NAMIC Wiki - User contributions [en]

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T15:02:43Z

Semwal: /* Key Investigators */

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

</gallery>

==Key Investigators==

*SK Semwal, Ph.D., University of Colorado, Colorado Springs
*Steve Pieper, Ph.D., Isomics
*Lauren O'Donnell, MD. SPL
*Michael Halle, Ph.D., SPL
*Sonia Pujol, Ph.D., SPL
* Tina Kapur, Ph.D., SPL
* Ron Kikinis, MD, BWH
* Sarah Frisken, MD, SPL

==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;"
|

* To start a collaboration at SPL and learn about Slicer
|

* Measuring topological variations, especially around cancer tissues, could provide effective medicine and cancer treatment.
*Computational tools on volume data sets and algorithms implemented into existing platforms such as slicer (3DSlicer.org) can prove useful if they can help with margins during the operations so that only those cells which needed to be out are taken out, not less not more.
*Dynamically measuring the topological and anatomical variations of medical data sets could lead to applications such as image-guided surgery.
*The challenge is that it is necessary to differentiate between cancer cell and healthy tissue, and because of the technology both false positive and negative cases have been observed along with deformations, which in volume terms means that same spatial voxels are now occupied by different values.
*Caveat: it can also mean that different tissues have the same values as well. One of the demos in the conference clarified that the interface has minimal effect in the process during operation (so as not to burden the surgeon) and also has to be better than what the surgeon is used to seeing.

|

*It is easier to learn from tutorials and they seemed to work quickly -- they are easy to follow.
*For example, first three tutorials are easy and provide effective guidance to run the slicer and write a simple python code as an extension.
*If one is trying to change the basic functionality of the Slicer by implementing something deeper insider the main source code then you will have to consider what you are replacing MUST be better than what is already there – this is a hard task as the code which has made in the core of the slicer support many projects so things should not be worse than before.
*From the commonGL point of view, some other site to consider are glslsandbox.com threeJS.org, lux renderer, 4 page of cheat-sheet for webGL as well, for implementing and experimenting with initial ideas.
|}

==Background and References==

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T14:57:29Z

Semwal: /* Project Description */

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

</gallery>

==Key Investigators==

*SK Semwal, Ph.D., University of Colorado, Colorado Springs
*Steve Pieper, Ph.D., Isomics
*Lauren O'Donnell, MD. SPL
*Michael Halle, Ph.D., SPL
*Sonia Pujol, Ph.D., SPL
* Tina Kapur, Ph.D., SPL
* Ron Kikinis, MD, SPL

==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;"
|

* To start a collaboration at SPL and learn about Slicer
|

* Measuring topological variations, especially around cancer tissues, could provide effective medicine and cancer treatment.
*Computational tools on volume data sets and algorithms implemented into existing platforms such as slicer (3DSlicer.org) can prove useful if they can help with margins during the operations so that only those cells which needed to be out are taken out, not less not more.
*Dynamically measuring the topological and anatomical variations of medical data sets could lead to applications such as image-guided surgery.
*The challenge is that it is necessary to differentiate between cancer cell and healthy tissue, and because of the technology both false positive and negative cases have been observed along with deformations, which in volume terms means that same spatial voxels are now occupied by different values.
*Caveat: it can also mean that different tissues have the same values as well. One of the demos in the conference clarified that the interface has minimal effect in the process during operation (so as not to burden the surgeon) and also has to be better than what the surgeon is used to seeing.

|

*It is easier to learn from tutorials and they seemed to work quickly -- they are easy to follow.
*For example, first three tutorials are easy and provide effective guidance to run the slicer and write a simple python code as an extension.
*If one is trying to change the basic functionality of the Slicer by implementing something deeper insider the main source code then you will have to consider what you are replacing MUST be better than what is already there – this is a hard task as the code which has made in the core of the slicer support many projects so things should not be worse than before.
*From the commonGL point of view, some other site to consider are glslsandbox.com threeJS.org, lux renderer, 4 page of cheat-sheet for webGL as well, for implementing and experimenting with initial ideas.
|}

==Background and References==

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T14:56:47Z

Semwal: /* Project Description */

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

</gallery>

==Key Investigators==

*SK Semwal, Ph.D., University of Colorado, Colorado Springs
*Steve Pieper, Ph.D., Isomics
*Lauren O'Donnell, MD. SPL
*Michael Halle, Ph.D., SPL
*Sonia Pujol, Ph.D., SPL
* Tina Kapur, Ph.D., SPL
* Ron Kikinis, MD, SPL

==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;"
|

* To start a collaboration at SPL and learn about Slicer
|

* Measuring topological variations, especially around cancer tissues, could provide effective medicine and cancer treatment.
*Computational tools on volume data sets and algorithms implemented into existing platforms such as slicer (3DSlicer.org) can prove useful if they can help with margins during the operations so that only those cells which needed to be out are taken out, not less not more.
*Dynamically measuring the topological and anatomical variations of medical data sets could lead to applications such as image-guided surgery.
*The challenge is that it is necessary to differentiate between cancer cell and healthy tissue, and because of the technology both false positive and negative cases have been observed along with deformations, which in volume terms means that same spatial voxels are now occupied by different values.
*Caveat: it can also mean that different tissues have the same values as well. One of the demos in the conference clarified that the interface has minimal effect in the process during operation (so as not to burden the surgeon) and also has to be better than what the surgeon is used to seeing.

|

*It is easier to learn from tutorials and they seemed to work quickly -- they are easy to follow.
*For example, first three tutorials are easy and provide effective guidance to run the slicer and write a simple python code as an extension.
*If one is trying to change the basic functionality of the Slicer by implementing something deeper insider the main source code then you will have to consider what you are replacing MUST be better than what is already there – this is a hard task as the code which has made in the core of the slicer support many projects so things should not be worse than before.
*From the commonGL point of view, some other site to consider areL glslsandbox.com threeJS.org, lux renderer, 4 page of cheat-sheet for webGL as well, for implementing and experimenting with initial ideas.
|}

==Background and References==

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T14:55:38Z

Semwal: /* Project Description */

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

</gallery>

==Key Investigators==

*SK Semwal, Ph.D., University of Colorado, Colorado Springs
*Steve Pieper, Ph.D., Isomics
*Lauren O'Donnell, MD. SPL
*Michael Halle, Ph.D., SPL
*Sonia Pujol, Ph.D., SPL
* Tina Kapur, Ph.D., SPL
* Ron Kikinis, MD, SPL

==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;"
|

* To start a collaboration at SPL and learn about Slicer
|

* Measuring topological variations, especially around cancer tissues, could provide effective medicine and cancer treatment. Computational tools on volume data sets and algorithms implemented into existing platforms such as slicer (3DSlicer.org) can prove useful if they can help with margins during the operations so that only those cells which needed to be out are taken out, not less not more. Dynamically measuring the topological and anatomical variations of medical data sets could lead to applications such as image-guided surgery. The challenge is that it is necessary to differentiate between cancer cell and healthy tissue, and because of the technology both false positive and negative cases have been observed along with deformations, which in volume terms means that same spatial voxels are now occupied by different values. Caveat: it can also mean that different tissues have the same values as well. One of the demos in the conference clarified that the interface has minimal effect in the process during operation (so as not to burden the surgeon) and also has to be better than what the surgeon is used to seeing.

|

*It is easier to learn from tutorials and they seemed to work quickly -- they are easy to follow. For example, first three tutorials are easy and provide effective guidance to run the slicer and write a simple python code as an extension. However, if you are trying to change the basic functionality of the Slicer by implementing something deeper insider the main source code then you will have to consider what you are replacing MUST be better than what is already there – this is a hard task as the code which has made in the core of the slicer support many projects so things should not be worse than before.
*From the commonGL point of view, some other site to consider areL glslsandbox.com threeJS.org, lux renderer, 4 page of cheat-sheet for webGL as well, for implementing and experimenting with initial ideas.
|}

==Background and References==

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T14:55:12Z

Semwal: /* Project Description */

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

</gallery>

==Key Investigators==

*SK Semwal, Ph.D., University of Colorado, Colorado Springs
*Steve Pieper, Ph.D., Isomics
*Lauren O'Donnell, MD. SPL
*Michael Halle, Ph.D., SPL
*Sonia Pujol, Ph.D., SPL
* Tina Kapur, Ph.D., SPL
* Ron Kikinis, MD, SPL

==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;"
|

* To start a collaboration at SPL and learn about Slicer
|

* Measuring topological variations, especially around cancer tissues, could provide effective medicine and cancer treatment. Computational tools on volume data sets and algorithms implemented into existing platforms such as slicer (3DSlicer.org) can prove useful if they can help with margins during the operations so that only those cells which needed to be out are taken out, not less not more. Dynamically measuring the topological and anatomical variations of medical data sets could lead to applications such as image-guided surgery. The challenge is that it is necessary to differentiate between cancer cell and healthy tissue, and because of the technology both false positive and negative cases have been observed along with deformations, which in volume terms means that same spatial voxels are now occupied by different values. Caveat: it can also mean that different tissues have the same values as well. One of the demos in the conference clarified that the interface has minimal effect in the process during operation (so as not to burden the surgeon) and also has to be better than what the surgeon is used to seeing.

|

*It is easier to learn from tutorials and they seemed to work quickly -- they are easy to follow. For example, first three tutorials are easy and provide effective guidance to run the slicer and write a simple python code as an extension. However, if you are trying to change the basic functionality of the Slicer by implementing something deeper insider the main source code then you will have to consider what you are replacing MUST be better than what is already there – this is a hard task as the code which has made in the core of the slicer support many projects so things should not be worse than before.
From the commonGL point of view, some other site to consider areL glslsandbox.com threeJS.org, lux renderer, 4 page of cheat-sheet for webGL as well, for implementing and experimenting with initial ideas.
|}

==Background and References==

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T14:50:01Z

Semwal: /* Project Description */

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

</gallery>

==Key Investigators==

*SK Semwal, Ph.D., University of Colorado, Colorado Springs
*Steve Pieper, Ph.D., Isomics
*Lauren O'Donnell, MD. SPL
*Michael Halle, Ph.D., SPL
*Sonia Pujol, Ph.D., SPL
* Tina Kapur, Ph.D., SPL
* Ron Kikinis, MD, SPL

==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;"
|

* To start a collaboration at SPL and learn about Slicer
|

* Measuring topological variations, especially around cancer tissues, could provide effective medicine and cancer treatment. What I learnt quickly was that, from my point of view, computational tools on volume data sets and algorithms implementing into existing platforms such as slicer (3DSlicer.org) can prove useful if they can help with margins during the operations so that only those cells which needed to be out are taken out, not less not more. Dynamically measuring the topological and anatomical variations of medical data sets could lead to applications such as image-guided surgery. The challenge is that it is necessary to differentiate between cancer cell and healthy tissue, and because of the technology both false positive and negative cases have been observed along with deformations, which in volume terms means that same spatial voxels are now occupied by different values. Ofcourse, it can also mean that different tissues have the same values as well. One of the demos in the conference clarified that the interface has minimally effect the process during operation (so as not to burden the surgeon) and also has to be better than what the surgeon is used to seeing.

|

*From Beginner’s point of view – it is easier to learn from tutorials and then seemed to work quickly. For example, first three tutorials are easy and provide effective guidance to run the slicer and write a simple python code as an extension. However, if you are trying to change the basic functionality of the Slicer by implementing something deeper insider the main source code then you will have to consider what you are replacing MUST be better than what is already there – this is a hard task as the code which has made in the core of the slicer support many projects so things should not be worse than before.
Finally he recommended, that I play with glslsandbox.com threeJS.org, lux renderer, 4 page of cheat-sheet for webGL as well for implementing and experimenting with initial ideas.
|}

==Background and References==

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T14:49:42Z

Semwal: /* Project Description */

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

</gallery>

==Key Investigators==

*SK Semwal, Ph.D., University of Colorado, Colorado Springs
*Steve Pieper, Ph.D., Isomics
*Lauren O'Donnell, MD. SPL
*Michael Halle, Ph.D., SPL
*Sonia Pujol, Ph.D., SPL
* Tina Kapur, Ph.D., SPL
* Ron Kikinis, MD, SPL

==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;"
|

* To start a collaboration at SPL and learn about Slicer
|

* Measuring topological variations, especially around cancer tissues, could provide effective medicine and cancer treatment. What I learnt quickly was that, from my point of view, computational tools on volume data sets and algorithms implementing into existing platforms such as slicer (3DSlicer.org) can prove useful if they can help with margins during the operations so that only those cells which needed to be out are taken out, not less not more. Dynamically measuring the topological and anatomical variations of medical data sets could lead to applications such as image-guided surgery. The challenge is that it is necessary to differentiate between cancer cell and healthy tissue, and because of the technology both false positive and negative cases have been observed along with deformations, which in volume terms means that same spatial voxels are now occupied by different values. Ofcourse, it can also mean that different tissues have the same values as well. One of the demos in the conference clarified that the interface has minimally effect the process during operation (so as not to burden the surgeon) and also has to be better than what the surgeon is used to seeing.
From Beginner’s point of view – it is easier to learn from tutorials and then seemed to work quickly. For example, first three tutorials are easy and provide effective guidance to run the slicer and write a simple python code as an extension. However, if you are trying to change the basic functionality of the Slicer by implementing something deeper insider the main source code then you will have to consider what you are replacing MUST be better than what is already there – this is a hard task as the code which has made in the core of the slicer support many projects so things should not be worse than before.
Finally he recommended, that I play with glslsandbox.com threeJS.org, lux renderer, 4 page of cheat-sheet for webGL as well for implementing and experimenting with initial ideas.

|

*From Beginner’s point of view – it is easier to learn from tutorials and then seemed to work quickly. For example, first three tutorials are easy and provide effective guidance to run the slicer and write a simple python code as an extension. However, if you are trying to change the basic functionality of the Slicer by implementing something deeper insider the main source code then you will have to consider what you are replacing MUST be better than what is already there – this is a hard task as the code which has made in the core of the slicer support many projects so things should not be worse than before.
Finally he recommended, that I play with glslsandbox.com threeJS.org, lux renderer, 4 page of cheat-sheet for webGL as well for implementing and experimenting with initial ideas.
|}

==Background and References==

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T14:48:58Z

Semwal: /* Project Description */

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

</gallery>

==Key Investigators==

*SK Semwal, Ph.D., University of Colorado, Colorado Springs
*Steve Pieper, Ph.D., Isomics
*Lauren O'Donnell, MD. SPL
*Michael Halle, Ph.D., SPL
*Sonia Pujol, Ph.D., SPL
* Tina Kapur, Ph.D., SPL
* Ron Kikinis, MD, SPL

==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;"
|

* To start a collaboration at SPL and learn about Slicer
|

* Measuring topological variations, especially around cancer tissues, could provide effective medicine and cancer treatment. What I learnt quickly was that, from my point of view, computational tools on volume data sets and algorithms implementing into existing platforms such as slicer (3DSlicer.org) can prove useful if they can help with margins during the operations so that only those cells which needed to be out are taken out, not less not more. Dynamically measuring the topological and anatomical variations of medical data sets could lead to applications such as image-guided surgery. The challenge is that it is necessary to differentiate between cancer cell and healthy tissue, and because of the technology both false positive and negative cases have been observed along with deformations, which in volume terms means that same spatial voxels are now occupied by different values. Ofcourse, it can also mean that different tissues have the same values as well. One of the demos in the conference clarified that the interface has minimally effect the process during operation (so as not to burden the surgeon) and also has to be better than what the surgeon is used to seeing.
From Beginner’s point of view – it is easier to learn from tutorials and then seemed to work quickly. For example, first three tutorials are easy and provide effective guidance to run the slicer and write a simple python code as an extension. However, if you are trying to change the basic functionality of the Slicer by implementing something deeper insider the main source code then you will have to consider what you are replacing MUST be better than what is already there – this is a hard task as the code which has made in the core of the slicer support many projects so things should not be worse than before.
Finally he recommended, that I play with glslsandbox.com threeJS.org, lux renderer, 4 page of cheat-sheet for webGL as well for implementing and experimenting with initial ideas.

|

*
|}

==Background and References==

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T14:47:37Z

Semwal: /* Key Investigators */

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T14:44:52Z

Semwal: /* Key Investigators */

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T14:44:03Z

Semwal: /* Key Investigators */

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T14:32:36Z

Semwal: /* Project Description */

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T14:30:53Z

Semwal: /* Key Investigators */

2016 Winter Project Week/Projects/ExploringCollaborationVisualization

2016-01-08T14:30:21Z

Semwal: Created page with "__NOTOC__ <gallery> Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the left..."

2016 Winter Project Week

2016-01-08T14:29:30Z

Semwal: /* Infrastructure */

__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)
* [[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/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/CongenitalHeart | Interactive patch-based segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)
* [[2016_Winter_Project_Week/Projects/DSCAnalysis | Dynamic Susceptibility Contrast (DSC) MRI Analysis]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)

* [[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/CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week/Projects/Data Persisting | Mechanism to Persist Clinical User Data from Different Modules Based on SQLite and/or other Database Engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/Workflows | Workflow Module that Enables the Navigation and Data Sharing between Different Modules in a Clinical Workflow ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/AIMInteroperability | AIM for Interoperability]] (Hans Meine, Andrey Fedorov, ??)
* [[2016_Winter_Project_Week/Projects/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