NAMIC Wiki - User contributions [en]

File:ProofOfConcept.gif

2017-01-13T16:36:16Z

Johan.andruejol: Johan.andruejol uploaded a new version of File:ProofOfConcept.gif

2017 Winter Project Week/SlicerGeometryModifier

2017-01-13T16:33:12Z

Johan.andruejol: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
Image:InterfaceExample.png|Mock-up of an interface in Slicer as of now.
Image:TranslationInBender.png|Example Of Translation in Blender.
Image:RotationInBender.png|Example Of Rotation in Blender.
Image:ScalingInBender.png|Example Of Scaling Blender.

</gallery>

==Key Investigators==

* Johan Andruejol (Kitware, Inc.)
* Beatriz Paniagua (Kitware, Inc.)

==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;"
|

* Slicer lacks interactive support for moving, rotating and scaling objects in the user interface. It would be nice to be able to interact directly with an object.
* The main objective of this project would be to allow user to change a transform parameters with through interaction. The objects under that transform should be automatically updated accordingly and the interaction representation should always match the transform properties.
* We would also like to explore adding new markup types in Slicer such as planes and paths. Those would be integrated using the infrastructure in place.
|

* Add a translation widget which:
** Allows the user to move the objects under a transform.
** Updates the transform interactively.
** Updates itself whenever the transform is changed.
** At this point, we would ask for feedback to the community.
* Explore the addition of a simple markup type like a plane.
|

* Discussions about design and what the feature should ultimately look like:
** The 3D widget should encompass all the nodes that are about to be transformed (around their bounding box).
** The 2D widget should be fairly simple, like an ROI around the node to be transformed
** Interaction between interaction widgets and transform vizualisation to be determined once the feature is more mature.
* Proof of concept: [[File:ProofOfConcept.gif|thumbnail|Proof of concept]]
|}

==Background and References==

* Other good examples
** https://threejs.org/editor/
** http://download.autodesk.com/us/maya/2010help/index.html?url=Transforming_objects_Use_manipulators.htm,topicNumber=d0e65921
** http://download.autodesk.com/us/maya/2010help/index.html?url=Transforming_objects_Use_the_Universal_Manipulator.htm,topicNumber=d0e66424

2017 Winter Project Week/SlicerGeometryModifier

2017-01-13T15:11:46Z

Johan.andruejol: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
Image:InterfaceExample.png|Mock-up of an interface in Slicer as of now.
Image:TranslationInBender.png|Example Of Translation in Blender.
Image:RotationInBender.png|Example Of Rotation in Blender.
Image:ScalingInBender.png|Example Of Scaling Blender.

</gallery>

==Key Investigators==

* Johan Andruejol (Kitware, Inc.)
* Beatriz Paniagua (Kitware, Inc.)

==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;"
|

* Slicer lacks interactive support for moving, rotating and scaling objects in the user interface. It would be nice to be able to interact directly with an object.
* The main objective of this project would be to allow user to change a transform parameters with through interaction. The objects under that transform should be automatically updated accordingly and the interaction representation should always match the transform properties.
* We would also like to explore adding new markup types in Slicer such as planes and paths. Those would be integrated using the infrastructure in place.
|

* Add a translation widget which:
** Allows the user to move the objects under a transform.
** Updates the transform interactively.
** Updates itself whenever the transform is changed.
** At this point, we would ask for feedback to the community.
* Explore the addition of a simple markup type like a plane.
|

* Discussions about design and what the feature should ultimately look like.
* Proof of concept: [[File:ProofOfConcept.gif|thumbnail|Proof of concept]]
|}

==Background and References==

* Other good examples
** https://threejs.org/editor/
** http://download.autodesk.com/us/maya/2010help/index.html?url=Transforming_objects_Use_manipulators.htm,topicNumber=d0e65921
** http://download.autodesk.com/us/maya/2010help/index.html?url=Transforming_objects_Use_the_Universal_Manipulator.htm,topicNumber=d0e66424

File:ProofOfConcept.gif

2017-01-12T14:05:54Z

Johan.andruejol:

2017 Winter Project Week/SlicerGeometryModifier

2017-01-12T14:04:13Z

Johan.andruejol:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
Image:InterfaceExample.png|Mock-up of an interface in Slicer as of now.
Image:TranslationInBender.png|Example Of Translation in Blender.
Image:RotationInBender.png|Example Of Rotation in Blender.
Image:ScalingInBender.png|Example Of Scaling Blender.

</gallery>

==Key Investigators==

* Johan Andruejol (Kitware, Inc.)
* Beatriz Paniagua (Kitware, Inc.)

==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;"
|

* Slicer lacks interactive support for moving, rotating and scaling objects in the user interface. It would be nice to be able to interact directly with an object.
* The main objective of this project would be to allow user to change a transform parameters with through interaction. The objects under that transform should be automatically updated accordingly and the interaction representation should always match the transform properties.
* We would also like to explore adding new markup types in Slicer such as planes and paths. Those would be integrated using the infrastructure in place.
|

* Add a translation widget which:
** Allows the user to move the objects under a transform.
** Updates the transform interactively.
** Updates itself whenever the transform is changed.
** At this point, we would ask for feedback to the community.
* Explore the addition of a simple markup type like a plane.
|

* [[File:ProofOfConcept.gif|thumbnail|Proof of concept]]
|}

==Background and References==

* Other good examples
** https://threejs.org/editor/
** http://download.autodesk.com/us/maya/2010help/index.html?url=Transforming_objects_Use_manipulators.htm,topicNumber=d0e65921
** http://download.autodesk.com/us/maya/2010help/index.html?url=Transforming_objects_Use_the_Universal_Manipulator.htm,topicNumber=d0e66424

2017 Winter Project Week/Dinner

2017-01-06T18:30:13Z

Johan.andruejol: /* RSVPs */

==Dinner Specs==

*Date and Time: Thursday, January 12, 6pm
*Location: Desi Dhaba, 401 Massachusetts Ave, Cambridge (about 10 minute walk from MIT)
*Food: Indian. (Veg and non-veg options, naan, rice)
*Cost: (TBD, last year was $25) - CASH ONLY! To be given to Katie Mastrogiacomo (kmast@bwh) during the week. She will provide receipts.
*Drinks: tap water is included in this price. Beyond that each person pays individually for their drinks.

==RSVPs==

#Curt Lisle
#Tina Kapur
# Andrey Fedorov
# Csaba Pinter
# Simon Drouin
# Alireza Mehrtash
# Henrik G. Jensen
# Beatriz Paniagua
# Beatriz Paniagua's +1
# Hans Meine
# Johan Andruejol

2017 Winter Project Week/SlicerGeometryModifier

2017-01-03T16:17:48Z

Johan.andruejol: Bender -> Blender

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
Image:InterfaceExample.png|Mock-up of an interface in Slicer as of now.
Image:TranslationInBender.png|Example Of Translation in Blender.
Image:RotationInBender.png|Example Of Rotation in Blender.
Image:ScalingInBender.png|Example Of Scaling Blender.

</gallery>

==Key Investigators==

* Johan Andruejol (Kitware, Inc.)
* Beatriz Paniagua (Kitware, Inc.)

==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;"
|

* Slicer lacks interactive support for moving, rotating and scaling objects in the user interface. It would be nice to be able to interact directly with an object.
* The main objective of this project would be to allow user to change a transform parameters with through interaction. The objects under that transform should be automatically updated accordingly and the interaction representation should always match the transform properties.
* We would also like to explore adding new markup types in Slicer such as planes and paths. Those would be integrated using the infrastructure in place.
|

* Add a translation widget which:
** Allows the user to move the objects under a transform.
** Updates the transform interactively.
** Updates itself whenever the transform is changed.
** At this point, we would ask for feedback to the community.
* Explore the addition of a simple markup type like a plane.
|

*
|}

==Background and References==

2017 Winter Project Week/SlicerGeometryModifier

2017-01-03T16:02:27Z

Johan.andruejol: Move image to gallery

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
Image:InterfaceExample.png|Mock-up of an interface in Slicer as of now.
Image:TranslationInBender.png|Example Of Translation in Bender.
Image:RotationInBender.png|Example Of Rotation in Bender.
Image:ScalingInBender.png|Example Of Scaling Bender.

</gallery>

==Key Investigators==

* Johan Andruejol (Kitware, Inc.)
* Beatriz Paniagua (Kitware, Inc.)

==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;"
|

* Slicer lacks interactive support for moving, rotating and scaling objects in the user interface. It would be nice to be able to interact directly with an object.
* The main objective of this project would be to allow user to change a transform parameters with through interaction. The objects under that transform should be automatically updated accordingly and the interaction representation should always match the transform properties.
* We would also like to explore adding new markup types in Slicer such as planes and paths. Those would be integrated using the infrastructure in place.
|

* Add a translation widget which:
** Allows the user to move the objects under a transform.
** Updates the transform interactively.
** Updates itself whenever the transform is changed.
** At this point, we would ask for feedback to the community.
* Explore the addition of a simple markup type like a plane.
|

*
|}

==Background and References==

2017 Winter Project Week

2017-01-03T15:53:22Z

Johan.andruejol: Move SlicerGeometryModifier to 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.
*'''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, Tina Kapur)
* [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)

== Web Technologies ==
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer)
* [[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle)
* [[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)

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

== 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)
* [[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)

==dMRI==
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (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-Frederik Westin)
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, 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/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)
* [[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
* [[2017 Winter Project Week/DiPy_in_Slicer | DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)
* [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
* [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua)

==To be Categorized==

* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
* [[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
* [[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
* [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)

= '''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].

# A, Zeina :: SHBOUL
# 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
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital
# Chae, Michael :: Monash University
# Chauvin, Laurent :: ETS
# Dalca, Adrian :: Massachusetts Institute of Technology
# Fedorov, Andriy :: Brigham and Women's Hospital
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.
# Girault, Alexis :: Kitware, Inc.
# Golland, Polina :: Massachusetts Institute of Technology
# Gollub, Randy :: Massachusetts General Hospital
# Gong, Shun :: Brigham and Women's Hospital
# Guerrier de Dumast, Priscille :: University of Michigan
# Harris, Gordon :: Massachusetts General Hospital
# Herz, Christian :: Brigham and Women's Hospital
# Hong, Sungmin :: New York University
# Hosny, Ahmed :: Dana-Farber
# Jagadeesan, Jayender :: Brigham and Women's Hospital
# Kapur, Tina :: Brigham and Women's Hospital
# Kikinis, Ron :: Brigham and Women's Hospital
# 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
# 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
# Sharp, Gregory :: Massachusetts General Hospital
# Sridharan, Patmaa :: University of Pennsylvania-CBICA
# Vidyaratne, Lasitha :: Old Dominion University
# Ye, Wu :: Brigham and Women's Hospital
# Zeleznik, Roman :: DFCI
# Zhang, Fan :: Brigham and Women's Hospital
# Zhang, Miaomiao :: Massachusetts Institute of Technology
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital

2017 Winter Project Week/SlicerGeometryModifier

2017-01-03T14:48:39Z

Johan.andruejol: Remove JC from contributors

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

</gallery>

==Key Investigators==

* Johan Andruejol (Kitware, Inc.)
* Beatriz Paniagua (Kitware, Inc.)

==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;"
|

* Slicer lacks interactive support for moving, rotating and scaling objects in the user interface. It would be nice to be able to interact directly with an object.
* The main objective of this project would be to allow user to change a transform parameters with through interaction. The objects under that transform should be automatically updated accordingly and the interaction representation should always match the transform properties.
* We would also like to explore adding new markup types in Slicer such as planes and paths. Those would be integrated using the infrastructure in place.
|

* Add a translation widget which:
** Allows the user to move the objects under a transform.
** Updates the transform interactively.
** Updates itself whenever the transform is changed.
** At this point, we would ask for feedback to the community.
* Explore the addition of a simple markup type like a plane.
|

*
|}

==Background and References==

[[File:InterfaceExample.png|thumb|center|Mock-up of an interface in Slicer as of now.]]
[[File:TranslationInBender.png|thumb|center|Example Of Translation in Bender]]
[[File:RotationInBender.png|thumb|center|Example Of Rotation in Bender]]
[[File:ScalingInBender.png|thumb|center|Example Of Scaling Bender]]

2017 Winter Project Week/SlicerGeometryModifier

2017-01-03T14:45:25Z

Johan.andruejol: Image resize 2

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

</gallery>

==Key Investigators==

* Johan Andruejol (Kitware, Inc.)
* JC Fillon-Robin (Kitware, Inc.)
* Beatriz Paniagua (Kitware, Inc.)

==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;"
|

* Slicer lacks interactive support for moving, rotating and scaling objects in the user interface. It would be nice to be able to interact directly with an object.
* The main objective of this project would be to allow user to change a transform parameters with through interaction. The objects under that transform should be automatically updated accordingly and the interaction representation should always match the transform properties.
* We would also like to explore adding new markup types in Slicer such as planes and paths. Those would be integrated using the infrastructure in place.
|

* Add a translation widget which:
** Allows the user to move the objects under a transform.
** Updates the transform interactively.
** Updates itself whenever the transform is changed.
** At this point, we would ask for feedback to the community.
* Explore the addition of a simple markup type like a plane.
|

*
|}

==Background and References==

[[File:InterfaceExample.png|thumb|center|Mock-up of an interface in Slicer as of now.]]
[[File:TranslationInBender.png|thumb|center|Example Of Translation in Bender]]
[[File:RotationInBender.png|thumb|center|Example Of Rotation in Bender]]
[[File:ScalingInBender.png|thumb|center|Example Of Scaling Bender]]

2017 Winter Project Week/SlicerGeometryModifier

2017-01-03T14:43:54Z

Johan.andruejol: Image resize

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

</gallery>

==Key Investigators==

* Johan Andruejol (Kitware, Inc.)
* JC Fillon-Robin (Kitware, Inc.)
* Beatriz Paniagua (Kitware, Inc.)

==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;"
|

* Slicer lacks interactive support for moving, rotating and scaling objects in the user interface. It would be nice to be able to interact directly with an object.
* The main objective of this project would be to allow user to change a transform parameters with through interaction. The objects under that transform should be automatically updated accordingly and the interaction representation should always match the transform properties.
* We would also like to explore adding new markup types in Slicer such as planes and paths. Those would be integrated using the infrastructure in place.
|

* Add a translation widget which:
** Allows the user to move the objects under a transform.
** Updates the transform interactively.
** Updates itself whenever the transform is changed.
** At this point, we would ask for feedback to the community.
* Explore the addition of a simple markup type like a plane.
|

*
|}

==Background and References==

[[File:InterfaceExample.png|thumb|Mock-up of an interface in Slicer as of now.]]
[[File:TranslationInBender.png|Example Of Translation in Bender]]
[[File:RotationInBender.png|Example Of Rotation in Bender]]
[[File:ScalingInBender.png|Example Of Scaling Bender]]

2017 Winter Project Week/SlicerGeometryModifier

2017-01-03T14:41:11Z

Johan.andruejol: Add images

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

</gallery>

==Key Investigators==

* Johan Andruejol (Kitware, Inc.)
* JC Fillon-Robin (Kitware, Inc.)
* Beatriz Paniagua (Kitware, Inc.)

==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;"
|

* Slicer lacks interactive support for moving, rotating and scaling objects in the user interface. It would be nice to be able to interact directly with an object.
* The main objective of this project would be to allow user to change a transform parameters with through interaction. The objects under that transform should be automatically updated accordingly and the interaction representation should always match the transform properties.
* We would also like to explore adding new markup types in Slicer such as planes and paths. Those would be integrated using the infrastructure in place.
|

* Add a translation widget which:
** Allows the user to move the objects under a transform.
** Updates the transform interactively.
** Updates itself whenever the transform is changed.
** At this point, we would ask for feedback to the community.
* Explore the addition of a simple markup type like a plane.
|

*
|}

==Background and References==

[[File:InterfaceExample.png|Mock-up of an interface in Slicer as of now.]]
[[File:TranslationInBender.png|Example Of Translation in Bender]]
[[File:RotationInBender.png|Example Of Rotation in Bender]]
[[File:ScalingInBender.png|Example Of Scaling Bender]]

File:ScalingInBender.png

2017-01-03T14:40:48Z

Johan.andruejol:

File:RotationInBender.png

2017-01-03T14:40:26Z

Johan.andruejol:

File:TranslationInBender.png

2017-01-03T14:39:37Z

Johan.andruejol:

File:InterfaceExample.png

2017-01-03T14:39:12Z

Johan.andruejol:

2017 Winter Project Week/SlicerGeometryModifier

2017-01-03T14:38:44Z

Johan.andruejol: /* 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==

* Johan Andruejol (Kitware, Inc.)
* JC Fillon-Robin (Kitware, Inc.)
* Beatriz Paniagua (Kitware, Inc.)

==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;"
|

* Slicer lacks interactive support for moving, rotating and scaling objects in the user interface. It would be nice to be able to interact directly with an object.
* The main objective of this project would be to allow user to change a transform parameters with through interaction. The objects under that transform should be automatically updated accordingly and the interaction representation should always match the transform properties.
* We would also like to explore adding new markup types in Slicer such as planes and paths. Those would be integrated using the infrastructure in place.
|

* Add a translation widget which:
** Allows the user to move the objects under a transform.
** Updates the transform interactively.
** Updates itself whenever the transform is changed.
** At this point, we would ask for feedback to the community.
* Explore the addition of a simple markup type like a plane.
|

*
|}

==Background and References==

[[File:InterfaceExample.png|thumbnail|Mock-up of an interface in Slicer as of now.]]
[[File:TranslationInBender.png|thumbnail|Example Of Translation in Bender]]
[[File:RotationInBender.png|thumbnail|Example Of Rotation in Bender]]
[[File:ScalingInBender.png|thumbnail|Example Of Scaling Bender]]

2017 Winter Project Week/SlicerGeometryModifier

2017-01-03T14:30:41Z

Johan.andruejol:

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

</gallery>

==Key Investigators==

* Johan Andruejol (Kitware, Inc.)
* JC Fillon-Robin (Kitware, Inc.)
* Beatriz Paniagua (Kitware, Inc.)

==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;"
|

* Slicer lacks interactive support for moving, rotating and scaling objects in the user interface. It would be nice to be able to interact directly with an object.
* The main objective of this project would be to allow user to change a transform parameters with through interaction. The objects under that transform should be automatically updated accordingly and the interaction representation should always match the transform properties.
* We would also like to explore adding new markup types in Slicer such as planes and paths. Those would be integrated using the infrastructure in place.
|

* Add a translation widget which:
** Allows the user to move the objects under a transform.
** Updates the transform interactively.
** Updates itself whenever the transform is changed.
** At this point, we would ask for feedback to the community.
* Explore the addition of a simple markup type like a plane.
|

*
|}

==Background and References==

2017 Winter Project Week/SlicerGeometryModifier

2017-01-03T14:29:01Z

Johan.andruejol: First draft of SlicerGeometryModifier page

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

</gallery>

==Key Investigators==

* Johan Andruejol (Kitware, Inc.)
* JC Fillon-Robin (Kitware, Inc.)
* Beatriz Paniagua (Kitware, Inc.)

==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;"
|

* Slicer lacks interactive support for moving, rotating and scaling objects in the user interface. It would be nice to be able to interact directly with an object.
* The main objective of this project would be to allow user to change a transform parameters with through interaction. The objects under that transform should be automatically updated accordingly and the interaction representation should always match the transform properties.
* We would also like to explore adding new markup types in Slicer such as planes and paths. Those would be integrated using the infrastructure in place.
|

* Add a translation widget which:
** Allows the user to move the objects under a transform.
** Updates the transform interactively.
** Updates itself whenever the transform is changed.
** At this point, we would ask for feedback to the community.
* Explore the addition of a simple markup type like a plane.
|

*
|}

==Background and References==


==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;"
|

*
|

*
|

*
|}

==Background and References==

2016 Winter Project Week/Projects/CLIImprovement

2016-01-08T15:18:17Z

Johan.andruejol: /* Project Description */

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

</gallery>

==Key Investigators==
* Johan Andruejol (Kitware Inc)

==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;"
|

* Improve the CLI piping robustness
* Improve the CLI testing coverage
* Explore the creation of an utility to pipe CLIs easily
|

* Fix the issue raised by this pull request: https://github.com/Slicer/Slicer/pull/358
* Add simple python testing to call multiple CLIs in a row
* Add testing for running CLIs in parrallel
|

* Completed:
** CLI testing: Pull request here to solve issue for runnning CLIs in parallel and in a row: https://github.com/Slicer/Slicer/pull/438
**-> Integrated in r24834
* TODO:
** More testing for CLI behavior: https://github.com/Slicer/Slicer/pull/441
** Experimental branch for CLIPipeline: https://github.com/vovythevov/Slicer/blob/CLIPipelineNode/Modules/Scripted/CLIPipelineModule/CLIPipelineModule.py#L350-L377
|}

==Background and References==

2016 Winter Project Week/Projects/CLIImprovement

2016-01-08T15:17:45Z

Johan.andruejol: /* Project Description */

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

</gallery>

==Key Investigators==
* Johan Andruejol (Kitware Inc)

==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;"
|

* Improve the CLI piping robustness
* Improve the CLI testing coverage
* Explore the creation of an utility to pipe CLIs easily
|

* Fix the issue raised by this pull request: https://github.com/Slicer/Slicer/pull/358
* Add simple python testing to call multiple CLIs in a row
* Add testing for running CLIs in parrallel
|

* Completed:
** CLI testing: Pull request here to solve issue for runnning CLIs in parallel and in a row: https://github.com/Slicer/Slicer/pull/438
**-> Integrated in r24834
* TODO:
** More testing for CLI behavior: https://github.com/Slicer/Slicer/pull/441

** Experimental branch for CLIPipeline: https://github.com/vovythevov/Slicer/blob/CLIPipelineNode/Modules/Scripted/CLIPipelineModule/CLIPipelineModule.py#L350-L377
|}

==Background and References==

2016 Winter Project Week/Projects/CLIImprovement

2016-01-08T15:07:40Z

Johan.andruejol: /* Project Description */

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

</gallery>

==Key Investigators==
* Johan Andruejol (Kitware Inc)

==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;"
|

* Improve the CLI piping robustness
* Improve the CLI testing coverage
* Explore the creation of an utility to pipe CLIs easily
|

* Fix the issue raised by this pull request: https://github.com/Slicer/Slicer/pull/358
* Add simple python testing to call multiple CLIs in a row
* Add testing for running CLIs in parrallel
|

* Completed:
** CLI testing: Pull request here to solve issue for runnning CLIs in parallel and in a row: https://github.com/Slicer/Slicer/pull/438
**-> Integrated in r24834
* TODO:
** Experimental branch for CLIPipeline: https://github.com/vovythevov/Slicer/blob/CLIPipelineNode/Modules/Scripted/CLIPipelineModule/CLIPipelineModule.py#L350-L377
** More testing for CLI behavior: https://github.com/Slicer/Slicer/pull/441
|}

==Background and References==

2016 Winter Project Week/Projects/CLIImprovement

2016-01-08T14:14:13Z

Johan.andruejol: /* Project Description */

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

</gallery>

==Key Investigators==
* Johan Andruejol (Kitware Inc)

==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;"
|

* Improve the CLI piping robustness
* Improve the CLI testing coverage
* Explore the creation of an utility to pipe CLIs easily
|

* Fix the issue raised by this pull request: https://github.com/Slicer/Slicer/pull/358 (Fixed)
* Add simple python testing to call multiple CLIs in a row (Fixed)
* Add testing for running CLIs in parrallel (Fixed)
|

* Pull request here to solve issue for runnning CLIs in parallel and in a row: https://github.com/Slicer/Slicer/pull/438
-> Integrated in r24834
* Experimental branch for CLIPipeline: https://github.com/vovythevov/Slicer/blob/CLIPipelineNode/Modules/Scripted/CLIPipelineModule/CLIPipelineModule.py#L350-L377
* More testing for CLI behavior: https://github.com/Slicer/Slicer/pull/441
|}

==Background and References==

2016 Winter Project Week/Projects/CLIImprovement

2016-01-08T14:13:31Z

Johan.andruejol: /* Project Description */

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

</gallery>

==Key Investigators==
* Johan Andruejol (Kitware Inc)

==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;"
|

* Improve the CLI piping robustness
* Improve the CLI testing coverage
* Explore the creation of an utility to pipe CLIs easily
|

* Fix the issue raised by this pull request: https://github.com/Slicer/Slicer/pull/358
* Add simple python testing to call multiple CLIs in a row
* Add testing for running CLIs in parrallel
|

* Pull request here to solve issue for runnning CLIs in parallel and in a row: https://github.com/Slicer/Slicer/pull/438
-> Integrated in r24834
* Experimental branch for CLIPipeline: https://github.com/vovythevov/Slicer/blob/CLIPipelineNode/Modules/Scripted/CLIPipelineModule/CLIPipelineModule.py#L350-L377
* More testing for CLI behavior: https://github.com/Slicer/Slicer/pull/441
|}

==Background and References==

2016 Winter Project Week/Dinner

2016-01-05T19:21:09Z

Johan.andruejol: /* RSVPs */

==Dinner Specs==

*Date and Time: Thursday, January 7th, 6pm
*Location: Desi Dhaba, 401 Massachusetts Ave, Cambridge (about 10 minute walk from Project Week)
*Food: Indian. (Veg and non-veg options, naan, rice)
*Cost: $25 to be paid in cash when you get to the restaurant (for BWH attendees, this is reimbursable)
*Drinks: tap water is included in this price. Beyond that each person pays individually for their drinks - alcohol or otherwise

Disclaimer: We went yesterday (Monday) and they were not serving alcohol. - Adam Rankin

==RSVPs==
#Tina Kapur
#Ron Kikinis
#Steve Pieper
# Andrey Fedorov
# Sonia Pujol
#Hans Meine
#Michael Onken
# Junichi Tokuda
# Dan Blezek
# Johan Andruejol

2016 Winter Project Week/Projects/CLIImprovement

2016-01-05T18:15:06Z

Johan.andruejol:

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

</gallery>

==Key Investigators==
* Johan Andruejol (Kitware Inc)

==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;"
|

* Improve the CLI piping robustness
* Improve the CLI testing coverage
* Explore the creation of an utility to pipe CLIs easily
|

* Fix the issue raised by this pull request: https://github.com/Slicer/Slicer/pull/358
* Add simple python testing to call multiple CLIs in a row
* Add testing for running CLIs in parrallel
|

* Pull request here to solve issue for runnning CLIs in parallel and in a row: https://github.com/Slicer/Slicer/pull/438
|}

==Background and References==

2016 Winter Project Week/Projects/CLIImprovement

2016-01-04T19:22:58Z

Johan.andruejol: /* Project Description */

2016 Winter Project Week/Projects/CLIImprovement

2016-01-04T18:24:37Z

Johan.andruejol:

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

</gallery>

==Key Investigators==
* Johan Andruejol (Kitware Inc)

==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;"
|

* Improve the CLI robustness
* Improve the CLI testing coverage
* Explore the creation of an utility to pipe CLIs easily
|

* Fix the issue raised by this pull request: https://github.com/Slicer/Slicer/pull/358
* Add simple python testing to call multiple CLIs in a row
* Add testing for running CLIs in parrallel
|

*
|}

==Background and References==

2016 Winter Project Week/Projects/CLIImprovement

2016-01-04T18:22:44Z

Johan.andruejol: /* Project Description */

2016 Winter Project Week/Projects/CLIImprovement

2016-01-03T22:55:29Z

Johan.andruejol:

2016 Winter Project Week/Projects/CLIImprovement

2016-01-03T22:55:16Z

Johan.andruejol: 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

2016-01-03T22:47:24Z

Johan.andruejol: /* 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"|
|
|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''' TBD 
'''9:30-10:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Image-guided Neurosurgery| Clinical perspective on Image Guided Neurosurgery]] (Alexandra Golby) 
'''10:30-11:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Multiparametric MRI| Clinical perspective on Multiparametric MRI]] (Fiona Fennessy) 
'''11:30am-12:30pm''' TBD 
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ----------------- 
'''12pm:''' [[Events:TutorialContestJanuary2016|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]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

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

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

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

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

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

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

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

= '''Logistics''' =

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

= '''Registrants''' =

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

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