2017 Winter Project Week/PyRadiomics

2017-01-13T16:30:48Z

Fedorov: /* Background and References */

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


</gallery>

==Key Investigators==

* Joost van Griethuysen
* Hugo Aerts
* Steve Pieper
* Jean-Christophe Fillion-Robin
* Andrey Fedorov

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

* Introduce PyRadiomics to the community
|

* Present, meet collaborators...
* Discuss issues related to integration with Slicer: external packages, numpy version, Slicer module UI
* Discuss issues related to enhancing performance using C code
|

* Introduced PyRadiomics to the community
* There are still some issues with the packaging of the extension, SlicerRadiomics. Numpy issue is resolved, PyRadiomics works with numpy 1.9.2, adjusted minimum requirements. Once these issues are resolved, it will be made publicly available in the [http://github.com/Radiomics Github Radiomics Organisation].
* C code performance enhancement is written, but is still causing some issues during compilation. Switch setup to use skbuild and cmake. Latest (offline) tests work with setup.py develop and setup.py test.
* Issues related to building SlicerRadiomics have been fixed, extension can now be built and used in the built version in the basic form
* Issues related to packaging SlicerRadiomics have been identified (limitations of Slicer infrastructure packaging external python packages); JC identified the solution approach, and the issue will be resolved soon, we expect the extension to be available publicly within a month
|}

==Background and References==

* [https://Github.com/Radiomics/pyradiomics GitHub Repository]
* [http://pyradiomics.readthedocs.io Documentation]
* https://Github.com/Radiomics/SlicerRadiomics

2017 Winter Project Week/PyRadiomics

2017-01-13T16:30:22Z

Fedorov: /* Project Description */

File:SlicerRadiomics.jpg

2017-01-13T16:26:13Z

Fedorov:

2017 Winter Project Week/PyRadiomics

2017-01-13T16:25:33Z

Fedorov:

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


</gallery>

==Key Investigators==

* Joost van Griethuysen
* Hugo Aerts
* Steve Pieper
* Jean-Christophe Fillion-Robin
* Andrey Fedorov

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

* Introduce PyRadiomics to the community
|

* Present, meet collaborators...
* Discuss issues related to integration with Slicer: external packages, numpy version, Slicer module UI
* Discuss issues related to enhancing performance using C code
|

* Introduced PyRadiomics to the community
* There are still some issues with the packaging of the extension, SlicerRadiomics. Numpy issue is resolved, PyRadiomics works with numpy 1.9.2, adjusted minimum requirements. Once these issues are resolved, it will be made publicly available in the [http://github.com/Radiomics Github Radiomics Organisation].
* C code performance enhancement is written, but is still causing some issues during compilation. Switch setup to use skbuild and cmake. Latest (offline) tests work with setup.py develop and setup.py test.
|}

==Background and References==

* [https://Github.com/Radiomics/pyradiomics GitHub Repository]
* [http://pyradiomics.readthedocs.io Documentation]

2017 Winter Project Week/dcmqi

2017-01-13T15:58:38Z

Fedorov: /* Project Description */

2017 Winter Project Week/UpdatingCommunityForums

2017-01-13T15:45:48Z

Fedorov: /* Background and References */

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

</gallery>

==Key Investigators==
* Andrey Fedorov
* Andras Lasso
* Mike Halle
* Steve Pieper
* Isaiah Norton
* Tina Kapur
* Teodora Szasz
* The COMMUNITY

==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;"
|

* Discuss the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Consider mailing list proposal to move Slicer and possibly several related discussion forums to the Discourse platform.
* Discuss new community-interaction possibilities such as Gitter.
* Consider the long-discussed proposals to move to github hosting for the web site
|

* Breakfast breakout discussion - Tuesday 8:30am - Ron is confirmed to join!
* Document the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Discourse
** Assess Discourse with broader community.
** Identify funding mechanism.
** Logistics to move if chosen:
*** Hosting: fully-managed service? vs DigitalOcean or other provider?
*** Domain name: 'discourse.slicer.org'?
*** SSL certificate for domain: can use Letsencrypt after host and DNS record are configured
*** SMTP service: included in hosted option. For self-hosting: strongly recommended, and mandatory for email-only signup and mailing list mode; not mandatory if using only oauth provider (GitHub/Google/etc.)
* GitHub
** Identify remaining action items to complete the long-awaited move of Slicer source hosting to GitHub.
* Web-site
** Organize web-site content on github
** Consider moving hosting to github
|

* Discussion took place about general principles of the decision making process (outlined below)
** Participants: Ron, JC, Steve, Andras, Isaiah, Csaba, Andrey
** Specific to mailing list to forum migration, Ron's main concern is that with recurring payments there is a possibility of things falling through the cracks and potential interruption of the service
* Gitter
** in a small group discussion, decided against using gitter for Slicer community at least for now; although it would provide an advantage of having a place for developers to chat in real time and get quick help, we cannot guarantee critical mass of experienced developers participating, and it would not replace mailing list or forum
** to support project week communication, propose to use gitter channel under [https://github.com/NA-MIC github NA-MIC community] that JC already created (contact JC to join); we could use that community to discuss projects and connect people in advance of the next project week
|}

==Decision-making policy draft==
1. Given the topic of interest, initiate discussion on the mailing list

2. Identify a small circle of community members that are interested to study the topic in more depth

3. Take the discussion off the general list, work on the analysis of options and alternatives, summarize findings on the wiki or similar

4. Announce the in-depth discussion of the topic for the Slicer Community hangout, encourage anyone that is interested in weighing in on the topic to join the discussion. If there is someone who is interested to participate in the discussion, but cannot join the meeting due to conflict, they should notify the leaders of the given project and identify the time suitable for everyone. (Note: we might want to advertise Slicer Hangout appropriately, include agenda in the announcement email directly, and advertise the event to Slicer users as well as developers)

5. Hopefully, reach consensus at the hangout and proceed with the agreed plan.

==Background and References==
* Discourse discussion / proposal on the Slicer mailing list
** http://slicer-users.65878.n3.nabble.com/Starting-Q-A-Community-on-StackExchange-tp4031469p4031496.html
* Discussions of GitHub hosting:
** http://slicer-devel.65872.n3.nabble.com/Slicer-binary-download-is-extremely-slow-consider-github-for-hosting-packaged-binaries-td4036985.html
* [https://meta.discourse.org/t/discourse-and-slack-or-other-group-chat-apps-like-irc-hipchat-gitter-etc/39630 Discourse and Slack (or other group chat apps like IRC, HipChat, Gitter, etc)]
* https://www.slicer.org/wiki/Documentation/Labs/DocumentationImprovments
* NodeBB - like Discourse https://nodebb.org/pricing
* https://experts.feverbee.com/t/discourse-vs-nodebb/1384/6
* Comparison of forum software: https://en.wikipedia.org/wiki/Comparison_of_Internet_forum_software
* NA-MIC community on github: https://github.com/NA-MIC

==Requirements==
* [high] Get email notification about specific themes (releases, announcements, sub-community, such as shape analysis, RT, ...)
* [high] Import existing users
* [high] Code highlight
* [high] indexing by Google
* [medium] Authentication with github
* [medium] Option for yearly billing
* [medium] Polls (vote on features to be developed, collect community feedback for decisions, etc)
* [medium] Permalinks of thread for easy sharing by email
* [low] Answer posts through email
* [low] Vote for good answers, mark accepted answer
* [low] Support cross referencing of Github issues

2017 Winter Project Week/UpdatingCommunityForums

2017-01-13T15:45:31Z

Fedorov: /* Project Description */

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

</gallery>

==Key Investigators==
* Andrey Fedorov
* Andras Lasso
* Mike Halle
* Steve Pieper
* Isaiah Norton
* Tina Kapur
* Teodora Szasz
* The COMMUNITY

==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;"
|

* Discuss the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Consider mailing list proposal to move Slicer and possibly several related discussion forums to the Discourse platform.
* Discuss new community-interaction possibilities such as Gitter.
* Consider the long-discussed proposals to move to github hosting for the web site
|

* Breakfast breakout discussion - Tuesday 8:30am - Ron is confirmed to join!
* Document the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Discourse
** Assess Discourse with broader community.
** Identify funding mechanism.
** Logistics to move if chosen:
*** Hosting: fully-managed service? vs DigitalOcean or other provider?
*** Domain name: 'discourse.slicer.org'?
*** SSL certificate for domain: can use Letsencrypt after host and DNS record are configured
*** SMTP service: included in hosted option. For self-hosting: strongly recommended, and mandatory for email-only signup and mailing list mode; not mandatory if using only oauth provider (GitHub/Google/etc.)
* GitHub
** Identify remaining action items to complete the long-awaited move of Slicer source hosting to GitHub.
* Web-site
** Organize web-site content on github
** Consider moving hosting to github
|

* Discussion took place about general principles of the decision making process (outlined below)
** Participants: Ron, JC, Steve, Andras, Isaiah, Csaba, Andrey
** Specific to mailing list to forum migration, Ron's main concern is that with recurring payments there is a possibility of things falling through the cracks and potential interruption of the service
* Gitter
** in a small group discussion, decided against using gitter for Slicer community at least for now; although it would provide an advantage of having a place for developers to chat in real time and get quick help, we cannot guarantee critical mass of experienced developers participating, and it would not replace mailing list or forum
** to support project week communication, propose to use gitter channel under [https://github.com/NA-MIC github NA-MIC community] that JC already created (contact JC to join); we could use that community to discuss projects and connect people in advance of the next project week
|}

==Decision-making policy draft==
1. Given the topic of interest, initiate discussion on the mailing list

2. Identify a small circle of community members that are interested to study the topic in more depth

3. Take the discussion off the general list, work on the analysis of options and alternatives, summarize findings on the wiki or similar

4. Announce the in-depth discussion of the topic for the Slicer Community hangout, encourage anyone that is interested in weighing in on the topic to join the discussion. If there is someone who is interested to participate in the discussion, but cannot join the meeting due to conflict, they should notify the leaders of the given project and identify the time suitable for everyone. (Note: we might want to advertise Slicer Hangout appropriately, include agenda in the announcement email directly, and advertise the event to Slicer users as well as developers)

5. Hopefully, reach consensus at the hangout and proceed with the agreed plan.

==Background and References==
* Discourse discussion / proposal on the Slicer mailing list
** http://slicer-users.65878.n3.nabble.com/Starting-Q-A-Community-on-StackExchange-tp4031469p4031496.html
* Discussions of GitHub hosting:
** http://slicer-devel.65872.n3.nabble.com/Slicer-binary-download-is-extremely-slow-consider-github-for-hosting-packaged-binaries-td4036985.html
* [https://meta.discourse.org/t/discourse-and-slack-or-other-group-chat-apps-like-irc-hipchat-gitter-etc/39630 Discourse and Slack (or other group chat apps like IRC, HipChat, Gitter, etc)]
* https://www.slicer.org/wiki/Documentation/Labs/DocumentationImprovments
* NodeBB - like Discourse https://nodebb.org/pricing
* https://experts.feverbee.com/t/discourse-vs-nodebb/1384/6
* Comparison of forum software: https://en.wikipedia.org/wiki/Comparison_of_Internet_forum_software

==Requirements==
* [high] Get email notification about specific themes (releases, announcements, sub-community, such as shape analysis, RT, ...)
* [high] Import existing users
* [high] Code highlight
* [high] indexing by Google
* [medium] Authentication with github
* [medium] Option for yearly billing
* [medium] Polls (vote on features to be developed, collect community feedback for decisions, etc)
* [medium] Permalinks of thread for easy sharing by email
* [low] Answer posts through email
* [low] Vote for good answers, mark accepted answer
* [low] Support cross referencing of Github issues

2017 Tutorial Contest

2017-01-12T19:44:52Z

Fedorov: /* Tutorials */

[[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=
*[http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerPathology Slicer Pathology] (Erich Bremer/Andriy Fedorov)
*[[Media:SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pptx| Simple Python Tool for Quality Control of DWI data (Laurent Chauvin)]]
*[https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM (Beatriz Paniagua)]
*[http://www.na-mic.org/Wiki/images/a/a6/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing] (Csaba Pinter)
*[[Media:ROSIGTLTutorial_Tokuda_Jan2017.pptx| Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink (Junichi Tokuda)]]
*[[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.
*Judges:
**Rebekka Lauer, Humboldt-University, Berlin
**Parvin Mousavi, Brigham and Women's Hospital
**Peter Anderson
**Hongtao Zhang, Hebei General Hospital
**Michael Chae, Monash University

=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

2017-01-12T19:44:42Z

Fedorov: /* Tutorials */

[[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=
*[wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerPathology Slicer Pathology] (Erich Bremer/Andriy Fedorov)
*[[Media:SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pptx| Simple Python Tool for Quality Control of DWI data (Laurent Chauvin)]]
*[https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM (Beatriz Paniagua)]
*[http://www.na-mic.org/Wiki/images/a/a6/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing] (Csaba Pinter)
*[[Media:ROSIGTLTutorial_Tokuda_Jan2017.pptx| Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink (Junichi Tokuda)]]
*[[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.
*Judges:
**Rebekka Lauer, Humboldt-University, Berlin
**Parvin Mousavi, Brigham and Women's Hospital
**Peter Anderson
**Hongtao Zhang, Hebei General Hospital
**Michael Chae, Monash University

=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 Winter Project Week/UpdatingCommunityForums

2017-01-11T23:18:25Z

Fedorov: /* Requirements */

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

</gallery>

==Key Investigators==
* Andrey Fedorov
* Andras Lasso
* Mike Halle
* Steve Pieper
* Isaiah Norton
* Tina Kapur
* Teodora Szasz
* The COMMUNITY

==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;"
|

* Discuss the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Consider mailing list proposal to move Slicer and possibly several related discussion forums to the Discourse platform.
* Discuss new community-interaction possibilities such as Gitter.
* Consider the long-discussed proposals to move to github hosting for the web site
|

* Breakfast breakout discussion - Tuesday 8:30am - Ron is confirmed to join!
* Document the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Discourse
** Assess Discourse with broader community.
** Identify funding mechanism.
** Logistics to move if chosen:
*** Hosting: fully-managed service? vs DigitalOcean or other provider?
*** Domain name: 'discourse.slicer.org'?
*** SSL certificate for domain: can use Letsencrypt after host and DNS record are configured
*** SMTP service: included in hosted option. For self-hosting: strongly recommended, and mandatory for email-only signup and mailing list mode; not mandatory if using only oauth provider (GitHub/Google/etc.)
* GitHub
** Identify remaining action items to complete the long-awaited move of Slicer source hosting to GitHub.
* Web-site
** Organize web-site content on github
** Consider moving hosting to github
|

* Discussion took place about general principles of the decision making process (outlined below)
** Participants: Ron, JC, Steve, Andras, Isaiah, Csaba, Andrey
** Specific to mailing list to forum migration, Ron's main concern is that with recurring payments there is a possibility of things falling through the cracks and potential interruption of the service
|}

==Decision-making policy draft==
1. Given the topic of interest, initiate discussion on the mailing list

2. Identify a small circle of community members that are interested to study the topic in more depth

3. Take the discussion off the general list, work on the analysis of options and alternatives, summarize findings on the wiki or similar

4. Announce the in-depth discussion of the topic for the Slicer Community hangout, encourage anyone that is interested in weighing in on the topic to join the discussion. If there is someone who is interested to participate in the discussion, but cannot join the meeting due to conflict, they should notify the leaders of the given project and identify the time suitable for everyone. (Note: we might want to advertise Slicer Hangout appropriately, include agenda in the announcement email directly, and advertise the event to Slicer users as well as developers)

5. Hopefully, reach consensus at the hangout and proceed with the agreed plan.

==Background and References==
* Discourse discussion / proposal on the Slicer mailing list
** http://slicer-users.65878.n3.nabble.com/Starting-Q-A-Community-on-StackExchange-tp4031469p4031496.html
* Discussions of GitHub hosting:
** http://slicer-devel.65872.n3.nabble.com/Slicer-binary-download-is-extremely-slow-consider-github-for-hosting-packaged-binaries-td4036985.html
* [https://meta.discourse.org/t/discourse-and-slack-or-other-group-chat-apps-like-irc-hipchat-gitter-etc/39630 Discourse and Slack (or other group chat apps like IRC, HipChat, Gitter, etc)]
* https://www.slicer.org/wiki/Documentation/Labs/DocumentationImprovments
* NodeBB - like Discourse https://nodebb.org/pricing
* https://experts.feverbee.com/t/discourse-vs-nodebb/1384/6
* Comparison of forum software: https://en.wikipedia.org/wiki/Comparison_of_Internet_forum_software

==Requirements==
* [high] Get email notification about specific themes (releases, announcements, sub-community, such as shape analysis, RT, ...)
* [high] Import existing users
* [high] Code highlight
* [high] indexing by Google
* [medium] Authentication with github
* [medium] Option for yearly billing
* [medium] Polls (vote on features to be developed, collect community feedback for decisions, etc)
* [medium] Permalinks of thread for easy sharing by email
* [low] Answer posts through email
* [low] Vote for good answers, mark accepted answer
* [low] Support cross referencing of Github issues

2017 Winter Project Week/UpdatingCommunityForums

2017-01-11T03:55:38Z

Fedorov: /* Background and References */

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

</gallery>

==Key Investigators==
* Andrey Fedorov
* Andras Lasso
* Mike Halle
* Steve Pieper
* Isaiah Norton
* Tina Kapur
* Teodora Szasz
* The COMMUNITY

==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;"
|

* Discuss the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Consider mailing list proposal to move Slicer and possibly several related discussion forums to the Discourse platform.
* Discuss new community-interaction possibilities such as Gitter.
* Consider the long-discussed proposals to move to github hosting for the web site
|

* Breakfast breakout discussion - Tuesday 8:30am - Ron is confirmed to join!
* Document the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Discourse
** Assess Discourse with broader community.
** Identify funding mechanism.
** Logistics to move if chosen:
*** Hosting: fully-managed service? vs DigitalOcean or other provider?
*** Domain name: 'discourse.slicer.org'?
*** SSL certificate for domain: can use Letsencrypt after host and DNS record are configured
*** SMTP service: included in hosted option. For self-hosting: strongly recommended, and mandatory for email-only signup and mailing list mode; not mandatory if using only oauth provider (GitHub/Google/etc.)
* GitHub
** Identify remaining action items to complete the long-awaited move of Slicer source hosting to GitHub.
* Web-site
** Organize web-site content on github
** Consider moving hosting to github
|

* Discussion took place about general principles of the decision making process (outlined below)
** Participants: Ron, JC, Steve, Andras, Isaiah, Csaba, Andrey
** Specific to mailing list to forum migration, Ron's main concern is that with recurring payments there is a possibility of things falling through the cracks and potential interruption of the service
|}

==Decision-making policy draft==
1. Given the topic of interest, initiate discussion on the mailing list

2. Identify a small circle of community members that are interested to study the topic in more depth

3. Take the discussion off the general list, work on the analysis of options and alternatives, summarize findings on the wiki or similar

4. Announce the in-depth discussion of the topic for the Slicer Community hangout, encourage anyone that is interested in weighing in on the topic to join the discussion. If there is someone who is interested to participate in the discussion, but cannot join the meeting due to conflict, they should notify the leaders of the given project and identify the time suitable for everyone. (Note: we might want to advertise Slicer Hangout appropriately, include agenda in the announcement email directly, and advertise the event to Slicer users as well as developers)

5. Hopefully, reach consensus at the hangout and proceed with the agreed plan.

==Background and References==
* Discourse discussion / proposal on the Slicer mailing list
** http://slicer-users.65878.n3.nabble.com/Starting-Q-A-Community-on-StackExchange-tp4031469p4031496.html
* Discussions of GitHub hosting:
** http://slicer-devel.65872.n3.nabble.com/Slicer-binary-download-is-extremely-slow-consider-github-for-hosting-packaged-binaries-td4036985.html
* [https://meta.discourse.org/t/discourse-and-slack-or-other-group-chat-apps-like-irc-hipchat-gitter-etc/39630 Discourse and Slack (or other group chat apps like IRC, HipChat, Gitter, etc)]
* https://www.slicer.org/wiki/Documentation/Labs/DocumentationImprovments
* NodeBB - like Discourse https://nodebb.org/pricing
* https://experts.feverbee.com/t/discourse-vs-nodebb/1384/6
* Comparison of forum software: https://en.wikipedia.org/wiki/Comparison_of_Internet_forum_software

2017 Winter Project Week/UpdatingCommunityForums

2017-01-11T03:47:41Z

Fedorov: /* Decision-making policy draft */

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

</gallery>

==Key Investigators==
* Andrey Fedorov
* Andras Lasso
* Mike Halle
* Steve Pieper
* Isaiah Norton
* Tina Kapur
* Teodora Szasz
* The COMMUNITY

==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;"
|

* Discuss the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Consider mailing list proposal to move Slicer and possibly several related discussion forums to the Discourse platform.
* Discuss new community-interaction possibilities such as Gitter.
* Consider the long-discussed proposals to move to github hosting for the web site
|

* Breakfast breakout discussion - Tuesday 8:30am - Ron is confirmed to join!
* Document the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Discourse
** Assess Discourse with broader community.
** Identify funding mechanism.
** Logistics to move if chosen:
*** Hosting: fully-managed service? vs DigitalOcean or other provider?
*** Domain name: 'discourse.slicer.org'?
*** SSL certificate for domain: can use Letsencrypt after host and DNS record are configured
*** SMTP service: included in hosted option. For self-hosting: strongly recommended, and mandatory for email-only signup and mailing list mode; not mandatory if using only oauth provider (GitHub/Google/etc.)
* GitHub
** Identify remaining action items to complete the long-awaited move of Slicer source hosting to GitHub.
* Web-site
** Organize web-site content on github
** Consider moving hosting to github
|

* Discussion took place about general principles of the decision making process (outlined below)
** Participants: Ron, JC, Steve, Andras, Isaiah, Csaba, Andrey
** Specific to mailing list to forum migration, Ron's main concern is that with recurring payments there is a possibility of things falling through the cracks and potential interruption of the service
|}

==Decision-making policy draft==
1. Given the topic of interest, initiate discussion on the mailing list

2. Identify a small circle of community members that are interested to study the topic in more depth

3. Take the discussion off the general list, work on the analysis of options and alternatives, summarize findings on the wiki or similar

4. Announce the in-depth discussion of the topic for the Slicer Community hangout, encourage anyone that is interested in weighing in on the topic to join the discussion. If there is someone who is interested to participate in the discussion, but cannot join the meeting due to conflict, they should notify the leaders of the given project and identify the time suitable for everyone. (Note: we might want to advertise Slicer Hangout appropriately, include agenda in the announcement email directly, and advertise the event to Slicer users as well as developers)

5. Hopefully, reach consensus at the hangout and proceed with the agreed plan.

==Background and References==
* Discourse discussion / proposal on the Slicer mailing list
** http://slicer-users.65878.n3.nabble.com/Starting-Q-A-Community-on-StackExchange-tp4031469p4031496.html
* Discussions of GitHub hosting:
** http://slicer-devel.65872.n3.nabble.com/Slicer-binary-download-is-extremely-slow-consider-github-for-hosting-packaged-binaries-td4036985.html
* [https://meta.discourse.org/t/discourse-and-slack-or-other-group-chat-apps-like-irc-hipchat-gitter-etc/39630 Discourse and Slack (or other group chat apps like IRC, HipChat, Gitter, etc)]
* https://www.slicer.org/wiki/Documentation/Labs/DocumentationImprovments
* NodeBB - like Discourse https://nodebb.org/pricing
* https://experts.feverbee.com/t/discourse-vs-nodebb/1384/6

2017 Winter Project Week/UpdatingCommunityForums

2017-01-11T03:46:25Z

Fedorov: /* Decision-making policy draft */

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

</gallery>

==Key Investigators==
* Andrey Fedorov
* Andras Lasso
* Mike Halle
* Steve Pieper
* Isaiah Norton
* Tina Kapur
* Teodora Szasz
* The COMMUNITY

==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;"
|

* Discuss the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Consider mailing list proposal to move Slicer and possibly several related discussion forums to the Discourse platform.
* Discuss new community-interaction possibilities such as Gitter.
* Consider the long-discussed proposals to move to github hosting for the web site
|

* Breakfast breakout discussion - Tuesday 8:30am - Ron is confirmed to join!
* Document the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Discourse
** Assess Discourse with broader community.
** Identify funding mechanism.
** Logistics to move if chosen:
*** Hosting: fully-managed service? vs DigitalOcean or other provider?
*** Domain name: 'discourse.slicer.org'?
*** SSL certificate for domain: can use Letsencrypt after host and DNS record are configured
*** SMTP service: included in hosted option. For self-hosting: strongly recommended, and mandatory for email-only signup and mailing list mode; not mandatory if using only oauth provider (GitHub/Google/etc.)
* GitHub
** Identify remaining action items to complete the long-awaited move of Slicer source hosting to GitHub.
* Web-site
** Organize web-site content on github
** Consider moving hosting to github
|

* Discussion took place about general principles of the decision making process (outlined below)
** Participants: Ron, JC, Steve, Andras, Isaiah, Csaba, Andrey
** Specific to mailing list to forum migration, Ron's main concern is that with recurring payments there is a possibility of things falling through the cracks and potential interruption of the service
|}

==Decision-making policy draft==
1. Given the topic of interest, initiate discussion on the mailing list

2. Identify a small circle of community members that are interested to study the topic in more depth

3. Take the discussion off the general list, work on the analysis of options and alternatives, summarize findings on the wiki or similar

4. Announce the in-depth discussion of the topic for the Slicer Community hangout, encourage anyone that is interested in weighing in on the topic to join the discussion (Note: we might want to advertise Slicer Hangout appropriately, include agenda in the announcement email directly, and advertise the event to Slicer users as well as developers)

5. Hopefully, reach consensus at the hangout and proceed with the agreed plan.

==Background and References==
* Discourse discussion / proposal on the Slicer mailing list
** http://slicer-users.65878.n3.nabble.com/Starting-Q-A-Community-on-StackExchange-tp4031469p4031496.html
* Discussions of GitHub hosting:
** http://slicer-devel.65872.n3.nabble.com/Slicer-binary-download-is-extremely-slow-consider-github-for-hosting-packaged-binaries-td4036985.html
* [https://meta.discourse.org/t/discourse-and-slack-or-other-group-chat-apps-like-irc-hipchat-gitter-etc/39630 Discourse and Slack (or other group chat apps like IRC, HipChat, Gitter, etc)]
* https://www.slicer.org/wiki/Documentation/Labs/DocumentationImprovments
* NodeBB - like Discourse https://nodebb.org/pricing
* https://experts.feverbee.com/t/discourse-vs-nodebb/1384/6

2017 Winter Project Week/UpdatingCommunityForums

2017-01-11T03:46:03Z

Fedorov:

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

</gallery>

==Key Investigators==
* Andrey Fedorov
* Andras Lasso
* Mike Halle
* Steve Pieper
* Isaiah Norton
* Tina Kapur
* Teodora Szasz
* The COMMUNITY

==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;"
|

* Discuss the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Consider mailing list proposal to move Slicer and possibly several related discussion forums to the Discourse platform.
* Discuss new community-interaction possibilities such as Gitter.
* Consider the long-discussed proposals to move to github hosting for the web site
|

* Breakfast breakout discussion - Tuesday 8:30am - Ron is confirmed to join!
* Document the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Discourse
** Assess Discourse with broader community.
** Identify funding mechanism.
** Logistics to move if chosen:
*** Hosting: fully-managed service? vs DigitalOcean or other provider?
*** Domain name: 'discourse.slicer.org'?
*** SSL certificate for domain: can use Letsencrypt after host and DNS record are configured
*** SMTP service: included in hosted option. For self-hosting: strongly recommended, and mandatory for email-only signup and mailing list mode; not mandatory if using only oauth provider (GitHub/Google/etc.)
* GitHub
** Identify remaining action items to complete the long-awaited move of Slicer source hosting to GitHub.
* Web-site
** Organize web-site content on github
** Consider moving hosting to github
|

* Discussion took place about general principles of the decision making process (outlined below)
** Participants: Ron, JC, Steve, Andras, Isaiah, Csaba, Andrey
** Specific to mailing list to forum migration, Ron's main concern is that with recurring payments there is a possibility of things falling through the cracks and potential interruption of the service
|}

==Decision-making policy draft==
1. Given the topic of interest, initiate discussion on the mailing list
2. Identify a small circle of community members that are interested to study the topic in more depth
3. Take the discussion off the general list, work on the analysis of options and alternatives, summarize findings on the wiki or similar
4. Announce the in-depth discussion of the topic for the Slicer Community hangout, encourage anyone that is interested in weighing in on the topic to join the discussion (Note: we might want to advertise Slicer Hangout appropriately, include agenda in the announcement email directly, and advertise the event to Slicer users as well as developers)
5. Hopefully, reach consensus at the hangout and proceed with the agreed plan.

==Background and References==
* Discourse discussion / proposal on the Slicer mailing list
** http://slicer-users.65878.n3.nabble.com/Starting-Q-A-Community-on-StackExchange-tp4031469p4031496.html
* Discussions of GitHub hosting:
** http://slicer-devel.65872.n3.nabble.com/Slicer-binary-download-is-extremely-slow-consider-github-for-hosting-packaged-binaries-td4036985.html
* [https://meta.discourse.org/t/discourse-and-slack-or-other-group-chat-apps-like-irc-hipchat-gitter-etc/39630 Discourse and Slack (or other group chat apps like IRC, HipChat, Gitter, etc)]
* https://www.slicer.org/wiki/Documentation/Labs/DocumentationImprovments
* NodeBB - like Discourse https://nodebb.org/pricing
* https://experts.feverbee.com/t/discourse-vs-nodebb/1384/6

2017 Winter Project Week/UpdatingCommunityForums

2017-01-11T03:41:45Z

Fedorov: /* Project Description */

2017 Winter Project Week/PkModeling

2017-01-11T02:54:26Z

Fedorov: /* Key Investigators */

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

</gallery>

==Key Investigators==
* Andrew Beers, Jayashree Kalpathy-Cramer, MGH
* Jim Miller, GE

==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;"
|

* PkModeling, a Slicer module meant to derive DCE pharmokinetic parameters via the two and three parameter Tofts model, has not had perfect accuracy on phantoms for the Tofts model. We intend to troubleshoot and address these errors, which we have determined from our previous research to be problems with the implementations of the Tofts model.
* Make the module more usable and/or intuitive to casual users.
* Although it may be a larger Slicer infrastructure project, add support to Slicer for 4D Niftis, the main file format of our lab.
|

* Debug the module with several test cases and deconstruct the models steps to see where error is introduced to its calculations.
* Model UI off of successful modules, and seek advice from attendants of Project Week.
* Probe conversion between MultiVolumes and 4D Nifti files.
|

*
|}

==Background and References==

2017 Winter Project Week/QuantitativeReporting

2017-01-11T02:33:12Z

Fedorov: /* Background and References */

==Key Investigators==

* Christian Herz, BWH
* Andrey Fedorov, BWH
* Andras Lasso, Queen's
* Csaba Pinter, Queen's

==Project Description==
An extension of 3D Slicer to support segmentation-based measurements with DICOM-based import and export of the results.
{| 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;"
|

* utilizes dcmqi library for reading/writing of DICOM SEG/SR
* demonstrate Quantitative Reporting extension
* improve documentation
* discuss next steps and specific open issues
|

* get rid of hacks that hide SegmentEditor components individually by iterating over GUI components
* add functionality for continuing a saved report
* communication of measurements tables and integrated support into Slicer Table node (CSV/JSON/other approaches - see https://github.com/QIICR/QuantitativeReporting/issues/105)
* integration of measurement quantities/units into Slicer for volume nodes
|

|}

[[image:QuantitativeReporting-screenshot.jpg|1024px]]

==Background and References==

* dcmqi home page: http://github.com/qiicr/dcmqi
* Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2016) DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research. PeerJ 4:e2057 https://doi.org/10.7717/peerj.2057

2017 Winter Project Week/dcmqi

2017-01-11T02:32:33Z

Fedorov: /* Background and References */

2017 Winter Project Week/UpdatingCommunityForums

2017-01-09T19:57:02Z

Fedorov: /* Key Investigators */

2017 Winter Project Week/UpdatingCommunityForums

2017-01-09T18:32:41Z

Fedorov: /* Project Description */