicer Web Infrastructure]] (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]] (Nicole Aucoin, Csaba Pinter, 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/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/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)
* [[2016_Winter_Project_Week/Projects/ExploringCollaborationVisualization| Exploring a collaboration in visualization]] (SK Semwal)

= '''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
#Beatriz 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
#Kelli 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
#Jorge Onieva, BWH
#James Ross, BWH
#Raul SanJose, BWH
#Jayashree Kalpathy-Cramer, MGH/HMS
#Daniel Glazer, BWH
#Valentin Demeusy, SPL Intern
#Ameet Jain, Phillips Research
#Utsav Soni, BWH
#Matthew Toews, Ecole de Technologie Superieure
#Isaiah Norton, BWH
#Sean Doyle, MGH
#Stuart Pomerantz, MGH
#Randy Gollub, MGH
#Melissa Mallory, BWH
#Axel Krieger, Children's National Medical Center
#Nobuhiko Hata, BWH
#Carl-Fredrik Westin, BWH/HMS
#Terry Yoo, NLM-NIH/Harvard IACS

2016 Winter Project Week/Projects/TractographyModuleDevelop&Test

2016-01-08T15:06:13Z

Fan: /* Project Description */

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

</gallery>

==Key Investigators==

* Fan Zhang, BWH
* Pegah Kahaliardabili, BWH
* Isaiah Norton, BWH
* Lauren O'Donnell, BWH
* others

==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;"
|
* Update the existing modules in Tractography category of 3D Slicer, and add testing cases .
* Develop new modules for tractography processing.
|
* FiberTractMeasurements (in Slicer now): Compute a set of different scalar measurements (such as FA and trace) from fiber tracts.
* FiberTractClean: Using an input whole brain mask, remove spurious fibers that are very parallel to the surface of the mask (e.g. in skull or CSF). Also remove very short fibers (by default those with fewer than 2 points, which are just an artifact of unsuccessful seeding).
* FiberEndPointFromLabelMap: Allow a user to calculate the number of fiber endpoints touching certain regions according to a label map. The label map is provided by users, which can be generated from, e.g., Freesurfer.
|
* Coding - Finishing
* Testing - Finishing
* Integration - Ongoing
|}

==Background and References==