NAMIC Wiki - User contributions [en]

Project Week 25/Human-Computer Interaction under sterile conditions

2017-06-30T12:11:17Z

Lasso: /* Illustrations */

__TOC__
Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==
*[http://isgwww.cs.uni-magdeburg.de/cas/ Christian Hansen] (University of Magdeburg, Germany)
*[http://isgwww.cs.uni-magdeburg.de/cas/team.php Julian Hettig] (University of Magdeburg, Germany)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (PerkLab, Queen's)
*[http://isgwww.cs.uni-magdeburg.de/cas/team.php Benjamin Hatscher] (University of Magdeburg, Germany)
*[http://www.researchgate.net/profile/David_Black11 David Black] (University of Bremen; Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany)
*[http://www.dkfz.de/en/mic/team/people/Marco_Nolden.html Marco Nolden] (German Cancer Research Center (DKFZ), Germany)
*[http://juanruizalzola.com/about-juan/ Juan Ruiz Alzola] (University of Las Palmas de Gran Canaria, Spain)
*[http://www.imagenglab.com/newsite/salvatore_scaramuzzino/ Salvatore Scaramuzzino] ("Magna Graecia" University - ASL Vercelli, Italy)

==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;"
|
Human-Computer Interaction under Sterile Conditions.
* Review of state of the art (tochless interaction)
* Development of new user interfaces to support surgical interterventions

|

# Long, intensive conceptualization (2 days) of possibilities for gesture interaction and audio feedback for it
## We will need moderation kit (paper, pencil, markers, etc)
# Prototypes of possible auditory/visual feedback based on conceptualization
## With OSC communication protocol, David will make quick, flexible sound methods
## foot/eye interaction (?)

|


# Connected Slicer to OSC: added SlicerSoundControl extension (https://github.com/SlicerIGT/SlicerSoundControl), see below for necessary OSC message names
# Tested avoidance warning with experimental integration into breast lumpectomy navigation module (LumpNav): https://youtu.be/gSz8IHmogMo
# tried using gestures to zoom windows in and out

|}

==Illustrations==

{| class="wikitable"
! style="text-align: left; width:50%" | [[image:OpenSoundControl.png|400px]] OpenSoundControl module for configuring and testing OpenSoundControl server communication
! style="text-align: left; width:50%" | [[image:SoundNavigation.png|400px]] SoundNavigation module for automatically generating OpenSoundControl messages for tool navigation, from tool and reference transform nodes
|- style="vertical-align:top;"
|}

<embedvideo service="youtube">https://youtu.be/gSz8IHmogMo</embedvideo>

==SlicerSoundControl==
see https://github.com/SlicerIGT/SlicerSoundControl

=== Environment for Testing Slicer Sound Control ===

OSC Message names:

Base name: /SoundNav/Instrument/

Translation: each fro 0 to 100 mm
* /TranslationX
* /TranslationY
* /TranslationZ
* /Distance (absolute distance)

Translation: each from 0 to 180 degrees
* /OrientationX
* /OrientationY
* /OrientationZ
* /Orientation (overall orientation)

GUI for test:
[[File:OSCTest GUI.png|500px|frameless|OSCTest GUI]]

=== Environment for Sterile Gestures (planned, not yet implemented) ===
* In/ out
** --> "/InOut 0" out
** --> "/InOut 1" in
* Edge distance (0 to 3 cm?)
** --> "/EdgeDist x" where x is float between 0 and 3

=== Ambient ===
* Overall acceleration
** --> "/OverallAccel x" where x is float between 0 and 1
* Background noise
* Absolute position (x/y, not depth) to show current selected window
** --> "/AbsPolX x" where x is float between 0 and 1
** --> "/AbsPolY x" where x is float between 0 and 1

=== Gestures ===
* select image
** --> "/SelectGesture x" where x is gesture number
* zoom to left window
* zoom to right window
* put back into small viewer

==Background==
[[File:Screen Shot 2017-06-26 at 12.14.57.png|500px|example HCI with freehand gestures for sound]]


Example of previous related work using standard surgical gloves and OR compatible plastic draping confirmed to be compatible with sterile requirements at BWH AMIGO:
]
<embedvideo service="youtube">https://www.youtube.com/watch?v=zSqO2pUEodw</embedvideo>

== References==

[http://isgwww.cs.uni-magdeburg.de/cas/pub/2017_IJCARS_MewesHensenWackerHansen.pdf Mewes et al. (2017) Touchless Interaction with Software in Interventional Radiology and Surgery: A Systematic Literature Review]

[http://isgwww.cs.uni-magdeburg.de/cas/pub/2017_Hettig_JCARS.pdf Hettig et al. (2017) Comparison of Gesture and Conventional Interaction Techniques for Interventional Neuroradiology]

Project Week 25/Human-Computer Interaction under sterile conditions

2017-06-30T12:10:41Z

Lasso: /* Illustrations */

__TOC__
Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==
*[http://isgwww.cs.uni-magdeburg.de/cas/ Christian Hansen] (University of Magdeburg, Germany)
*[http://isgwww.cs.uni-magdeburg.de/cas/team.php Julian Hettig] (University of Magdeburg, Germany)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (PerkLab, Queen's)
*[http://isgwww.cs.uni-magdeburg.de/cas/team.php Benjamin Hatscher] (University of Magdeburg, Germany)
*[http://www.researchgate.net/profile/David_Black11 David Black] (University of Bremen; Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany)
*[http://www.dkfz.de/en/mic/team/people/Marco_Nolden.html Marco Nolden] (German Cancer Research Center (DKFZ), Germany)
*[http://juanruizalzola.com/about-juan/ Juan Ruiz Alzola] (University of Las Palmas de Gran Canaria, Spain)
*[http://www.imagenglab.com/newsite/salvatore_scaramuzzino/ Salvatore Scaramuzzino] ("Magna Graecia" University - ASL Vercelli, Italy)

==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;"
|
Human-Computer Interaction under Sterile Conditions.
* Review of state of the art (tochless interaction)
* Development of new user interfaces to support surgical interterventions

|

# Long, intensive conceptualization (2 days) of possibilities for gesture interaction and audio feedback for it
## We will need moderation kit (paper, pencil, markers, etc)
# Prototypes of possible auditory/visual feedback based on conceptualization
## With OSC communication protocol, David will make quick, flexible sound methods
## foot/eye interaction (?)

|


# Connected Slicer to OSC: added SlicerSoundControl extension (https://github.com/SlicerIGT/SlicerSoundControl), see below for necessary OSC message names
# Tested avoidance warning with experimental integration into breast lumpectomy navigation module (LumpNav): https://youtu.be/gSz8IHmogMo
# tried using gestures to zoom windows in and out

|}

==Illustrations==

{| class="wikitable"
! style="text-align: left; width:50%" | [[image:20170629_OpenSoundControl.png|400px]] OpenSoundControl module for configuring and testing OpenSoundControl server communication
! style="text-align: left; width:50%" | [[image:20170629_SoundNavigation.png|400px]] SoundNavigation module for automatically generating OpenSoundControl messages for tool navigation, from tool and reference transform nodes
|- style="vertical-align:top;"
|}

<embedvideo service="youtube">https://youtu.be/gSz8IHmogMo</embedvideo>

==SlicerSoundControl==
see https://github.com/SlicerIGT/SlicerSoundControl

=== Environment for Testing Slicer Sound Control ===

OSC Message names:

Base name: /SoundNav/Instrument/

Translation: each fro 0 to 100 mm
* /TranslationX
* /TranslationY
* /TranslationZ
* /Distance (absolute distance)

Translation: each from 0 to 180 degrees
* /OrientationX
* /OrientationY
* /OrientationZ
* /Orientation (overall orientation)

GUI for test:
[[File:OSCTest GUI.png|500px|frameless|OSCTest GUI]]

=== Environment for Sterile Gestures (planned, not yet implemented) ===
* In/ out
** --> "/InOut 0" out
** --> "/InOut 1" in
* Edge distance (0 to 3 cm?)
** --> "/EdgeDist x" where x is float between 0 and 3

=== Ambient ===
* Overall acceleration
** --> "/OverallAccel x" where x is float between 0 and 1
* Background noise
* Absolute position (x/y, not depth) to show current selected window
** --> "/AbsPolX x" where x is float between 0 and 1
** --> "/AbsPolY x" where x is float between 0 and 1

=== Gestures ===
* select image
** --> "/SelectGesture x" where x is gesture number
* zoom to left window
* zoom to right window
* put back into small viewer

==Background==
[[File:Screen Shot 2017-06-26 at 12.14.57.png|500px|example HCI with freehand gestures for sound]]


Example of previous related work using standard surgical gloves and OR compatible plastic draping confirmed to be compatible with sterile requirements at BWH AMIGO:
]
<embedvideo service="youtube">https://www.youtube.com/watch?v=zSqO2pUEodw</embedvideo>

== References==

[http://isgwww.cs.uni-magdeburg.de/cas/pub/2017_IJCARS_MewesHensenWackerHansen.pdf Mewes et al. (2017) Touchless Interaction with Software in Interventional Radiology and Surgery: A Systematic Literature Review]

[http://isgwww.cs.uni-magdeburg.de/cas/pub/2017_Hettig_JCARS.pdf Hettig et al. (2017) Comparison of Gesture and Conventional Interaction Techniques for Interventional Neuroradiology]

File:SoundNavigation.png

2017-06-30T12:08:17Z

Lasso: https://github.com/SlicerIGT/SlicerSoundControl

https://github.com/SlicerIGT/SlicerSoundControl

File:OpenSoundControl.png

2017-06-30T12:08:01Z

Lasso: https://github.com/SlicerIGT/SlicerSoundControl

https://github.com/SlicerIGT/SlicerSoundControl

Project Week 25/Human-Computer Interaction under sterile conditions

2017-06-30T12:07:11Z

Lasso:

__TOC__
Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==
*[http://isgwww.cs.uni-magdeburg.de/cas/ Christian Hansen] (University of Magdeburg, Germany)
*[http://isgwww.cs.uni-magdeburg.de/cas/team.php Julian Hettig] (University of Magdeburg, Germany)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (PerkLab, Queen's)
*[http://isgwww.cs.uni-magdeburg.de/cas/team.php Benjamin Hatscher] (University of Magdeburg, Germany)
*[http://www.researchgate.net/profile/David_Black11 David Black] (University of Bremen; Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany)
*[http://www.dkfz.de/en/mic/team/people/Marco_Nolden.html Marco Nolden] (German Cancer Research Center (DKFZ), Germany)
*[http://juanruizalzola.com/about-juan/ Juan Ruiz Alzola] (University of Las Palmas de Gran Canaria, Spain)
*[http://www.imagenglab.com/newsite/salvatore_scaramuzzino/ Salvatore Scaramuzzino] ("Magna Graecia" University - ASL Vercelli, Italy)

==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;"
|
Human-Computer Interaction under Sterile Conditions.
* Review of state of the art (tochless interaction)
* Development of new user interfaces to support surgical interterventions

|

# Long, intensive conceptualization (2 days) of possibilities for gesture interaction and audio feedback for it
## We will need moderation kit (paper, pencil, markers, etc)
# Prototypes of possible auditory/visual feedback based on conceptualization
## With OSC communication protocol, David will make quick, flexible sound methods
## foot/eye interaction (?)

|


# Connected Slicer to OSC: added SlicerSoundControl extension (https://github.com/SlicerIGT/SlicerSoundControl), see below for necessary OSC message names
# Tested avoidance warning with experimental integration into breast lumpectomy navigation module (LumpNav): https://youtu.be/gSz8IHmogMo
# tried using gestures to zoom windows in and out

|}

==Illustrations==

[[File:OpenSoundControl.png|200px|thumb|left|OpenSoundControl module for configuring and testing OpenSoundControl server communication]]

[[File:SoundNavigation.png|200px|thumb|left|SoundNavigation module for automatically generating OpenSoundControl messages for tool navigation, from tool and reference transform nodes]]

<embedvideo service="youtube">https://youtu.be/gSz8IHmogMo</embedvideo>

==SlicerSoundControl==
see https://github.com/SlicerIGT/SlicerSoundControl

=== Environment for Testing Slicer Sound Control ===

OSC Message names:

Base name: /SoundNav/Instrument/

Translation: each fro 0 to 100 mm
* /TranslationX
* /TranslationY
* /TranslationZ
* /Distance (absolute distance)

Translation: each from 0 to 180 degrees
* /OrientationX
* /OrientationY
* /OrientationZ
* /Orientation (overall orientation)

GUI for test:
[[File:OSCTest GUI.png|500px|frameless|OSCTest GUI]]

=== Environment for Sterile Gestures (planned, not yet implemented) ===
* In/ out
** --> "/InOut 0" out
** --> "/InOut 1" in
* Edge distance (0 to 3 cm?)
** --> "/EdgeDist x" where x is float between 0 and 3

=== Ambient ===
* Overall acceleration
** --> "/OverallAccel x" where x is float between 0 and 1
* Background noise
* Absolute position (x/y, not depth) to show current selected window
** --> "/AbsPolX x" where x is float between 0 and 1
** --> "/AbsPolY x" where x is float between 0 and 1

=== Gestures ===
* select image
** --> "/SelectGesture x" where x is gesture number
* zoom to left window
* zoom to right window
* put back into small viewer

==Background==
[[File:Screen Shot 2017-06-26 at 12.14.57.png|500px|example HCI with freehand gestures for sound]]


Example of previous related work using standard surgical gloves and OR compatible plastic draping confirmed to be compatible with sterile requirements at BWH AMIGO:
]
<embedvideo service="youtube">https://www.youtube.com/watch?v=zSqO2pUEodw</embedvideo>

== References==

[http://isgwww.cs.uni-magdeburg.de/cas/pub/2017_IJCARS_MewesHensenWackerHansen.pdf Mewes et al. (2017) Touchless Interaction with Software in Interventional Radiology and Surgery: A Systematic Literature Review]

[http://isgwww.cs.uni-magdeburg.de/cas/pub/2017_Hettig_JCARS.pdf Hettig et al. (2017) Comparison of Gesture and Conventional Interaction Techniques for Interventional Neuroradiology]

Project Week 25/Human-Computer Interaction under sterile conditions

2017-06-30T12:00:42Z

Lasso:

__TOC__
Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==
*[http://isgwww.cs.uni-magdeburg.de/cas/ Christian Hansen] (University of Magdeburg, Germany)
*[http://isgwww.cs.uni-magdeburg.de/cas/team.php Julian Hettig] (University of Magdeburg, Germany)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (PerkLab, Queen's)
*[http://isgwww.cs.uni-magdeburg.de/cas/team.php Benjamin Hatscher] (University of Magdeburg, Germany)
*[http://www.researchgate.net/profile/David_Black11 David Black] (University of Bremen; Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany)
*[http://www.dkfz.de/en/mic/team/people/Marco_Nolden.html Marco Nolden] (German Cancer Research Center (DKFZ), Germany)
*[http://juanruizalzola.com/about-juan/ Juan Ruiz Alzola] (University of Las Palmas de Gran Canaria, Spain)
*[http://www.imagenglab.com/newsite/salvatore_scaramuzzino/ Salvatore Scaramuzzino] ("Magna Graecia" University - ASL Vercelli, Italy)

==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;"
|
Human-Computer Interaction under Sterile Conditions.
* Review of state of the art (tochless interaction)
* Development of new user interfaces to support surgical interterventions

|

# Long, intensive conceptualization (2 days) of possibilities for gesture interaction and audio feedback for it
## We will need moderation kit (paper, pencil, markers, etc)
# Prototypes of possible auditory/visual feedback based on conceptualization
## With OSC communication protocol, David will make quick, flexible sound methods
## foot/eye interaction (?)
# [[File:OSC Test Input.pd.zip|thumb|Test incoming OSC messages using PureData]]
##Here is a test patch for incoming messages, also makes sound. Need to [https://puredata.info/downloads/pd-extended download PD-Extended] to use this.

|


# Connected Slicer to OSC: added SlicerSoundControl extension (https://github.com/SlicerIGT/SlicerSoundControl)
# Tested avoidance warning with experimental integration into breast lumpectomy navigation module (LumpNav): https://youtu.be/gSz8IHmogMo
# tried using gestures to zoom windows in and out

|}

==Necessary Parameters==
see https://github.com/SlicerIGT/SlicerSoundControl

/BlackLegend

=== Environment ===
* In/ out
** --> "/InOut 0" out
** --> "/InOut 1" in
* Edge distance (0 to 3 cm?)
** --> "/EdgeDist x" where x is float between 0 and 3

=== Ambient ===
* Overall acceleration
** --> "/OverallAccel x" where x is float between 0 and 1
* Background noise
* Absolute position (x/y, not depth) to show current selected window
** --> "/AbsPolX x" where x is float between 0 and 1
** --> "/AbsPolY x" where x is float between 0 and 1

=== Gestures ===
* select image
** --> "/SelectGesture x" where x is gesture number
* zoom to left window
* zoom to right window
* put back into small viewer

==Background==
[[File:Screen Shot 2017-06-26 at 12.14.57.png|500px|example HCI with freehand gestures for sound]]


Example of previous related work using standard surgical gloves and OR compatible plastic draping confirmed to be compatible with sterile requirements at BWH AMIGO:
]
<embedvideo service="youtube">https://www.youtube.com/watch?v=zSqO2pUEodw</embedvideo>

== References==

[http://isgwww.cs.uni-magdeburg.de/cas/pub/2017_IJCARS_MewesHensenWackerHansen.pdf Mewes et al. (2017) Touchless Interaction with Software in Interventional Radiology and Surgery: A Systematic Literature Review]

[http://isgwww.cs.uni-magdeburg.de/cas/pub/2017_Hettig_JCARS.pdf Hettig et al. (2017) Comparison of Gesture and Conventional Interaction Techniques for Interventional Neuroradiology]

Project Week 25/Slice-to-Volume Registration to Support MRI guided Interventions

2017-06-26T10:33:11Z

Lasso:

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[http://isgwww.cs.uni-magdeburg.de/cas/team.php Gino Gulamhussene] (University of Magdeburg, Germany)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
* The objective of this project is to drive the discussion under which circumstances medical image registration can be used to support MRI guided liver interventions.
* Furthermore a simple implementation of a state of the art method to register iMRI to MRI shall show the principle possibility of such an approach.

|
* discuss the applicability of Slice-to-Volume registration of intra-interventional MRI to pre-interventional MRI to support liver interventions. (insights from radiologists would be valuable)
* give an overview of factors that determin the applicability of (StV) registration to support liver interventions in MRI
* implement state of the art algorithm to register orthogonal iMRI slices to MRI volume

|

|}

==Illustrations==



==Background and References==

* [[2011_Winter_Project_Week:Intra-ProceduralProstateMotion]]

Project Week 25

2017-06-26T09:59:32Z

Lasso: /* Calendar */

__NOTOC__
Back to [[Events]]

A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].

[[image:PW25.png|300px]] [[image:IEL_logo.png|225px]]
<br>

=Welcome to the web page for the 25th Project Week!=
It is a pleasure to announce that the 25th Project week will be held in [https://goo.gl/maps/b9CpkFxNyWN2 Catanzaro Lido] (Calabria, Italy) on June 26-30, 2017. This is the first time in Italy for the Slicer Community, and the event is organized in cooperation with [http://www.imagenglab.com ImagEngLab]. Catanzaro Lido is a city on the Ionian Sea, in the middle of Squillace Gulf where, according to the ancient legend, Odysseus started his journey back to Ithaca. Of course bring your swimsuit...the conference room and the hotel are 20 meters far away from the beach!

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

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

===Local Organizing Committee===
*[http://www.imagenglab.com/newsite/mf_spadea/ Maria Francesca Spadea, PhD]
*[http://www.imagenglab.com/newsite/paolo_zaffino/ Paolo Zaffino, PhD].

==Logistics==
*'''Dates:''' June 26-30, 2017. Details in the calendar below.
*'''Location:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. [mailto:prenotazioni@hotelperladelporto.it Booking]. Subject line: "Slicer Summer Project Week 2017". Special rates: Single room, full bed, 79 € per night (1 person)/ Single room, queen bed 89 € per night (1 person)/ Double room, queen bed 99 € per night (2 people)/Triple room, 110 € (3 people)
*'''Registration:''' To register please visit this [http://www.imagenglab.com/newsite/project-week page]
*'''Registration Fee:''' 320€ and it includes lunches, coffee breaks and airport connections
*'''Hotel:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. The closest airport is [http://www.lameziaairport.it/english/ Lamezia Terme Airport (IATA: SUF)].
*'''Transportation from Airport to Hotel:''' Your registration fee includes ground transportation [https://www.google.com/maps/dir/Lamezia+Terme+International+Airport,+Via+Aeroporto,+88046+Lamezia+Terme+CZ,+Italy/BEST+WESTERN+PLUS+Hotel+Perla+Del+Porto,+Via+Martiri+di+Cefalonia,+64,+88100+Catanzaro,+Italy/@38.868758,16.1564814,10z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x133fe15a3cbed47f:0x544ab120c3de78a6!2m2!1d16.2434017!2d38.9065845!1m5!1m1!1s0x134003d668252a13:0x2989caf676f45a72!2m2!1d16.6312407!2d38.827712!3e0 to/from the hotel and airport]. Please fill out this [https://goo.gl/forms/7vmhxZSHy8Z1A62z2 form] to request transportation
*'''Local points of interest (pubs, restaurants, bar):''' [https://www.google.com/maps/d/viewer?mid=1FU63ik9Do3zzP6K2kvLVTtM2at8&ll=38.86221979925013%2C16.44292274999998&z=12 map] (constantly updated)

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NA-MIC Project Week (Timezone is Italy / GMT+02.)
|view=WEEK
|dates=20170626/20170701
}}

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

Breakout sessions:
* [[Project_Week_25/Neuro-navigation_breakout_session|Neuro-navigation breakout session]]
* Segment editor
* Deep learning?

=Projects=

<big>Please duplicate [https://na-mic.org/wiki/Project_Week_Template this template] to create a page for your project. </big>

Please put a brief preliminary title for your project here with some names in parenthesis for potential team members
==Deep Learning Applications==
#[[Project_Week_25/NeedleSegmentation |CNN for Needle Segmentation from MRI Images]]
#[[Project_Week_25/CNN_for_multi-plane_prostate_segmentation | CNN for multi-plane prostate segmentation]]
#[[Project_Week_25/CNN for PseudoCT Generation from T1T2 MR|CNN for PseudoCT Generation from T1/T2 MRI]]
#[[Project_Week_25/Breast Cancer Analysis in DCE-MRI | Breast Cancer Segmentation in DCE-MRI via Deep Learning Approaches]]

==Augmented Reality and Virtual Reality==
#[[Project_Week_25/Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification | Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification]]
# [[Project_Week_25/Next_Generation_GPU_Volume_Rendering | Next Generation of Volume Rendering in VTK ]]
#[[Project_Week_25/Development_and_Evaluation_of_New_AR_Visualization_Techniques_to_Support_Radiological_Interventions | Development and Evaluation of New AR Visualization Techniques to Support Radiological Interventions]]
#[[Project_Week_25/Intra-operative deformable_registration_based_on_dense_point_cloud_reconstruction |Intra-operative Deformable Registration Based on Dense Point Cloud Reconstruction for Augmented Reality in Laproscopic Surgery]]
#[[Project_Week_25/Slicer Export to VR | Slicer Export to VR]]

==Navigating Ultrasound==
# [[Project_Week_25/Tracked-Ultrasound-Standardization-IV | Tracked Ultrasound Standardization IV: Controlling US Acquisition]]
#[[Project_Week_25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation |Segmentation for Improving Image Registration of Preoperative MRI with Intraoperative Ultrasound Images for Neuro-navigation]]
==DICOM==
#[[Project_Week_25/DICOM_for_Quantitative_Imaging_and_Integration_with_Processing_Applications|DICOM for Quantitative Imaging and Integration with Processing Applications]]
#[[Project_Week_25/Conversion of DICOM Single Frame MR to Enhanced Multiframe | Conversion of DICOM Single Frame MR to Enhanced Multiframe]]
#[[Project_Week_25/DICOM Segmentation Support for Cornerstone and OHIF Viewer | DICOM Segmentation Support for Cornerstone/ OHIF Viewer]]

==Chest Image Processing==
#[[Project_Week_25/SlicerCIP_Bronchiectasis | SlicerCIP: Tool for Quantitative Analysis of Bronchiectasis]]
#[[Project_Week_25/SlicerCIP_ReportsTool | SlicerCIP: Tool for Creation of Reports for Quantitive Analysis]]
==Platform==
#[[Project_Week_25/Interactive_Manipulation_of_Plots_and_Graphs | Interactive Manipulation of Plots and Graphs]]
#[[Project_Week_25/Internationalizing Slicer Modules|Internationalizing Slicer Modules]]
#[[Project_Week_25/Interfacing Slicer to Mobile Phone-controlled Sensors|Interfacing Slicer to Mobile Phone-controlled Sensors]]
#[[Project_Week_25/Slicer and 3D Printing|Slicer and 3D Printing]]
#[[Project_Week_25/Multimodal: | Multimodal, Multiresolution, Multivolume Data]]
#[[Project_Week_25/Human-Computer_Interaction_under_sterile_conditions |Human-Computer Interaction under Sterile Conditions]]

==Applications Smorgasbord==
#[[Project_Week_25/Steerable Catheters Path Planner Extension for Brain Surgery Applications | Steerable Catheters Path Planner Extension for Brain Surgery Applications]]
#[[Project_Week_25/Slice-to-Volume Registration to Support MRI guided Interventions | Slice-to-Volume Registration to Support MRI guided Interventions ]]
#[[Project_Week_25/Surgical_Planning_In_Stereotaxy | Surgical Planning In Stereotaxy ]]
#[[Project_Week_25/SALT_Spatiotemporal_Modeling: | Slicer SALT Validation: Spatiotemporal Modeling of Subcortical Structures ]]
#[[Project_Week_25/Wrist_Kinematics: | Kinematic Analysis of the Wrist from Dynamic MRI]]
#[[Project_Week_25/EBP | External Beam Planning]]

=Registrants=

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [http://www.imagenglab.com/newsite/project-week/ registration site].

# Kikinis, Ron :: Brigham and Women's Hospital, Harvard Medical School, USA
# Pieper, Steve :: Isomics, Inc., USA
# Kapur, Tina :: Brigham and Women's Hospital, Harvard Medical School, USA
# Spadea, Maria Francesca :: Magna Graecia University, Italy
# Zaffino, Paolo :: Magna Graecia University, Italy
# Scaramuzzino, Salvatore :: Magna Graecia University/ASL Vercelli, Italy
# Pileggi, Giampaolo :: Magna Graecia University, Italy/German Cancer Research Center (DKFZ), Germany
# Rackerseder, Julia :: Technical University of Munich, Germany
# Pinter, Csaba :: Queen's University, Canada
# Kraß, Scheherazade :: University of Bremen, Germany
# Gerig, Guido :: NYU Tandon School of Engineering, USA
# Punzo, Davide :: Kapteyn Astronomical Institute, University of Groningen, The Netherlands
# Drouin, Simon :: NeuroImaging and Surgical Technologies (NIST) Lab, Canada
# Lasso, Andras :: School of Computing, Queen's University, Canada
# Favaro, Alberto :: Politecnico di Milano, Italy
# Leger, Etienne :: Concordia University, Canada
# Ziegler, Erik :: Ziegler Consult SAS
# Onken, Michael :: Open Connections GmbH, Germany
# Pinzi, Marlene :: Imperial College, UK
# Nitsch, Jennifer :: University of Bremen, Germany
# Moccia, Sara :: Politecnico di Milano, Italy
# Black, David :: Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany
# Penzkofer, Tobias :: Charité Universitätsmedizin, Berlin, Germany
# Hansen, Christian :: University of Magdeburg, Germany
# Vegard Solberg, Ole :: Norway
# Heinrich, Florian :: University of Magdeburg, Germany
# Mewes, André :: University of Magdeburg, Germany
# Hatscher, Benjamin :: University of Magdeburg, Germany
# Hettig, Julian :: University of Magdeburg, Germany
# Meyer, Anneke :: University of Magdeburg, Germany
# Gulamhussene, Gino :: University of Magdeburg, Germany
# Cassetta, Roberto :: Politecnico di Milano, Italy
# Fillion-Robin, Jean-Christophe :: Kitware, Inc., USA
# Metzger, Jasmin :: German Cancer Research Center (DKFZ), Germany
# Fishbaugh, James :: NYU Tandon School of Engineering, USA
# Nolden, Marco :: German Cancer Research Center (DKFZ), Germany
# Nehrkorn, Jorge Quintero :: Canary Islands, Spain
# Perez Garcia, Fernando :: ICM Brain & Spine Institute, Paris, France
# De Momi, Elena :: Politecnico di Milano, Italy
# Piantadosi, Gabriele :: DIETI, Federico II di Napoli, Italy
# Pernelle, Guillaume :: Imperial College, UK
# San Jose, Raul :: Brigham and Women's Hospital, Harvard Medical School, USA
# Nardelli, Pietro :: Brigham and Women's Hospital, Harvard Medical School, USA
# Fernandez Vidal, Sara :: ICM Brain & Spine Institute, Paris, France
# Sharp, Gregory :: Massachusetts General Hospital, Harvard Medical School, USA
# Moiraghi, Alessandro :: Università degli Studi di Milano, Italy
# Seco, Joao :: German Cancer Research Center (DKFZ), Germany
# Pumar Carreras, Nayra :: Canary Islands, Spain
# Afonso Suarez, Maria Dolores :: Canary Islands, Spain
# Alzola Ruiz, Juan :: Canary Islands, Spain
# Pujol, Sonia :: Brigham and Women's Hospital, Harvard Medical School, USA

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-26T09:45:16Z

Lasso: /* Key Investigators */

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[http://www.rug.nl/staff/davide.punzo/ Davide Punzo] (Kapteyn Astronomical Institute, University of Groningen, The Netherlands)
*[http://www.spl.harvard.edu/pages/People/pieper Steve Pieper] (Isomics Inc., USA)
*[https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin] (Kitware Inc., USA)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)

==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;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|
|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (blue object in the 3D View) directly from the plotting window.

[[image:SlicerAstroWiki13.png|1200px]]

==Background and References==
*https://www.slicer.org/wiki/Developer_Meetings/20170425
*http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
*http://www.jqplot.com/examples/zooming.php
*[https://github.com/Punzo/SlicerAstro/wiki/ SlicerAstro]

[[image:SlicerAstroLogo.png|400px]]

*(Just for fun: how the gas in a galaxy looks like in 3D https://www.youtube.com/watch?v=yLjW9nbdO8g )

Project Week 25

2017-06-26T08:59:17Z

Lasso: /* Calendar */

__NOTOC__
Back to [[Events]]

A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].

[[image:PW25.png|300px]] [[image:IEL_logo.png|225px]]
<br>

=Welcome to the web page for the 25th Project Week!=
It is a pleasure to announce that the 25th Project week will be held in [https://goo.gl/maps/b9CpkFxNyWN2 Catanzaro Lido] (Calabria, Italy) on June 26-30, 2017. This is the first time in Italy for the Slicer Community, and the event is organized in cooperation with [http://www.imagenglab.com ImagEngLab]. Catanzaro Lido is a city on the Ionian Sea, in the middle of Squillace Gulf where, according to the ancient legend, Odysseus started his journey back to Ithaca. Of course bring your swimsuit...the conference room and the hotel are 20 meters far away from the beach!

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

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

===Local Organizing Committee===
*[http://www.imagenglab.com/newsite/mf_spadea/ Maria Francesca Spadea, PhD]
*[http://www.imagenglab.com/newsite/paolo_zaffino/ Paolo Zaffino, PhD].

==Logistics==
*'''Dates:''' June 26-30, 2017. Details in the calendar below.
*'''Location:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. [mailto:prenotazioni@hotelperladelporto.it Booking]. Subject line: "Slicer Summer Project Week 2017". Special rates: Single room, full bed, 79 € per night (1 person)/ Single room, queen bed 89 € per night (1 person)/ Double room, queen bed 99 € per night (2 people)/Triple room, 110 € (3 people)
*'''Registration:''' To register please visit this [http://www.imagenglab.com/newsite/project-week page]
*'''Registration Fee:''' 320€ and it includes lunches, coffee breaks and airport connections
*'''Hotel:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. The closest airport is [http://www.lameziaairport.it/english/ Lamezia Terme Airport (IATA: SUF)].
*'''Transportation from Airport to Hotel:''' Your registration fee includes ground transportation [https://www.google.com/maps/dir/Lamezia+Terme+International+Airport,+Via+Aeroporto,+88046+Lamezia+Terme+CZ,+Italy/BEST+WESTERN+PLUS+Hotel+Perla+Del+Porto,+Via+Martiri+di+Cefalonia,+64,+88100+Catanzaro,+Italy/@38.868758,16.1564814,10z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x133fe15a3cbed47f:0x544ab120c3de78a6!2m2!1d16.2434017!2d38.9065845!1m5!1m1!1s0x134003d668252a13:0x2989caf676f45a72!2m2!1d16.6312407!2d38.827712!3e0 to/from the hotel and airport]. Please fill out this [https://goo.gl/forms/7vmhxZSHy8Z1A62z2 form] to request transportation
*'''Local points of interest (pubs, restaurants, bar):''' [https://www.google.com/maps/d/viewer?mid=1FU63ik9Do3zzP6K2kvLVTtM2at8&ll=38.86221979925013%2C16.44292274999998&z=12 map] (constantly updated)

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NA-MIC Project Week (Timezone is Italy / GMT+02.)
|view=WEEK
|dates=20170626/20170701
}}

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

Breakout sessions:
* [[Project_Week_25/Neuro-navigation_breakout_session|Neuro-navigation breakout session]]
* Deep learning?

=Projects=

<big>Please duplicate [https://na-mic.org/wiki/Project_Week_Template this template] to create a page for your project. </big>

Please put a brief preliminary title for your project here with some names in parenthesis for potential team members
==Deep Learning Applications==
#[[Project_Week_25/NeedleSegmentation |CNN for Needle Segmentation from MRI Images]]
#[[Project_Week_25/CNN_for_multi-plane_prostate_segmentation | CNN for multi-plane prostate segmentation]]
#[[Project_Week_25/CNN for PseudoCT Generation from T1T2 MR|CNN for PseudoCT Generation from T1/T2 MRI]]
#[[Project_Week_25/Breast Cancer Analysis in DCE-MRI | Breast Cancer Segmentation in DCE-MRI via Deep Learning Approaches]]

==Augmented Reality and Virtual Reality==
#[[Project_Week_25/Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification | Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification]]
# [[Project_Week_25/Next_Generation_GPU_Volume_Rendering | Next Generation of Volume Rendering in VTK ]]
#[[Project_Week_25/Development_and_Evaluation_of_New_AR_Visualization_Techniques_to_Support_Radiological_Interventions | Development and Evaluation of New AR Visualization Techniques to Support Radiological Interventions]]
#[[Project_Week_25/Intra-operative deformable_registration_based_on_dense_point_cloud_reconstruction |Intra-operative Deformable Registration Based on Dense Point Cloud Reconstruction for Augmented Reality in Laproscopic Surgery]]
#[[Project_Week_25/Slicer Export to VR | Slicer Export to VR]]

==Navigating Ultrasound==
# [[Project_Week_25/Tracked-Ultrasound-Standardization-IV | Tracked Ultrasound Standardization IV: Controlling US Acquisition]]
#[[Project_Week_25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation |Segmentation for Improving Image Registration of Preoperative MRI with Intraoperative Ultrasound Images for Neuro-navigation]]
==DICOM==
#[[Project_Week_25/DICOM_for_Quantitative_Imaging_and_Integration_with_Processing_Applications|DICOM for Quantitative Imaging and Integration with Processing Applications]]
#[[Project_Week_25/Conversion of DICOM Single Frame MR to Enhanced Multiframe | Conversion of DICOM Single Frame MR to Enhanced Multiframe]]
#[[Project_Week_25/DICOM Segmentation Support for Cornerstone and OHIF Viewer | DICOM Segmentation Support for Cornerstone/ OHIF Viewer]]

==Chest Image Processing==
#[[Project_Week_25/SlicerCIP_Bronchiectasis | SlicerCIP: Tool for Quantitative Analysis of Bronchiectasis]]
#[[Project_Week_25/SlicerCIP_ReportsTool | SlicerCIP: Tool for Creation of Reports for Quantitive Analysis]]
==Platform==
#[[Project_Week_25/Interactive_Manipulation_of_Plots_and_Graphs | Interactive Manipulation of Plots and Graphs]]
#[[Project_Week_25/Internationalizing Slicer Modules|Internationalizing Slicer Modules]]
#[[Project_Week_25/Interfacing Slicer to Mobile Phone-controlled Sensors|Interfacing Slicer to Mobile Phone-controlled Sensors]]
#[[Project_Week_25/Slicer and 3D Printing|Slicer and 3D Printing]]
#[[Project_Week_25/Multimodal: | Multimodal, Multiresolution, Multivolume Data]]
#[[Project_Week_25/Human-Computer_Interaction_under_sterile_conditions |Human-Computer Interaction under Sterile Conditions]]

==Applications Smorgasbord==
#[[Project_Week_25/Steerable Catheters Path Planner Extension for Brain Surgery Applications | Steerable Catheters Path Planner Extension for Brain Surgery Applications]]
#[[Project_Week_25/Slice-to-Volume Registration to Support MRI guided Interventions | Slice-to-Volume Registration to Support MRI guided Interventions ]]
#[[Project_Week_25/Surgical_Planning_In_Stereotaxy | Surgical Planning In Stereotaxy ]]
#[[Project_Week_25/SALT_Spatiotemporal_Modeling: | Slicer SALT Validation: Spatiotemporal Modeling of Subcortical Structures ]]
#[[Project_Week_25/Wrist_Kinematics: | Kinematic Analysis of the Wrist from Dynamic MRI]]
#[[Project_Week_25/EBP | External Beam Planning]]

=Registrants=

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [http://www.imagenglab.com/newsite/project-week/ registration site].

# Kikinis, Ron :: Brigham and Women's Hospital, Harvard Medical School, USA
# Pieper, Steve :: Isomics, Inc., USA
# Kapur, Tina :: Brigham and Women's Hospital, Harvard Medical School, USA
# Spadea, Maria Francesca :: Magna Graecia University, Italy
# Zaffino, Paolo :: Magna Graecia University, Italy
# Scaramuzzino, Salvatore :: Magna Graecia University/ASL Vercelli, Italy
# Pileggi, Giampaolo :: Magna Graecia University, Italy/German Cancer Research Center (DKFZ), Germany
# Rackerseder, Julia :: Technical University of Munich, Germany
# Pinter, Csaba :: Queen's University, Canada
# Kraß, Scheherazade :: University of Bremen, Germany
# Gerig, Guido :: NYU Tandon School of Engineering, USA
# Punzo, Davide :: Kapteyn Astronomical Institute, University of Groningen, The Netherlands
# Drouin, Simon :: NeuroImaging and Surgical Technologies (NIST) Lab, Canada
# Lasso, Andras :: School of Computing, Queen's University, Canada
# Favaro, Alberto :: Politecnico di Milano, Italy
# Leger, Etienne :: Concordia University, Canada
# Ziegler, Erik :: Ziegler Consult SAS
# Onken, Michael :: Open Connections GmbH, Germany
# Pinzi, Marlene :: Imperial College, UK
# Nitsch, Jennifer :: University of Bremen, Germany
# Moccia, Sara :: Politecnico di Milano, Italy
# Black, David :: Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany
# Penzkofer, Tobias :: Charité Universitätsmedizin, Berlin, Germany
# Hansen, Christian :: University of Magdeburg, Germany
# Vegard Solberg, Ole :: Norway
# Heinrich, Florian :: University of Magdeburg, Germany
# Mewes, André :: University of Magdeburg, Germany
# Hatscher, Benjamin :: University of Magdeburg, Germany
# Hettig, Julian :: University of Magdeburg, Germany
# Meyer, Anneke :: University of Magdeburg, Germany
# Gulamhussene, Gino :: University of Magdeburg, Germany
# Cassetta, Roberto :: Politecnico di Milano, Italy
# Fillion-Robin, Jean-Christophe :: Kitware, Inc., USA
# Metzger, Jasmin :: German Cancer Research Center (DKFZ), Germany
# Fishbaugh, James :: NYU Tandon School of Engineering, USA
# Nolden, Marco :: German Cancer Research Center (DKFZ), Germany
# Nehrkorn, Jorge Quintero :: Canary Islands, Spain
# Perez Garcia, Fernando :: ICM Brain & Spine Institute, Paris, France
# De Momi, Elena :: Politecnico di Milano, Italy
# Piantadosi, Gabriele :: DIETI, Federico II di Napoli, Italy
# Pernelle, Guillaume :: Imperial College, UK
# San Jose, Raul :: Brigham and Women's Hospital, Harvard Medical School, USA
# Nardelli, Pietro :: Brigham and Women's Hospital, Harvard Medical School, USA
# Fernandez Vidal, Sara :: ICM Brain & Spine Institute, Paris, France
# Sharp, Gregory :: Massachusetts General Hospital, Harvard Medical School, USA
# Moiraghi, Alessandro :: Università degli Studi di Milano, Italy
# Seco, Joao :: German Cancer Research Center (DKFZ), Germany
# Pumar Carreras, Nayra :: Canary Islands, Spain
# Afonso Suarez, Maria Dolores :: Canary Islands, Spain
# Alzola Ruiz, Juan :: Canary Islands, Spain
# Pujol, Sonia :: Brigham and Women's Hospital, Harvard Medical School, USA

Project Week 25

2017-06-25T21:20:42Z

Lasso:

__NOTOC__
Back to [[Events]]

A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].

[[image:PW25.png|300px]] [[image:IEL_logo.png|225px]]
<br>

=Welcome to the web page for the 25th Project Week!=
It is a pleasure to announce that the 25th Project week will be held in [https://goo.gl/maps/b9CpkFxNyWN2 Catanzaro Lido] (Calabria, Italy) on June 26-30, 2017. This is the first time in Italy for the Slicer Community, and the event is organized in cooperation with [http://www.imagenglab.com ImagEngLab]. Catanzaro Lido is a city on the Ionian Sea, in the middle of Squillace Gulf where, according to the ancient legend, Odysseus started his journey back to Ithaca. Of course bring your swimsuit...the conference room and the hotel are 20 meters far away from the beach!

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

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

===Local Organizing Committee===
*[http://www.imagenglab.com/newsite/mf_spadea/ Maria Francesca Spadea, PhD]
*[http://www.imagenglab.com/newsite/paolo_zaffino/ Paolo Zaffino, PhD].

==Logistics==
*'''Dates:''' June 26-30, 2017. Details in the calendar below.
*'''Location:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. [mailto:prenotazioni@hotelperladelporto.it Booking]. Subject line: "Slicer Summer Project Week 2017". Special rates: Single room, full bed, 79 € per night (1 person)/ Single room, queen bed 89 € per night (1 person)/ Double room, queen bed 99 € per night (2 people)/Triple room, 110 € (3 people)
*'''Registration:''' To register please visit this [http://www.imagenglab.com/newsite/project-week page]
*'''Registration Fee:''' 320€ and it includes lunches, coffee breaks and airport connections
*'''Hotel:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. The closest airport is [http://www.lameziaairport.it/english/ Lamezia Terme Airport (IATA: SUF)].
*'''Transportation from Airport to Hotel:''' Your registration fee includes ground transportation [https://www.google.com/maps/dir/Lamezia+Terme+International+Airport,+Via+Aeroporto,+88046+Lamezia+Terme+CZ,+Italy/BEST+WESTERN+PLUS+Hotel+Perla+Del+Porto,+Via+Martiri+di+Cefalonia,+64,+88100+Catanzaro,+Italy/@38.868758,16.1564814,10z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x133fe15a3cbed47f:0x544ab120c3de78a6!2m2!1d16.2434017!2d38.9065845!1m5!1m1!1s0x134003d668252a13:0x2989caf676f45a72!2m2!1d16.6312407!2d38.827712!3e0 to/from the hotel and airport]. Please fill out this [https://goo.gl/forms/7vmhxZSHy8Z1A62z2 form] to request transportation
*'''Local points of interest (pubs, restaurants, bar):''' [https://www.google.com/maps/d/viewer?mid=1FU63ik9Do3zzP6K2kvLVTtM2at8&ll=38.86221979925013%2C16.44292274999998&z=12 map] (constantly updated)

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NA-MIC Project Week (Timezone is Italy / GMT+02.)
|view=WEEK
|dates=20170626/20170701
}}

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

Breakout sessions:
* [[Project_Week_25/Neuro-navigation_breakout_session|Neuro-navigation breakout session]]

=Projects=

<big>Please duplicate [https://na-mic.org/wiki/Project_Week_Template this template] to create a page for your project. </big>

Please put a brief preliminary title for your project here with some names in parenthesis for potential team members
==Deep Learning Applications==
#[[Project_Week_25/NeedleSegmentation |CNN for Needle Segmentation from MRI Images]]
#[[Project_Week_25/CNN_for_multi-plane_prostate_segmentation | CNN for multi-plane prostate segmentation]]
#[[Project_Week_25/CNN for PseudoCT Generation from T1T2 MR|CNN for PseudoCT Generation from T1/T2 MRI]]
#[[Project_Week_25/Breast Cancer Analysis in DCE-MRI | Breast Cancer Segmentation in DCE-MRI via Deep Learning Approaches]]

==Augmented Reality and Virtual Reality==
#[[Project_Week_25/Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification | Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification]]
# [[Project_Week_25/Next_Generation_GPU_Volume_Rendering | Next Generation of Volume Rendering in VTK ]]
#[[Project_Week_25/Development_and_Evaluation_of_New_AR_Visualization_Techniques_to_Support_Radiological_Interventions | Development and Evaluation of New AR Visualization Techniques to Support Radiological Interventions]]
#[[Project_Week_25/Intra-operative deformable_registration_based_on_dense_point_cloud_reconstruction |Intra-operative Deformable Registration Based on Dense Point Cloud Reconstruction for Augmented Reality in Laproscopic Surgery]]
#Slicer Export to VR (Juan Ruiz Alzola, Mike Halle)

==Navigating Ultrasound==
# [[Project_Week_25/Tracked-Ultrasound-Standardization-IV | Tracked Ultrasound Standardization IV: Controlling US Acquisition]]
#[[Project_Week_25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation |Segmentation for Improving Image Registration of Preoperative MRI with Intraoperative Ultrasound Images for Neuro-navigation]]
==DICOM==
#[[Project_Week_25/DICOM_for_Quantitative_Imaging_and_Integration_with_Processing_Applications|DICOM for Quantitative Imaging and Integration with Processing Applications]]
#[[Project_Week_25/Conversion of DICOM Single Frame MR to Enhanced Multiframe | Conversion of DICOM Single Frame MR to Enhanced Multiframe]]
#[[Project_Week_25/DICOM Segmentation Support for Cornerstone and OHIF Viewer | DICOM Segmentation Support for Cornerstone/ OHIF Viewer]]

==Chest Image Processing==
#[[Project_Week_25/SlicerCIP_Bronchiectasis | SlicerCIP: Tool for Quantitative Analysis of Bronchiectasis]]
#[[Project_Week_25/SlicerCIP_ReportsTool | SlicerCIP: Tool for Creation of Reports for Quantitive Analysis]]
==Platform==
#[[Project_Week_25/Interactive_Manipulation_of_Plots_and_Graphs | Interactive Manipulation of Plots and Graphs]]
#[[Project_Week_25/Internationalizing Slicer Modules|Internationalizing Slicer Modules]]
#[[Project_Week_25/Interfacing Slicer to Mobile Phone-controlled Sensors|Interfacing Slicer to Mobile Phone-controlled Sensors]]
#[[Project_Week_25/Slicer and 3D Printing|Slicer and 3D Printing]]
#[[Project_Week_25/Multimodal: | Multimodal, Multiresolution, Multivolume Data]]
#[[Project_Week_25/Human-Computer_Interaction_under_sterile_conditions |Human-Computer Interaction under Sterile Conditions]]

==Applications Smorgasbord==
#[[Project_Week_25/Steerable Catheters Path Planner Extension for Brain Surgery Applications | Steerable Catheters Path Planner Extension for Brain Surgery Applications]]
#[[Project_Week_25/Slice-to-Volume Registration to Support MRI guided Interventions | Slice-to-Volume Registration to Support MRI guided Interventions ]]
#[[Project_Week_25/SALT_Spatiotemporal_Modeling: | Slicer SALT Validation: Spatiotemporal Modeling of Subcortical Structures ]]
#[[Project_Week_25/Wrist_Kinematics: | Kinematic Analysis of the Wrist from Dynamic MRI]]

=Registrants=

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [http://www.imagenglab.com/newsite/project-week/ registration site].

# Kikinis, Ron :: Brigham and Women's Hospital, Harvard Medical School, USA
# Pieper, Steve :: Isomics, Inc., USA
# Kapur, Tina :: Brigham and Women's Hospital, Harvard Medical School, USA
# Spadea, Maria Francesca :: Magna Graecia University, Italy
# Zaffino, Paolo :: Magna Graecia University, Italy
# Scaramuzzino, Salvatore :: Magna Graecia University/ASL Vercelli, Italy
# Pileggi, Giampaolo :: Magna Graecia University, Italy/German Cancer Research Center (DKFZ), Germany
# Rackerseder, Julia :: Technical University of Munich, Germany
# Pinter, Csaba :: Queen's University, Canada
# Kraß, Scheherazade :: University of Bremen, Germany
# Gerig, Guido :: NYU Tandon School of Engineering, USA
# Punzo, Davide :: Kapteyn Astronomical Institute, University of Groningen, The Netherlands
# Drouin, Simon :: NeuroImaging and Surgical Technologies (NIST) Lab, Canada
# Lasso, Andras :: School of Computing, Queen's University, Canada
# Favaro, Alberto :: Politecnico di Milano, Italy
# Leger, Etienne :: Concordia University, Canada
# Ziegler, Erik :: Ziegler Consult SAS
# Onken, Michael :: Open Connections GmbH, Germany
# Pinzi, Marlene :: Imperial College, UK
# Nitsch, Jennifer :: University of Bremen, Germany
# Moccia, Sara :: Politecnico di Milano, Italy
# Black, David :: Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany
# Penzkofer, Tobias :: Charité Universitätsmedizin, Berlin, Germany
# Hansen, Christian :: University of Magdeburg, Germany
# Vegard Solberg, Ole :: Norway
# Heinrich, Florian :: University of Magdeburg, Germany
# Mewes, André :: University of Magdeburg, Germany
# Hatscher, Benjamin :: University of Magdeburg, Germany
# Hettig, Julian :: University of Magdeburg, Germany
# Meyer, Anneke :: University of Magdeburg, Germany
# Gulamhussene, Gino :: University of Magdeburg, Germany
# Cassetta, Roberto :: Politecnico di Milano, Italy
# Fillion-Robin, Jean-Christophe :: Kitware, Inc., USA
# Metzger, Jasmin :: German Cancer Research Center (DKFZ), Germany
# Fishbaugh, James :: NYU Tandon School of Engineering, USA
# Nolden, Marco :: German Cancer Research Center (DKFZ), Germany
# Nehrkorn, Jorge Quintero :: Canary Islands, Spain
# Perez Garcia, Fernando :: ICM Brain & Spine Institute, Paris, France
# De Momi, Elena :: Politecnico di Milano, Italy
# Piantadosi, Gabriele :: DIETI, Federico II di Napoli, Italy
# Pernelle, Guillaume :: Imperial College, UK
# San Jose, Raul :: Brigham and Women's Hospital, Harvard Medical School, USA
# Nardelli, Pietro :: Brigham and Women's Hospital, Harvard Medical School, USA
# Fernandez Vidal, Sara :: ICM Brain & Spine Institute, Paris, France
# Sharp, Gregory :: Massachusetts General Hospital, Harvard Medical School, USA
# Moiraghi, Alessandro :: Università degli Studi di Milano, Italy
# Seco, Joao :: German Cancer Research Center (DKFZ), Germany
# Pumar Carreras, Nayra :: Canary Islands, Spain
# Afonso Suarez, Maria Dolores :: Canary Islands, Spain
# Alzola Ruiz, Juan :: Canary Islands, Spain
# Pujol, Sonia :: Brigham and Women's Hospital, Harvard Medical School, USA

Project Week 25/Neuro-navigation breakout session

2017-06-25T21:15:33Z

Lasso: /* Participants */

= Introduction =

This will be an informal session that all project week participants that are interested in neuro-navigation should join. Just add your name to the participant list and show up at the session, optionally prepare 2-3 slides for introducing yourself to the group (tell about yourself, what you do in neuro-navigation, what your challenges are, what you plan to do). If you create slides then upload them to the wiki and add a link at your name.

* Time: Tuesday 2pm-3pm.
* Location: to be determined - it will be posted here.

= Participants =

If you do not have write access to the wiki then send your name (and slides) to Andras Lasso (lasso@queensu.ca).

# Andras Lasso ([http://perk.cs.queensu.ca PerkLab, Queen's]) - [[Media:20170625-NamicWeek-AndrasLassoIntro.pdf|intro slides]]

Project Week 25/Neuro-navigation breakout session

2017-06-25T21:13:38Z

Lasso: /* Participants */

= Introduction =

This will be an informal session that all project week participants that are interested in neuro-navigation should join. Just add your name to the participant list and show up at the session, optionally prepare 2-3 slides for introducing yourself to the group (tell about yourself, what you do in neuro-navigation, what your challenges are, what you plan to do). If you create slides then upload them to the wiki and add a link at your name.

* Time: Tuesday 2pm-3pm.
* Location: to be determined - it will be posted here.

= Participants =

If you do not have write access to the wiki then send your name (and slides) to Andras Lasso (lasso@queensu.ca).

# Andras Lasso - [[Media:20170625-NamicWeek-AndrasLassoIntro.pdf|intro slides]]

File:20170625-NamicWeek-AndrasLassoIntro.pdf

2017-06-25T21:12:26Z

Lasso:

Project Week 25/Neuro-navigation breakout session

2017-06-25T20:19:10Z

Lasso: Created page with "= Introduction = This will be an informal session that all project week participants that are interested in neuro-navigation should join. Just add your name to the participan..."

Project Week 25

2017-04-29T16:14:47Z

Lasso:

__NOTOC__
Back to [[Events]]

A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].

[[image:PW-Summer2017.png|300px]] [[image:IEL_logo.png|225px]]
<br>

=Welcome to the web page for the 25th Project Week!=

It is a pleasure to announce that the 25th Project week will be held in [https://goo.gl/maps/b9CpkFxNyWN2 Catanzaro Lido] (Calabria, Italy) on June 26-30, 2017. This is the first time in Italy for the Slicer Community, and the event is organized in cooperation with [http://www.imagenglab.com ImagEngLab]. Catanzaro Lido is a city on the Ionian Sea, in the middle of Squillace Gulf where, according to the ancient legend, Odysseus started his journey back to Ithaca. Of course bring your swimsuit...the conference room and the hotel are 20 meters far away from the beach!

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

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

===Local Organizing Committee===
*[http://www.imagenglab.com/newsite/mf_spadea/ Maria Francesca Spadea, PhD]
*[http://www.imagenglab.com/newsite/paolo_zaffino/ Paolo Zaffino, PhD].

==Hangouts for preparation==
#(Tina Kapur) Hangout #1: April 5th, 2017 - 9.00 AM Boston time: [https://plus.google.com/events/cjh9ag37hm1e7peplatphl7kh2g?authkey=COWc5cKc77jymgE event page] ([[PW25 Hangouts Notes|Notes]])
#(Steve Pieper) Hangout #2: Wednesday April 12, 2017, 9am EDT (GMT-4): Web browser based computing: Dockerized Slicer with remote computing and GPU computing; Cornerstone/LesionTracker OHIF; XTK->AMI (threejs); ePad; vtk.js; QWebEngine; [https://plus.google.com/hangouts/_/kitware.com/pw-25?hceid=a2l0d2FyZS5jb21fc2IwN2kxNzFvbGFjOWFhdmg0NmlyNDk1YzRAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ.fffs75fitbu0mvpl3vvmrcqf3s&authuser=0 hangout page]
#(Andras Lasso) Hangout #3: Wednesday April 19, 2017, 9am EDT (GMT-4) Connecting devices such as surgical navigation, ultrasound, 3D Slicer, PLUS, OpenIGTLink, Augmented reality; [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page]
#(Tina Kapur) Hangout #4: Wednesday April 26, 2017, 9am EDT (GMT-4) Deep Learning for Detection of Cancer and Instruments; [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page];
#(Simon Drouin) Hangout #5: Wednesday May 3, 2017, 9am EDT (GMT-4)Augmented Reality/Virtual Reality;
#(Tina Kapur) Hangout #6: Wednesday May 10, 2017, 9am EDT (GMT-4) For new participants: What is project week and how to get the most out of participating in it?
#(Andrey Fedorov, for phone call, not at project week) Hangout #7?: Wednesday May 17, 2017, 9am EDT (GMT-4) DICOM for Quantitative Imaging and integration with processing applications.

==Logistics==

*'''Dates:''' June 26-30, 2017. Consider staying for one more day (leaving Sunday morning), as a day off in a gorgeous sea place is planned on July 1st. More details will be posted soon.
*'''Location:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]
**[mailto:prenotazioni@hotelperladelporto.it Booking]. Subject line: "Slicer Summer Project Week 2017".
***Special rates are:
****Single room, full bed, 79 € per night (1 person)
****Single room, queen bed 89 € per night (1 person)
****Double room, queen bed 99 € per night (2 people)
****Triple room, 110 € (3 people)
*'''REGISTRATION:''' To register please visit this [http://www.imagenglab.com/newsite/project-week page]
*'''Registration Fee:''' 320€ and it includes lunches, coffee breaks and airport connections
*'''Hotel:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. The closest airport is [http://www.lameziaairport.it/english/ Lamezia Terme Airport (IATA: SUF)].
*'''Transportation from Airport to Hotel''' Your registration fee includes ground transportation [https://www.google.com/maps/dir/Lamezia+Terme+International+Airport,+Via+Aeroporto,+88046+Lamezia+Terme+CZ,+Italy/BEST+WESTERN+PLUS+Hotel+Perla+Del+Porto,+Via+Martiri+di+Cefalonia,+64,+88100+Catanzaro,+Italy/@38.868758,16.1564814,10z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x133fe15a3cbed47f:0x544ab120c3de78a6!2m2!1d16.2434017!2d38.9065845!1m5!1m1!1s0x134003d668252a13:0x2989caf676f45a72!2m2!1d16.6312407!2d38.827712!3e0 to/from the hotel and airport].
** Please fill out this form to request transportation https://goo.gl/forms/7vmhxZSHy8Z1A62z2
*'''Local points of interest (pubs, restaurants, bar):''' [https://www.google.com/maps/d/viewer?mid=1FU63ik9Do3zzP6K2kvLVTtM2at8&ll=38.86221979925013%2C16.44292274999998&z=12 map (constantly updated)]

==Calendar==

'''''<font color="maroon">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 June 26, 2017 to see the relevant events.</font>'''''<br>

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NA-MIC Project Week
|view=WEEK
|dates=20170626/20170701
}}

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

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [http://www.imagenglab.com/newsite/project-week/ registration site].

# Kikinis, Ron :: Brigham and Women's Hospital, Harvard Medical School, USA
# Pieper, Steve :: Isomics, Inc., USA
# Kapur, Tina :: Brigham and Women's Hospital, Harvard Medical School, USA
# Spadea, Maria Francesca :: Magna Graecia University, Italy
# Zaffino, Paolo :: Magna Graecia University, Italy
# Scaramuzzino, Salvatore :: Magna Graecia University/ASL Vercelli, Italy
# Pileggi, Giampaolo :: Magna Graecia University, Italy/DKFZ, Germany
# Rackerseder, Julia :: Technische Universität München, Germany
# Pinter, Csaba :: Queen's University, Canada
# Scheherazade, Kraß :: University of Bremen, Germany
# Gerig, Guido
# Punzo, Davide :: Kapteyn Astronomical Institute, Netherlands
# Drouin, Simon

Project Week 25

2017-03-13T16:45:29Z

Lasso:

__NOTOC__

[[image:PW-Summer2017.png|300px]] [[image:IEL_logo.png|225px]]
<br>

=Welcome to the web page for the 25th Project Week!=

It is a pleasure to announce that the 25th Project week will be held in [https://goo.gl/maps/b9CpkFxNyWN2 Catanzaro Lido] (Calabria, Italy) on June 26-30, 2017. This is the first time in Italy for the Slicer Community, and the event is organized in cooperation with [http://www.imagenglab.com ImagEngLab]. Catanzaro Lido is a city on the Ionian Sea, in the middle of Squillace Gulf where, according to the ancient legend, Odysseus started his journey back to Ithaca. Of course bring your swimsuit...the conference room and the hotel are 20 meters far away from the beach!

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

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

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

===Local Organizing Committee===
*[http://www.imagenglab.com/newsite/mf_spadea/ Maria Francesca Spadea, PhD]
*[http://www.imagenglab.com/newsite/paolo_zaffino/ Paolo Zaffino, PhD].

==Logistics==

*'''Dates:''' June 26-30, 2017. Consider staying for one more day (leaving Sunday morning), as a day off in a gorgeous seaplace is planned on July 1st. More details will be posted soon.
*'''Location:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]
**[mailto:prenotazioni@hotelperladelporto.it Booking]. Subject line: "Slicer Summer Project Week 2017". To guarantee the discount and room availability, reservation must be completed by '''June 1st, 2017'''.
*'''REGISTRATION:''' To register please visit this [http://www.imagenglab.com/newsite/project-week page]
*'''Registration Fee:''' 320€ and it includes lunches, coffee breaks and airport connections
*'''Hotel:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. The closest airport is [http://www.lameziaairport.it/english/ Lamezia Terme Airport (IATA: SUF)].

2017 Winter Project Week/ImprovementsToSegmentEditor

2017-01-16T17:44:26Z

Lasso: /* Feedbacks and status of implementation */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
Image:SegmentationHighlights01s.png|Highlights of segmentations 1
Image:SegmentationHighlights02s.png|Highlights of segmentations 2
Image:20160526_SegmentationObject.PNG|Segmentation object

</gallery>

==Key Investigators==
* Csaba Pinter (Queen's)
* Andras Lasso (Queen's)

==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;"
|

* Segment Editor is the new version of the Editor module used for segmentating structures from anatomical images
* The module is quite new, so we'd love to
** help people adopt the new module
** hear any feedback about the module
|

* Breakout session in Kiva room at 12PM on Wednesday
|

* About 30 participants. Presentation + demo + discussion
* Basics of the underlying Segmentations infrastructure presented (Csaba): [https://www.slicer.org/w/images/6/64/20160526_Segmentations.pptx these slides] ([https://www.slicer.org/w/images/a/ae/20160526_Segmentations.pdf PDF]) (This is a longer version of the slides presented. More information on the [https://www.slicer.org/wiki/Documentation/Nightly/Modules/Segmentations Segmentations module wiki page])
* Segment Editor features presented (Andras)
** CTACardio
*** Thresholding
**** Apply
**** Crop right arm with scissors in slice view, circle ROI
**** Create model
**** Undo
**** Use for paint
*** Paint:
**** Segment vessel in right arm
**** Create model
**** Change spacing
**** Sphere paint
*** Hollow model:
**** Copy segment
**** Grow segment
**** Subtract segment
**** Cut ends
*** Masking:
**** Editable area: inside all segments
**** Paint
**** Grow
**** New segment, Outside all segments
**** Grow
**** New segment, Overwrite other segments (default)
**** Paint
**** Overwrite other segments: None
** Auto-complete:
*** Geometric:
**** CTACardio
**** Abdominal muscles
*** Growcut
**** MRBrainTumor1
**** Growcut
**** Fix leakage
**** Smoothing
**** Segment stats
** Scissors:
*** CTChest, bone threshold
*** Island / Keep largest
*** Create surface
*** Create new segment (for ribs)
*** Editable: inside all
*** Scissors - fill outside
*** Split islands to segments
*** Separate lowest vertebra with 3d scissors
** Slice thickness is used by paint tool 2D size
** Segmentation on oblique slices
** Segmentation on vesselness filtering result
* '''Video coming soon'''
* Discussion meeting minutes
** Rename Apply for paint to Use as mask in all effects (in Threshold)
** Logical/Copy -> Copy from
** Threshold is easy to leave on, and then the result will be surprising (e.g. when expanding)
** Clipping circle, adding margin (Adam)
** First master volume resolution remains the segment resolution -> make it clearer?
*** Explain master volume in a tooltip or similar
** Auto-complete/Fill/Initialize -> rename to make it clear what it does (Preview?)
** Alexis' comments
*** Create surface button name and icon (suggests that it creates a model node) -> Show surface? (may be confusing due to the wait)
*** Confusion about Segmentations and Segment Editor (Add/Remove is possible in two places)
*** Auto-complete contains very different operations -> make it two buttons?
** Effect button size and layout issues -> Make it more similar to Quantitative Reporting? (Undo/redo under effects, remove the empty area in the effects box)
** Jump to center of the segment in the slice views (Greg) -> Actions in the table or similarly to markups?
** 3D cursor in the 3D view -> moves in slices if you are not super careful not to move the mouse before clicking
** Template effect extension
** Volume clip features in segment editor (Christian) -> User interactions might be problematic
|}

==Background and References==


== Feedbacks and status of implementation ==
* To be processed
** Rename Apply for paint to Use as mask in all effects (in Threshold)
** Logical/Copy -> Copy from
** Threshold is easy to leave on, and then the result will be surprising (e.g. when expanding)
** Clipping circle, adding margin (Adam)
** First master volume resolution remains the segment resolution -> make it clearer?
*** Explain master volume in a tooltip or similar
** Auto-complete/Fill/Initialize -> rename to make it clear what it does (Preview?)
** Create surface button name and icon (suggests that it creates a model node) -> Show surface? (may be confusing due to the wait)
** Confusion about Segmentations and Segment Editor (Add/Remove is possible in two places)
** Auto-complete contains very different operations -> make it two buttons?
** Effect button size and layout issues -> Make it more similar to Quantitative Reporting? (Undo/redo under effects, remove the empty area in the effects box)
** Jump to center of the segment in the slice views (Greg) -> Actions in the table or similarly to markups?
** 3D cursor in the 3D view -> moves in slices if you are not super careful not to move the mouse before clicking
** Template effect extension
** Volume clip features in segment editor (Christian) -> User interactions might be problematic
** Lots of wasted space around effect buttons
** Place large undo/redo buttons below effect list? -> would waste valuable vertical space
** Work more with meaningful icons/buttons (including tooltips) which would improve the overall user experience. Specifically:
*** Shrink and grow could be replaced by checkable buttons that symbolize shrink/grow
** Make effects work on grayscale images (maybe convert when we resample?)
** Draw text (on 3D, maybe on 2D; could be implemented by creating the mask by a scissor-like method and then grow or erode the segment)
** Mirror segment along axis (typically needed for using healthy side as a template for reconstructing damaged side)
** Fixed-radius circle scissors (allow define and accurate diameter using a spinbox and draw it by a single click)
** Add more keyboard shortcuts (not just for effect 1-6)

2017 Winter Project Week/ImprovementsToSegmentEditor

2017-01-16T17:34:33Z

Lasso:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
Image:SegmentationHighlights01s.png|Highlights of segmentations 1
Image:SegmentationHighlights02s.png|Highlights of segmentations 2
Image:20160526_SegmentationObject.PNG|Segmentation object

</gallery>

==Key Investigators==
* Csaba Pinter (Queen's)
* Andras Lasso (Queen's)

==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;"
|

* Segment Editor is the new version of the Editor module used for segmentating structures from anatomical images
* The module is quite new, so we'd love to
** help people adopt the new module
** hear any feedback about the module
|

* Breakout session in Kiva room at 12PM on Wednesday
|

* About 30 participants. Presentation + demo + discussion
* Basics of the underlying Segmentations infrastructure presented (Csaba): [https://www.slicer.org/w/images/6/64/20160526_Segmentations.pptx these slides] ([https://www.slicer.org/w/images/a/ae/20160526_Segmentations.pdf PDF]) (This is a longer version of the slides presented. More information on the [https://www.slicer.org/wiki/Documentation/Nightly/Modules/Segmentations Segmentations module wiki page])
* Segment Editor features presented (Andras)
** CTACardio
*** Thresholding
**** Apply
**** Crop right arm with scissors in slice view, circle ROI
**** Create model
**** Undo
**** Use for paint
*** Paint:
**** Segment vessel in right arm
**** Create model
**** Change spacing
**** Sphere paint
*** Hollow model:
**** Copy segment
**** Grow segment
**** Subtract segment
**** Cut ends
*** Masking:
**** Editable area: inside all segments
**** Paint
**** Grow
**** New segment, Outside all segments
**** Grow
**** New segment, Overwrite other segments (default)
**** Paint
**** Overwrite other segments: None
** Auto-complete:
*** Geometric:
**** CTACardio
**** Abdominal muscles
*** Growcut
**** MRBrainTumor1
**** Growcut
**** Fix leakage
**** Smoothing
**** Segment stats
** Scissors:
*** CTChest, bone threshold
*** Island / Keep largest
*** Create surface
*** Create new segment (for ribs)
*** Editable: inside all
*** Scissors - fill outside
*** Split islands to segments
*** Separate lowest vertebra with 3d scissors
** Slice thickness is used by paint tool 2D size
** Segmentation on oblique slices
** Segmentation on vesselness filtering result
* '''Video coming soon'''
* Discussion meeting minutes
** Rename Apply for paint to Use as mask in all effects (in Threshold)
** Logical/Copy -> Copy from
** Threshold is easy to leave on, and then the result will be surprising (e.g. when expanding)
** Clipping circle, adding margin (Adam)
** First master volume resolution remains the segment resolution -> make it clearer?
*** Explain master volume in a tooltip or similar
** Auto-complete/Fill/Initialize -> rename to make it clear what it does (Preview?)
** Alexis' comments
*** Create surface button name and icon (suggests that it creates a model node) -> Show surface? (may be confusing due to the wait)
*** Confusion about Segmentations and Segment Editor (Add/Remove is possible in two places)
*** Auto-complete contains very different operations -> make it two buttons?
** Effect button size and layout issues -> Make it more similar to Quantitative Reporting? (Undo/redo under effects, remove the empty area in the effects box)
** Jump to center of the segment in the slice views (Greg) -> Actions in the table or similarly to markups?
** 3D cursor in the 3D view -> moves in slices if you are not super careful not to move the mouse before clicking
** Template effect extension
** Volume clip features in segment editor (Christian) -> User interactions might be problematic
|}

==Background and References==


== Feedbacks and status of implementation ==
* To be processed
** Rename Apply for paint to Use as mask in all effects (in Threshold)
** Logical/Copy -> Copy from
** Threshold is easy to leave on, and then the result will be surprising (e.g. when expanding)
** Clipping circle, adding margin (Adam)
** First master volume resolution remains the segment resolution -> make it clearer?
*** Explain master volume in a tooltip or similar
** Auto-complete/Fill/Initialize -> rename to make it clear what it does (Preview?)
** Create surface button name and icon (suggests that it creates a model node) -> Show surface? (may be confusing due to the wait)
** Confusion about Segmentations and Segment Editor (Add/Remove is possible in two places)
** Auto-complete contains very different operations -> make it two buttons?
** Effect button size and layout issues -> Make it more similar to Quantitative Reporting? (Undo/redo under effects, remove the empty area in the effects box)
** Jump to center of the segment in the slice views (Greg) -> Actions in the table or similarly to markups?
** 3D cursor in the 3D view -> moves in slices if you are not super careful not to move the mouse before clicking
** Template effect extension
** Volume clip features in segment editor (Christian) -> User interactions might be problematic
** Lots of wasted space around effect buttons
** Place large undo/redo buttons below effect list? -> would waste valuable vertical space
** Work more with meaningful icons/buttons (including tooltips) which would improve the overall user experience. Specifically:
*** Shrink and grow could be replaced by checkable buttons that symbolize shrink/grow
** Make effects work on grayscale images (maybe convert when we resample?)
** Draw text (on 3D, maybe on 2D)
** Mirror segment along axis (typically needed for using healthy side as a template for reconstructing damaged side)
** Fixed-radius circle scissors (allow define and accurate diameter using a spinbox and draw it by a single click)
** Add more keyboard shortcuts (not just for effect 1-6)

2017 Winter Project Week/ImprovementsToSegmentEditor

2017-01-16T15:38:01Z

Lasso:

2017 Winter Project Week/UpdatingCommunityForums

2017-01-11T19:45:23Z

Lasso: /* Background and References */

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

</gallery>

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

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

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

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

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

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

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

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

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

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

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

==Requirements==
* [high] Get email notification about specific themes (releases, announcements, sub-community, such as shape analysis, RT, ...)
* [high] Import existing users
* [medium] Authentication with github
* [medium] Option for yearly billing
* [medium] Polls (vote on features to be developed, collect community feedback for decisions, etc)
* [low] Answer posts through email
* [low] Vote for good answers, mark accepted answer

2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction

2017-01-09T19:13:39Z

Lasso:

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

Image:Chae2015-Fig4.png
</gallery>

==Key Investigators==
* Michael Chae (Monash University, Australia)
* Andras Lasso (Queen’s University, Canada)
* David Garcia (Queen’s University, Canada)
* Julian Smith (Monash University, Australia)
* Warren Rozen (Monash University, Australia)
* David Hunter-Smith (Monash University, Australia)

==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;"
|


* Develop tools to help surgeons plan breast reconstructive surgeries in patients with breast cancer:
** Volumetric analysis based on surface scans and pre-op volumetric images
** 3D-printed surgical planning template
* Current method requires extensive manual handling and is subsequently slow. We are aiming to develop automated or semi-automated techniques.
* Implement interface for inexpensive 3D scanners (Intel RealSense cameras) in Slicer

|


* Volumetric analysis:
** Current method [Chae2014]: We can perform volumetric analysis on any imaging platforms (e.g. CT, MRI, 3D scanners). For CT/MRI scanners, we’d manually segment “areas of interest” (i.e. total breast tissue, mammary tissue, breast implants) on their axial slices in Osirix software. We’d refer to 3D-reconstructed image of the breasts (on 3D Slicer) to help guide areas that we’d need to segment. We’re increasing finding it easier to segment certain areas (i.e. mammary tissue, breast implants) from axial slices loaded on 3D slicer, instead of Osirix. For 3D Scanner-derived images, we’d upload the 3D file on to MeshMixer software, from which the file will be meshed (e.g. cutting, making planes). These files will be sent to Blender software for volume calculation.
** We have been collecting the thresholding values used for segmenting breast tissues. We’d like to use these metrics, or other means, to automate/semi-automate breast volumetric analysis techniques

* 3D printed surgical planning template: In autologous breast reconstruction, we raise a flap of tissue (i.e. abdominal wall fat) based on a perforator vessel called, DIEP (deep inferior epigastric artery perforators) perforators. These course through muscle called rectus abdominis (aka “six packs”). We’d like to 3D print the patient-specific DIEP perforators and their surrounding rectus abdominis muscle for surgical planning. Currently, we can achieve this on 3D Slicer (manual segmentation via watershed method, island effect tool, and thresholding) but this is very difficult and time-consuming. It’ll be a great opportunity to make this process easier and also automate/semi-automate it.

|

*
|}

==Background and References==


1 in 8 women in the US will be diagnosed with breast cancer in their lifetime. As genetic testing for breast cancer, such as BRCA1/2, becomes more available, an increasing number of women will be diagnosed early and evidences show that more and more women are opting for aggressive surgery (i.e. mastectomy) early on to achieve cure. As a result, post-mastectomy breast reconstruction has become an important component of the holistic treatment of patients with breast cancer. Breast reconstruction with autologous tissue (i.e. one’s own tissue) bypasses risks associated with traditional implants and provides a stable, natural-appearing, long-term volume replacement. The most ideal source of tissue for breast reconstruction is the abdominal wall. These tissues are raised as a free flap tissue based on small vessels, called perforators. Unfortunately, there is a significant variance in perforator size and locations between individuals. Advancements in modern imaging technologies, such as computed tomographic angiography (CTA), has enabled surgeons to select the appropriate perforator and facilitate flap design, leading to improvements in clinical outcomes. However, their efficacy is limited by being displayed on a two-dimensional (2D) surface. In contrast, imaging-guided 3D-printed surgical planning solution can provide tactile feedback and a superior appreciation of visuospatial relationship between anatomical structures. (1-4)

* [Chae2014] Chae, M. P., Hunter-Smith, D. J., Spychal, R. T., Rozen, W. M. 3D volumetric analysis for planning breast reconstructive surgery. Breast Cancer Res Treat 2014;146:457-460.
* Rozen, W. M., Phillips, T. J., Ashton, M. W., Stella, D. L., Gibson, R. N., Taylor, G. I. Preoperative imaging for DIEA perforator flaps: a comparative study of computed tomographic angiography and Doppler ultrasound. Plast Reconstr Surg 2008;121:9-16.
* Masia, J., Clavero, J. A., Larranaga, J. R., Alomar, X., Pons, G., Serret, P. Multidetector-row computed tomography in the planning of abdominal perforator flaps. J Plast Reconstr Aesthet Surg 2006;59:594-599.
* Chae, M. P., Rozen, W. M., McMenamin, P. G., Findlay, M. W., Spychal, R. T., Hunter-Smith, D. J. Emerging Applications of Bedside 3D Printing in Plastic Surgery. Front Surg 2015;2:25.
* Gerstle, T. L., Ibrahim, A. M., Kim, P. S., Lee, B. T., Lin, S. J. A plastic surgery application in evolution: three-dimensional printing. Plast Reconstr Surg 2014;133:446-451.

2017 Winter Project Week

2017-01-09T19:05:23Z

Lasso: /* IGT: Navigation, Robotics, Surgical Planning */

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

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

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

==Logistics==

*'''Dates:''' January 9-13, 2017.
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)
*'''Transportation:''' Public transportation is highly encouraged, as no parking permits will be issued by MIT. For a list of local garages, please see [http://web.mit.edu/facilities/transportation/parking/visitors/public_parking.html here]
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].

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

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

==Conference Calls for Preparation==

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

==Calendar==

'''''<font color="maroon">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.</font>'''''<br>

{{#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]]

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

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

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

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

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

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

== Infrastructure ==
#[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)
#[[2017 Winter Project Week/ImprovementsToSegmentEditor | Improvements to Segment Editor]] (Csaba Pinter, Andras Lasso)
#[[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
#[[2017 Winter Project Week/UpdatingCommunityForums | Updating Slicer Community Infrastructure (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)
#[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
#[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)
#[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault)
#[[2017 Winter Project Week/Integrative_Intraoperative_Interface | Integrative Interface for Intraoperative Software Applications ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)

==Training and Dissemination==
#[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)
#[[2017 Winter Project Week/2017 NVIDIA Demo Contest|NVIDIA Demo Contest]] (Abdul Halabi, Abel Brown)

==Next project week==
#[[2017 Winter Project Week/Next project week| Next project week]] (Paolo Zaffino, Maria Francesca Spadea, Tina Kapur)

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/2017projectweek registration site].

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

2017 Winter Project Week/Tracked Ultrasound Standardization

2017-01-09T19:01:24Z

Lasso:

__NOTOC__
[[Image:UltrasoundToolGuidance3dOnly.gif|right]]
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* Andras Lasso (Queen's University, Canada)
* [http://nist.mni.mcgill.ca/?page_id=369 Simon Drouin] (Montreal Neurological Institute, Canada)
* Junichi Tokuda (Brigham and Women's Hospital, Harvard Medical School, USA)
* Longquan Chen (Brigham and Women's Hospital, Harvard Medical School, USA)
* Adam Rankin (Robarts Research Institute, Canada)
* [http://www.sintef.no/en/all-employees/employee/?EmpID=2596 Janne Beate Bakeng] (SINTEF, Norway)

==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;"
|

* [http://www.plustoolkit.org Plus toolkit] provides access to numerous hardware devices (imaging devices, tracking devices, navigations systems, sensors, etc.) and makes it available through [http://www.openigtlink.org OpenIGTLink] protocol
* Create a common library that makes communication with Plus (and OpenIGTLink-compatible devices or software) very simple:
** Ensure software interoperability
** Share software maintenance workload
** Make it easy to share new features
* Add specific features for tracked ultrasound and surgical navigation
|

* Finish implementation of remote control of PlusServerLauncher
* Implement the ultrasound control messages
* Merge IGSIO/OpenIGTLink into OpenIGTLink and close the IGSIO/OpenIGTLink repository
* Reintegrate IGSIO/OpenIGTLinkIO in OpenIGTLinkIF
* Develop a common high-level GUI to control OpenIGTLinkIO devices
|

*
|}

==Background and References==
*Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]
*Summer 2016 [[ 2016 Summer Project Week/Tracked Ultrasound Standardization | project page]]

2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction

2017-01-09T18:59:03Z

Lasso:

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

Image:Chae2015-Fig4.png
</gallery>

==Key Investigators==
* Michael Chae (Monash University, Australia)
* Andras Lasso (Queen’s University, Canada)
* David Garcia (Queen’s University, Canada)
* Julian Smith (Monash University, Australia)
* Warren Rozen (Monash University, Australia)
* David Hunter-Smith (Monash University, Australia)

==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;"
|


* Develop tools to help surgeons plan breast reconstructive surgeries in patients with breast cancer:
** Volumetric analysis based on surface scans and pre-op volumetric images
** 3D-printed surgical planning template
* Current method requires extensive manual handling and is subsequently slow. We are aiming to develop automated or semi-automated techniques.

|


* Volumetric analysis:
** Current method [Chae2014]: We can perform volumetric analysis on any imaging platforms (e.g. CT, MRI, 3D scanners). For CT/MRI scanners, we’d manually segment “areas of interest” (i.e. total breast tissue, mammary tissue, breast implants) on their axial slices in Osirix software. We’d refer to 3D-reconstructed image of the breasts (on 3D Slicer) to help guide areas that we’d need to segment. We’re increasing finding it easier to segment certain areas (i.e. mammary tissue, breast implants) from axial slices loaded on 3D slicer, instead of Osirix. For 3D Scanner-derived images, we’d upload the 3D file on to MeshMixer software, from which the file will be meshed (e.g. cutting, making planes). These files will be sent to Blender software for volume calculation.
** We have been collecting the thresholding values used for segmenting breast tissues. We’d like to use these metrics, or other means, to automate/semi-automate breast volumetric analysis techniques

* 3D printed surgical planning template: In autologous breast reconstruction, we raise a flap of tissue (i.e. abdominal wall fat) based on a perforator vessel called, DIEP (deep inferior epigastric artery perforators) perforators. These course through muscle called rectus abdominis (aka “six packs”). We’d like to 3D print the patient-specific DIEP perforators and their surrounding rectus abdominis muscle for surgical planning. Currently, we can achieve this on 3D Slicer (manual segmentation via watershed method, island effect tool, and thresholding) but this is very difficult and time-consuming. It’ll be a great opportunity to make this process easier and also automate/semi-automate it.

|

*
|}

==Background and References==


1 in 8 women in the US will be diagnosed with breast cancer in their lifetime. As genetic testing for breast cancer, such as BRCA1/2, becomes more available, an increasing number of women will be diagnosed early and evidences show that more and more women are opting for aggressive surgery (i.e. mastectomy) early on to achieve cure. As a result, post-mastectomy breast reconstruction has become an important component of the holistic treatment of patients with breast cancer. Breast reconstruction with autologous tissue (i.e. one’s own tissue) bypasses risks associated with traditional implants and provides a stable, natural-appearing, long-term volume replacement. The most ideal source of tissue for breast reconstruction is the abdominal wall. These tissues are raised as a free flap tissue based on small vessels, called perforators. Unfortunately, there is a significant variance in perforator size and locations between individuals. Advancements in modern imaging technologies, such as computed tomographic angiography (CTA), has enabled surgeons to select the appropriate perforator and facilitate flap design, leading to improvements in clinical outcomes. However, their efficacy is limited by being displayed on a two-dimensional (2D) surface. In contrast, imaging-guided 3D-printed surgical planning solution can provide tactile feedback and a superior appreciation of visuospatial relationship between anatomical structures. (1-4)

* [Chae2014] Chae, M. P., Hunter-Smith, D. J., Spychal, R. T., Rozen, W. M. 3D volumetric analysis for planning breast reconstructive surgery. Breast Cancer Res Treat 2014;146:457-460.
* Rozen, W. M., Phillips, T. J., Ashton, M. W., Stella, D. L., Gibson, R. N., Taylor, G. I. Preoperative imaging for DIEA perforator flaps: a comparative study of computed tomographic angiography and Doppler ultrasound. Plast Reconstr Surg 2008;121:9-16.
* Masia, J., Clavero, J. A., Larranaga, J. R., Alomar, X., Pons, G., Serret, P. Multidetector-row computed tomography in the planning of abdominal perforator flaps. J Plast Reconstr Aesthet Surg 2006;59:594-599.
* Chae, M. P., Rozen, W. M., McMenamin, P. G., Findlay, M. W., Spychal, R. T., Hunter-Smith, D. J. Emerging Applications of Bedside 3D Printing in Plastic Surgery. Front Surg 2015;2:25.
* Gerstle, T. L., Ibrahim, A. M., Kim, P. S., Lee, B. T., Lin, S. J. A plastic surgery application in evolution: three-dimensional printing. Plast Reconstr Surg 2014;133:446-451.

File:Chae2015-Fig4.png

2017-01-09T18:57:39Z

Lasso: Figure 4 from Chae, M. P., Hunter-Smith, D. J., Spychal, R. T., Rozen, W. M. 3D volumetric analysis for planning breast reconstructive surgery. Breast Cancer Res Treat 2014;146:457-460.

Figure 4 from Chae, M. P., Hunter-Smith, D. J., Spychal, R. T., Rozen, W. M. 3D volumetric analysis for planning breast reconstructive surgery. Breast Cancer Res Treat 2014;146:457-460.

2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction

2017-01-09T18:56:43Z

Lasso:

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

Image:Chae2015-Fig4.png
</gallery>

==Key Investigators==
* Michael Chae (Monash University, Australia)
* Andras Lasso (Queen’s University, Canada)
* Julian Smith (Monash University, Australia)
* Warren Rozen (Monash University, Australia)
* David Hunter-Smith (Monash University, Australia)

==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;"
|


* Develop tools to help surgeons plan breast reconstructive surgeries in patients with breast cancer:
** Volumetric analysis based on surface scans and pre-op volumetric images
** 3D-printed surgical planning template
* Current method requires extensive manual handling and is subsequently slow. We are aiming to develop automated or semi-automated techniques.

|


* Volumetric analysis:
** Current method [Chae2014]: We can perform volumetric analysis on any imaging platforms (e.g. CT, MRI, 3D scanners). For CT/MRI scanners, we’d manually segment “areas of interest” (i.e. total breast tissue, mammary tissue, breast implants) on their axial slices in Osirix software. We’d refer to 3D-reconstructed image of the breasts (on 3D Slicer) to help guide areas that we’d need to segment. We’re increasing finding it easier to segment certain areas (i.e. mammary tissue, breast implants) from axial slices loaded on 3D slicer, instead of Osirix. For 3D Scanner-derived images, we’d upload the 3D file on to MeshMixer software, from which the file will be meshed (e.g. cutting, making planes). These files will be sent to Blender software for volume calculation.
** We have been collecting the thresholding values used for segmenting breast tissues. We’d like to use these metrics, or other means, to automate/semi-automate breast volumetric analysis techniques

* 3D printed surgical planning template: In autologous breast reconstruction, we raise a flap of tissue (i.e. abdominal wall fat) based on a perforator vessel called, DIEP (deep inferior epigastric artery perforators) perforators. These course through muscle called rectus abdominis (aka “six packs”). We’d like to 3D print the patient-specific DIEP perforators and their surrounding rectus abdominis muscle for surgical planning. Currently, we can achieve this on 3D Slicer (manual segmentation via watershed method, island effect tool, and thresholding) but this is very difficult and time-consuming. It’ll be a great opportunity to make this process easier and also automate/semi-automate it.

|

*
|}

==Background and References==


1 in 8 women in the US will be diagnosed with breast cancer in their lifetime. As genetic testing for breast cancer, such as BRCA1/2, becomes more available, an increasing number of women will be diagnosed early and evidences show that more and more women are opting for aggressive surgery (i.e. mastectomy) early on to achieve cure. As a result, post-mastectomy breast reconstruction has become an important component of the holistic treatment of patients with breast cancer. Breast reconstruction with autologous tissue (i.e. one’s own tissue) bypasses risks associated with traditional implants and provides a stable, natural-appearing, long-term volume replacement. The most ideal source of tissue for breast reconstruction is the abdominal wall. These tissues are raised as a free flap tissue based on small vessels, called perforators. Unfortunately, there is a significant variance in perforator size and locations between individuals. Advancements in modern imaging technologies, such as computed tomographic angiography (CTA), has enabled surgeons to select the appropriate perforator and facilitate flap design, leading to improvements in clinical outcomes. However, their efficacy is limited by being displayed on a two-dimensional (2D) surface. In contrast, imaging-guided 3D-printed surgical planning solution can provide tactile feedback and a superior appreciation of visuospatial relationship between anatomical structures. (1-4)

* [Chae2014] Chae, M. P., Hunter-Smith, D. J., Spychal, R. T., Rozen, W. M. 3D volumetric analysis for planning breast reconstructive surgery. Breast Cancer Res Treat 2014;146:457-460.
* Rozen, W. M., Phillips, T. J., Ashton, M. W., Stella, D. L., Gibson, R. N., Taylor, G. I. Preoperative imaging for DIEA perforator flaps: a comparative study of computed tomographic angiography and Doppler ultrasound. Plast Reconstr Surg 2008;121:9-16.
* Masia, J., Clavero, J. A., Larranaga, J. R., Alomar, X., Pons, G., Serret, P. Multidetector-row computed tomography in the planning of abdominal perforator flaps. J Plast Reconstr Aesthet Surg 2006;59:594-599.
* Chae, M. P., Rozen, W. M., McMenamin, P. G., Findlay, M. W., Spychal, R. T., Hunter-Smith, D. J. Emerging Applications of Bedside 3D Printing in Plastic Surgery. Front Surg 2015;2:25.
* Gerstle, T. L., Ibrahim, A. M., Kim, P. S., Lee, B. T., Lin, S. J. A plastic surgery application in evolution: three-dimensional printing. Plast Reconstr Surg 2014;133:446-451.

2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction

2017-01-09T18:40:39Z

Lasso: /* Project Description */

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

</gallery>

==Key Investigators==
* Michael Chae (Monash University, Australia)
* Andras Lasso (Queen’s University, Canada)
* Julian Smith (Monash University, Australia)
* Warren Rozen (Monash University, Australia)
* David Hunter-Smith (Monash University, Australia)

==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;"
|


* Develop tools to help surgeons plan breast reconstructive surgeries in patients with breast cancer:
** Volumetric analysis based on surface scans and pre-op volumetric images
** 3D-printed surgical planning template
* Current method requires extensive manual handling and is subsequently slow. We are aiming to develop automated or semi-automated techniques.

|


* Volumetric analysis:
** Current method [Chae2014]: We can perform volumetric analysis on any imaging platforms (e.g. CT, MRI, 3D scanners). For CT/MRI scanners, we’d manually segment “areas of interest” (i.e. total breast tissue, mammary tissue, breast implants) on their axial slices in Osirix software. We’d refer to 3D-reconstructed image of the breasts (on 3D Slicer) to help guide areas that we’d need to segment. We’re increasing finding it easier to segment certain areas (i.e. mammary tissue, breast implants) from axial slices loaded on 3D slicer, instead of Osirix. For 3D Scanner-derived images, we’d upload the 3D file on to MeshMixer software, from which the file will be meshed (e.g. cutting, making planes). These files will be sent to Blender software for volume calculation.
** We have been collecting the thresholding values used for segmenting breast tissues. We’d like to use these metrics, or other means, to automate/semi-automate breast volumetric analysis techniques

* 3D printed surgical planning template: In autologous breast reconstruction, we raise a flap of tissue (i.e. abdominal wall fat) based on a perforator vessel called, DIEP (deep inferior epigastric artery perforators) perforators. These course through muscle called rectus abdominis (aka “six packs”). We’d like to 3D print the patient-specific DIEP perforators and their surrounding rectus abdominis muscle for surgical planning. Currently, we can achieve this on 3D Slicer (manual segmentation via watershed method, island effect tool, and thresholding) but this is very difficult and time-consuming. It’ll be a great opportunity to make this process easier and also automate/semi-automate it.

|

*
|}

==Background and References==


1 in 8 women in the US will be diagnosed with breast cancer in their lifetime. As genetic testing for breast cancer, such as BRCA1/2, becomes more available, an increasing number of women will be diagnosed early and evidences show that more and more women are opting for aggressive surgery (i.e. mastectomy) early on to achieve cure. As a result, post-mastectomy breast reconstruction has become an important component of the holistic treatment of patients with breast cancer. Breast reconstruction with autologous tissue (i.e. one’s own tissue) bypasses risks associated with traditional implants and provides a stable, natural-appearing, long-term volume replacement. The most ideal source of tissue for breast reconstruction is the abdominal wall. These tissues are raised as a free flap tissue based on small vessels, called perforators. Unfortunately, there is a significant variance in perforator size and locations between individuals. Advancements in modern imaging technologies, such as computed tomographic angiography (CTA), has enabled surgeons to select the appropriate perforator and facilitate flap design, leading to improvements in clinical outcomes. However, their efficacy is limited by being displayed on a two-dimensional (2D) surface. In contrast, imaging-guided 3D-printed surgical planning solution can provide tactile feedback and a superior appreciation of visuospatial relationship between anatomical structures. (1-4)

* [Chae2014] Chae, M. P., Hunter-Smith, D. J., Spychal, R. T., Rozen, W. M. 3D volumetric analysis for planning breast reconstructive surgery. Breast Cancer Res Treat 2014;146:457-460.
* Rozen, W. M., Phillips, T. J., Ashton, M. W., Stella, D. L., Gibson, R. N., Taylor, G. I. Preoperative imaging for DIEA perforator flaps: a comparative study of computed tomographic angiography and Doppler ultrasound. Plast Reconstr Surg 2008;121:9-16.
* Masia, J., Clavero, J. A., Larranaga, J. R., Alomar, X., Pons, G., Serret, P. Multidetector-row computed tomography in the planning of abdominal perforator flaps. J Plast Reconstr Aesthet Surg 2006;59:594-599.
* Chae, M. P., Rozen, W. M., McMenamin, P. G., Findlay, M. W., Spychal, R. T., Hunter-Smith, D. J. Emerging Applications of Bedside 3D Printing in Plastic Surgery. Front Surg 2015;2:25.
* Gerstle, T. L., Ibrahim, A. M., Kim, P. S., Lee, B. T., Lin, S. J. A plastic surgery application in evolution: three-dimensional printing. Plast Reconstr Surg 2014;133:446-451.

2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction

2017-01-09T18:38:56Z

Lasso:

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

</gallery>

==Key Investigators==
* Michael Chae (Monash University, Australia)
* Andras Lasso (Queen’s University, Canada)
* Julian Smith (Monash University, Australia)
* Warren Rozen (Monash University, Australia)
* David Hunter-Smith (Monash University, Australia)

==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;"
|


* Develop tools to help surgeons plan breast reconstructive surgeries in patients with breast cancer:
** Volumetric analysis based on surface scans and pre-op volumetric images
** 3D-printed surgical planning template
* Current method requires extensive manual handling and is subsequently slow. We are aiming to develop automated or semi-automated techniques.

|


* Volumetric analysis:
** Current method ([Chae2014]): We can perform volumetric analysis on any imaging platforms (e.g. CT, MRI, 3D scanners). For CT/MRI scanners, we’d manually segment “areas of interest” (i.e. total breast tissue, mammary tissue, breast implants) on their axial slices in Osirix software. We’d refer to 3D-reconstructed image of the breasts (on 3D Slicer) to help guide areas that we’d need to segment. We’re increasing finding it easier to segment certain areas (i.e. mammary tissue, breast implants) from axial slices loaded on 3D slicer, instead of Osirix. For 3D Scanner-derived images, we’d upload the 3D file on to MeshMixer software, from which the file will be meshed (e.g. cutting, making planes). These files will be sent to Blender software for volume calculation.
** We have been collecting the thresholding values used for segmenting breast tissues. We’d like to use these metrics, or other means, to automate/semi-automate breast volumetric analysis techniques

* 3D printed surgical planning template: In autologous breast reconstruction, we raise a flap of tissue (i.e. abdominal wall fat) based on a perforator vessel called, DIEP (deep inferior epigastric artery perforators) perforators. These course through muscle called rectus abdominis (aka “six packs”). We’d like to 3D print the patient-specific DIEP perforators and their surrounding rectus abdominis muscle for surgical planning. Currently, we can achieve this on 3D Slicer (manual segmentation via watershed method, island effect tool, and thresholding) but this is very difficult and time-consuming. It’ll be a great opportunity to make this process easier and also automate/semi-automate it.

|

*
|}

==Background and References==


1 in 8 women in the US will be diagnosed with breast cancer in their lifetime. As genetic testing for breast cancer, such as BRCA1/2, becomes more available, an increasing number of women will be diagnosed early and evidences show that more and more women are opting for aggressive surgery (i.e. mastectomy) early on to achieve cure. As a result, post-mastectomy breast reconstruction has become an important component of the holistic treatment of patients with breast cancer. Breast reconstruction with autologous tissue (i.e. one’s own tissue) bypasses risks associated with traditional implants and provides a stable, natural-appearing, long-term volume replacement. The most ideal source of tissue for breast reconstruction is the abdominal wall. These tissues are raised as a free flap tissue based on small vessels, called perforators. Unfortunately, there is a significant variance in perforator size and locations between individuals. Advancements in modern imaging technologies, such as computed tomographic angiography (CTA), has enabled surgeons to select the appropriate perforator and facilitate flap design, leading to improvements in clinical outcomes. However, their efficacy is limited by being displayed on a two-dimensional (2D) surface. In contrast, imaging-guided 3D-printed surgical planning solution can provide tactile feedback and a superior appreciation of visuospatial relationship between anatomical structures. (1-4)

* [Chae2014] Chae, M. P., Hunter-Smith, D. J., Spychal, R. T., Rozen, W. M. 3D volumetric analysis for planning breast reconstructive surgery. Breast Cancer Res Treat 2014;146:457-460.
* Rozen, W. M., Phillips, T. J., Ashton, M. W., Stella, D. L., Gibson, R. N., Taylor, G. I. Preoperative imaging for DIEA perforator flaps: a comparative study of computed tomographic angiography and Doppler ultrasound. Plast Reconstr Surg 2008;121:9-16.
* Masia, J., Clavero, J. A., Larranaga, J. R., Alomar, X., Pons, G., Serret, P. Multidetector-row computed tomography in the planning of abdominal perforator flaps. J Plast Reconstr Aesthet Surg 2006;59:594-599.
* Chae, M. P., Rozen, W. M., McMenamin, P. G., Findlay, M. W., Spychal, R. T., Hunter-Smith, D. J. Emerging Applications of Bedside 3D Printing in Plastic Surgery. Front Surg 2015;2:25.
* Gerstle, T. L., Ibrahim, A. M., Kim, P. S., Lee, B. T., Lin, S. J. A plastic surgery application in evolution: three-dimensional printing. Plast Reconstr Surg 2014;133:446-451.

2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction

2017-01-09T18:37:06Z

Lasso:

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

</gallery>

==Key Investigators==
* Michael Chae (Monash University, Australia)
* Andras Lasso (Queen’s University, Canada)
* Julian Smith (Monash University, Australia)
* Warren Rozen (Monash University, Australia)
* David Hunter-Smith (Monash University, Australia)

==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;"
|


* Develop tools to help surgeons plan breast reconstructive surgeries in patients with breast cancer:
** Volumetric analysis
** 3D-printed surgical planning template
* Current method requires extensive manual handling and is subsequently slow. We are aiming to develop automated or semi-automated techniques.

|


* Volumetric analysis:
** Current method ([Chae2014]): We can perform volumetric analysis on any imaging platforms (e.g. CT, MRI, 3D scanners). For CT/MRI scanners, we’d manually segment “areas of interest” (i.e. total breast tissue, mammary tissue, breast implants) on their axial slices in Osirix software. We’d refer to 3D-reconstructed image of the breasts (on 3D Slicer) to help guide areas that we’d need to segment. We’re increasing finding it easier to segment certain areas (i.e. mammary tissue, breast implants) from axial slices loaded on 3D slicer, instead of Osirix. For 3D Scanner-derived images, we’d upload the 3D file on to MeshMixer software, from which the file will be meshed (e.g. cutting, making planes). These files will be sent to Blender software for volume calculation.
** We have been collecting the thresholding values used for segmenting breast tissues. We’d like to use these metrics, or other means, to automate/semi-automate breast volumetric analysis techniques

* 3D printed surgical planning template: In autologous breast reconstruction, we raise a flap of tissue (i.e. abdominal wall fat) based on a perforator vessel called, DIEP (deep inferior epigastric artery perforators) perforators. These course through muscle called rectus abdominis (aka “six packs”). We’d like to 3D print the patient-specific DIEP perforators and their surrounding rectus abdominis muscle for surgical planning. Currently, we can achieve this on 3D Slicer (manual segmentation via watershed method, island effect tool, and thresholding) but this is very difficult and time-consuming. It’ll be a great opportunity to make this process easier and also automate/semi-automate it.

|

*
|}

==Background and References==


1 in 8 women in the US will be diagnosed with breast cancer in their lifetime. As genetic testing for breast cancer, such as BRCA1/2, becomes more available, an increasing number of women will be diagnosed early and evidences show that more and more women are opting for aggressive surgery (i.e. mastectomy) early on to achieve cure. As a result, post-mastectomy breast reconstruction has become an important component of the holistic treatment of patients with breast cancer. Breast reconstruction with autologous tissue (i.e. one’s own tissue) bypasses risks associated with traditional implants and provides a stable, natural-appearing, long-term volume replacement. The most ideal source of tissue for breast reconstruction is the abdominal wall. These tissues are raised as a free flap tissue based on small vessels, called perforators. Unfortunately, there is a significant variance in perforator size and locations between individuals. Advancements in modern imaging technologies, such as computed tomographic angiography (CTA), has enabled surgeons to select the appropriate perforator and facilitate flap design, leading to improvements in clinical outcomes. However, their efficacy is limited by being displayed on a two-dimensional (2D) surface. In contrast, imaging-guided 3D-printed surgical planning solution can provide tactile feedback and a superior appreciation of visuospatial relationship between anatomical structures. (1-4)

* [Chae2014] Chae, M. P., Hunter-Smith, D. J., Spychal, R. T., Rozen, W. M. 3D volumetric analysis for planning breast reconstructive surgery. Breast Cancer Res Treat 2014;146:457-460.
* Rozen, W. M., Phillips, T. J., Ashton, M. W., Stella, D. L., Gibson, R. N., Taylor, G. I. Preoperative imaging for DIEA perforator flaps: a comparative study of computed tomographic angiography and Doppler ultrasound. Plast Reconstr Surg 2008;121:9-16.
* Masia, J., Clavero, J. A., Larranaga, J. R., Alomar, X., Pons, G., Serret, P. Multidetector-row computed tomography in the planning of abdominal perforator flaps. J Plast Reconstr Aesthet Surg 2006;59:594-599.
* Chae, M. P., Rozen, W. M., McMenamin, P. G., Findlay, M. W., Spychal, R. T., Hunter-Smith, D. J. Emerging Applications of Bedside 3D Printing in Plastic Surgery. Front Surg 2015;2:25.
* Gerstle, T. L., Ibrahim, A. M., Kim, P. S., Lee, B. T., Lin, S. J. A plastic surgery application in evolution: three-dimensional printing. Plast Reconstr Surg 2014;133:446-451.

2017 Winter Project Week/Dinner

2017-01-06T18:55:15Z

Lasso: /* 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==

#Andras Lasso
#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
# Katie Mastrogiacomo

2017 Winter Project Week

2017-01-03T20:22:46Z

Lasso: /* Projects */

2016 Summer Project Week/Tracked Ultrasound Standardization

2016-06-25T08:41:00Z

Lasso:

__NOTOC__
[[Image:UltrasoundToolGuidance3dOnly.gif|right]]
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:CustusX_PLUS_igtl.png|CustusX+PLUS
</gallery>

==Key Investigators==
* Andras Lasso (Queen's University, Canada)
* Christian Askeland (SINTEF, Norway)
* Simon Drouin (Montreal Neurological Institute, Canada)
* Junichi Tokuda (Brigham and Women's Hospital, Harvard Medical School, USA)
* Longquan Chen (Brigham and Women's Hospital, Harvard Medical School, USA)
* Adam Rankin (Robarts Research Institute, Canada)
* Thomas Kirchner (German Cancer Research Center, Germany)

==Background==
* NAMIC Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* [http://www.plustoolkit.org Plus toolkit] provides access to numerous hardware devices (imaging devices, tracking devices, navigations systems, sensors, etc.) and makes it available through [http://www.openigtlink.org OpenIGTLink] protocol
* Create a common library that makes communication with Plus (and OpenIGTLink-compatible devices or software) very simple:
** Ensure software interoperability
** Share software maintenance workload
** Make it easy to share new features
* Add specific features for tracked ultrasound and surgical navigation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Formalize and complete OpenIGTLink v3 specification: mostly completed during [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | NAMIC Winter Project Week 2016]]
* Implement OpenIGTLink v3 specification in OpenIGTLink: commands and custom attributes
* Implement OpenIGTLinkIO library for convenient connection setup, command handling, conversion to/from VTK data objects, legacy OpenIGTLink (v1 and v2) support
* Implement tests and examples
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* [https://github.com/IGSIO/igsio.github.io OpenIGTLink v3] is implemented in [https://github.com/IGSIO/OpenIGTLink OpenIGTLink] and [http://www.plustoolkit.org Plus] toolkits
* [https://github.com/IGSIO/OpenIGTLinkIO OpenIGTLinkIO library] basic features implemented, used in CustusX, IBIS, Plus (server launcher)
* Next steps: make OpenIGTLinkIO feature complete, use OpenIGTLinkIO also in 3D Slicer and Plus (for making them simpler and easier to maintain)
</div>
</div>

2016 Summer Project Week/Tracked Ultrasound Standardization

2016-06-25T08:39:56Z

Lasso:

__NOTOC__
[[Image:UltrasoundToolGuidance3dOnly.gif|right]]
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:CustusX_PLUS_igtl.png|CustusX+PLUS
</gallery>

==Key Investigators==
* Andras Lasso (Queen's University, Canada)
* Christian Askeland (SINTEF, Norway)
* Simon Drouin (Montreal Neurological Institute, Canada)
* Junichi Tokuda (Brigham and Women's Hospital, Harvard Medical School, USA)
* Longquan Chen (Brigham and Women's Hospital, Harvard Medical School, USA)
* Adam Rankin (Robarts Research Institute, Canada)
* Thomas Kirchner (German Cancer Research Center, Germany)

==Background==
* NAMIC Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* [http://www.plustoolkit.org Plus toolkit] provides access to numerous hardware devices (imaging devices, tracking devices, navigations systems, sensors, etc.) and makes it available through [http://www.openigtlink.org OpenIGTLink] protocol
* Create a common library that makes communication with Plus (and OpenIGTLink-compatible devices or software) very simple:
** Ensure software interoperability
** Share software maintenance workload
** Make it easy to share new features
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Formalize and complete OpenIGTLink v3 specification: mostly completed during [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | NAMIC Winter Project Week 2016]]
* Implement OpenIGTLink v3 specification in OpenIGTLink: commands and custom attributes
* Implement OpenIGTLinkIO library for convenient connection setup, command handling, conversion to/from VTK data objects, legacy OpenIGTLink (v1 and v2) support
* Implement tests and examples
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* [https://github.com/IGSIO/igsio.github.io OpenIGTLink v3] is implemented in [https://github.com/IGSIO/OpenIGTLink OpenIGTLink] and [http://www.plustoolkit.org Plus] toolkits
* [https://github.com/IGSIO/OpenIGTLinkIO OpenIGTLinkIO library] basic features implemented, used in CustusX, IBIS, Plus (server launcher)
* Next steps: make OpenIGTLinkIO feature complete, use OpenIGTLinkIO also in 3D Slicer and Plus (for making them simpler and easier to maintain)
</div>
</div>

2016 Summer Project Week/Tracked Ultrasound Standardization

2016-06-25T08:16:36Z

Lasso: /* Project Description */

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

==Key Investigators==
* Andras Lasso (Queen's University, Canada)
* Christian Askeland (SINTEF, Norway)
* Simon Drouin (Montreal Neurological Institute, Canada)
* Junichi Tokuda (Brigham and Women's Hospital, Harvard Medical School, USA)
* Longquan Chen (Brigham and Women's Hospital, Harvard Medical School, USA)
* Adam Rankin (Robarts Research Institute, Canada)
* Thomas Kirchner (German Cancer Research Center, Germany)

==Background==
* NAMIC Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* [http://www.plustoolkit.org Plus toolkit] provides access to numerous hardware devices (imaging devices, tracking devices, navigations systems, sensors, etc.) and makes it available through [http://www.openigtlink.org OpenIGTLink] protocol
* Create a common library that makes communication with Plus (and OpenIGTLink-compatible devices or software) very simple:
** Ensure software interoperability
** Share software maintenance workload
** Make it easy to share new features
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Formalize and complete OpenIGTLink v3 specification: mostly completed during [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | NAMIC Winter Project Week 2016]]
* Implement OpenIGTLink v3 specification in OpenIGTLink: commands and custom attributes
* Implement OpenIGTLinkIO library for convenient connection setup, command handling, conversion to/from VTK data objects, legacy OpenIGTLink (v1 and v2) support
* Implement tests and examples
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* [https://github.com/IGSIO/igsio.github.io OpenIGTLink v3] is implemented in [https://github.com/IGSIO/OpenIGTLink OpenIGTLink] and [http://www.plustoolkit.org Plus] toolkits
* [https://github.com/IGSIO/OpenIGTLinkIO OpenIGTLinkIO library] basic features implemented, used in CustusX, IBIS, Plus (server launcher)
* Next steps: make OpenIGTLinkIO feature complete, use OpenIGTLinkIO also in 3D Slicer and Plus (for making them simpler and easier to maintain)
</div>
</div>

2016 Summer Project Week/Tracked Ultrasound Standardization

2016-06-25T08:10:16Z

Lasso: /* Project Description */

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

==Key Investigators==
* Andras Lasso (Queen's University, Canada)
* Christian Askeland (SINTEF, Norway)
* Simon Drouin (Montreal Neurological Institute, Canada)
* Junichi Tokuda (Brigham and Women's Hospital, Harvard Medical School, USA)
* Longquan Chen (Brigham and Women's Hospital, Harvard Medical School, USA)
* Adam Rankin (Robarts Research Institute, Canada)
* Thomas Kirchner (German Cancer Research Center, Germany)

==Background==
* NAMIC Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a common library with a convenient API that every application that wants to use OpenIGTLink can easily integrate
** Ensure software interoperability
** Share software maintenance workload
** Make it easy to share new features
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Formalize and complete OpenIGTLink v3 specification: mostly completed during [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | NAMIC Winter Project Week 2016]]
* Implement OpenIGTLink v3 specification in OpenIGTLink: commands and custom attributes
* Implement OpenIGTLinkIO library for convenient connection setup, command handling, conversion to/from VTK data objects, legacy OpenIGTLink (v1 and v2) support
* Implement tests and examples
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* [https://github.com/IGSIO/igsio.github.io OpenIGTLink v3] is implemented in [https://github.com/IGSIO/OpenIGTLink OpenIGTLink] and [http://www.plustoolkit.org Plus] toolkits
* [https://github.com/IGSIO/OpenIGTLinkIO OpenIGTLinkIO library] basic features implemented, used in CustusX, IBIS, Plus (server launcher)
* Next steps: make OpenIGTLinkIO feature complete, use OpenIGTLinkIO also in 3D Slicer and Plus (for making them simpler and easier to maintain)
</div>
</div>

2016 Summer Project Week/Tracked Ultrasound Standardization

2016-06-25T08:09:54Z

Lasso:

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

==Key Investigators==
* Andras Lasso (Queen's University, Canada)
* Christian Askeland (SINTEF, Norway)
* Simon Drouin (Montreal Neurological Institute, Canada)
* Junichi Tokuda (Brigham and Women's Hospital, Harvard Medical School, USA)
* Longquan Chen (Brigham and Women's Hospital, Harvard Medical School, USA)
* Adam Rankin (Robarts Research Institute, Canada)
* Thomas Kirchner (German Cancer Research Center, Germany)

==Background==
* NAMIC Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a common library with a convenient API that every application that wants to use OpenIGTLink can easily integrate
** Ensure software interoperability
** Share software maintenance workload
** Make it easy to share new features
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Formalize and complete OpenIGTLink v3 specification: mostly completed during [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | NAMIC Winter Project Week 2016]]
* Implement OpenIGTLink v3 specification in OpenIGTLink: commands and custom attributes
* Implement OpenIGTLinkIO library for convenient connection setup, command handling, conversion to/from VTK data objects, legacy OpenIGTLink (v1 and v2) support
* Implement tests and examples
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* https://github.com/IGSIO/igsio.github.io OpenIGTLink v3] is implemented in [https://github.com/IGSIO/OpenIGTLink OpenIGTLink] and [http://www.plustoolkit.org Plus] toolkits
* [https://github.com/IGSIO/OpenIGTLinkIO OpenIGTLinkIO library] basic features implemented, used in CustusX, IBIS, Plus (server launcher)
* Next steps: make OpenIGTLinkIO feature complete, use OpenIGTLinkIO also in 3D Slicer and Plus (for making them simpler and easier to maintain)
</div>
</div>

2016 Summer Project Week/Tracked Ultrasound Standardization

2016-06-25T07:59:24Z

Lasso:

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

==Key Investigators==
* Andras Lasso (Queen's University, Canada)
* Christian Askeland (SINTEF, Norway)
* Simon Drouin (Montreal Neurological Institute, Canada)
* Junichi Tokuda (Brigham and Women's Hospital, Harvard Medical School, USA)
* Longquan Chen (Brigham and Women's Hospital, Harvard Medical School, USA)
* Adam Rankin (Robarts Research Institute, Canada)
* Thomas Kirchner (German Cancer Research Center, Germany)

==Background==
* NAMIC Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Formalize and complete OpenIGTLink v3 specification
* Complete [https://github.com/IGSIO/igsio.github.io OpenIGTLink v3 implementation]
** Add support for metadata fields in v3 messages
* Finalize implementation of OpenIGTLink v3 in PLUS
* Finalize implementation of OpenIGTLink v3 in OpenIGTLink
* Finalize implementation of OpenIGTLink v3 in OpenIGTLinkRemote (SlicerIGT)
* Finalize separation of internals in OpenIGTLinkIF to enable re-use
* Maintain backwards compatibility
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement OpenIGTLink v3 specification in OpenIGTLink: commands and custom attributes
* Implement OpenIGTLinkIO library for convenient connection setup, command handling, conversion to/from VTK data objects, legacy OpenIGTLink (v1 and v2) support
* Implement tests and examples
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* OpenIGTLink v3 is implemented in OpenIGTLink and Plus toolkits
* OpenIGTLinkIO basic features implemented, used in CustusX, IBIS, Plus (server launcher)
* Next steps: make OpenIGTLinkIO feature complete, use OpenIGTLinkIO also in 3D Slicer and Plus (for making them simpler and easier to maintain)
</div>
</div>

2016 Summer Project Week/Tracked Ultrasound Standardization

2016-06-25T07:58:01Z

Lasso: /* Project Description */

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

==Key Investigators==
* Andras Lasso (Queen's University, Canada)
* Christian Askeland (SINTEF, Norway)
* Simon Drouin (Montreal Neurological Institute, Canada)
* Junichi Tokuda (Brigham and Women's Hospital, Harvard Medical School, USA)
* Longquan Chen (Brigham and Women's Hospital, Harvard Medical School, USA)
* Adam Rankin (Robarts Research Institute, Canada)
* Thomas Kirchner (German Cancer Research Center, Germany)

==Background==
* NAMIC Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Formalize and complete OpenIGTLink v3 specification
* Complete OpenIGTLink v3 implementation
** Add support for metadata fields in v3 messages
* Finalize implementation of OpenIGTLink v3 in PLUS
* Finalize implementation of OpenIGTLink v3 in OpenIGTLink
* Finalize implementation of OpenIGTLink v3 in OpenIGTLinkRemote (SlicerIGT)
* Finalize separation of internals in OpenIGTLinkIF to enable re-use
* Maintain backwards compatibility
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement OpenIGTLink v3 specification in OpenIGTLink: commands and custom attributes
* Implement OpenIGTLinkIO library for convenient connection setup, command handling, conversion to/from VTK data objects, legacy OpenIGTLink (v1 and v2) support
* Implement tests and examples
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* OpenIGTLink v3 is implemented in OpenIGTLink and Plus toolkits
* OpenIGTLinkIO basic features implemented, used in CustusX, IBIS, Plus (server launcher)
* Next steps: make OpenIGTLinkIO feature complete, use OpenIGTLinkIO also in 3D Slicer and Plus (for making them simpler and easier to maintain)
</div>
</div>

2016 Summer Project Week

2016-06-24T08:41:31Z

Lasso:

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>

<font color="red" size="30">Please fill in the survey about project weeks today!
[https://hms.az1.qualtrics.com/jfe/form/SV_6gK6BFe4Ivfo9RH click here]
</font>

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

='''Logistics'''=
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
*'''Location:''' Heidelberg, Germany.
**'''Getting to Heidelberg:''' Most will fly into Frankfurt Main International (FRA). At the airport look for "long distance trains". There you can buy a ticket from the machine to Heidelberg Hauptbahnhof (main station), around EUR 25. It usually takes less than an hour, with a change in Mannheim to a regional train. https://www.bahn.de . If you arrive on Sunday you can take a bus from the station to the Old Town or where your hotel is. Heidelberg is pretty small, look for directions on Google Maps. If you arrive on Monday see below on how to get to DKFZ directly.
**'''Monday''' at German Cancer Research Center - DKFZ
*** Enter through the main lobby ( just north of https://goo.gl/maps/e3ZbcsM5KC82, you can't miss it, it's the tallest building on campus with a big "dkfz." on top). The meeting room is on the 8th floor (H824, "Glaskasten", "glass box"). We will leave some instructions how to get there at the reception. The meeting time in the lobby will be 8:45am for those who wish to be at the meeting room by 9am. Official activities will start at noon with lunch.
*** To get to DKFZ in the morning you can use the Google Maps link above, public transport information is available there. For people staying in the Old Town, near Bismarckplatz or coming from the station it will be most likely Bus #32, exit at stop "Chirurgische Klinik", which is the second one after crossing the Neckar river. More detailed timetables at [http://fahrplanauskunft.vrn.de/vrn/XSLT_TRIP_REQUEST2?language=en the local transportation services VRN]. If you are up early there is also a nice [https://goo.gl/maps/SRRG6x7KDNU2 walk along the river].
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
***Suggested place for meetings is the Marstall student center ([https://www.google.de/maps/place/Zeughaus-Mensa+im+Marstall/@49.4124525,8.7056926,349m/data=!3m1!1e3!4m5!3m4!1s0x0000000000000000:0x8fd41be2e27fc36e!8m2!3d49.412919!4d8.7044381 map])
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
*Preparatory Conference Calls:
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

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

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

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

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

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

An introduction and summary of all previous Project Events is available [[Project_Events|here]].

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

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

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

='''Equipment'''=
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)
*[[2016_Summer_Project_Week:Equipment_Requests|Specialized equipment that people would like to have]] '''Updated June 16 2016'''

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

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

=== Infrastructure ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)
* [[2016 Summer Project Week/3D Lasso Selection | Implementation and Testing Performance of 3-D Lasso Selection within the Segmentation Editor Infrastructure ]] (Davide Punzo, Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2016 Summer Project Week/Segmentations Integration | Integration of Segmentations Infrastructure and Related Modules to Slicer Core]] (Csaba Pinter, Andras Lasso)
* [[2016 Summer Project Week/DICOM Tractography Results | Finalizing DICOM Tractography Results Implementation in DCMTK for BWH Project]] (Lauren O'Donnell, Isaiah Norton, Michael Onken)
* [[2016 Summer Project Week/Feedback for Project Week | Measuring the Impact of Project Weeks]] (Tina Kapur)
* [[2016 Summer Project WEB and 3D DICOM viewer to the rest of us]] (Koji Kobayashi)

=== Augmented Reality ===
* [[2016 Summer Project Week/OpenVR_integration | OpenVR Integration]] (Adam Rankin, Andras Lasso)
* [[2016 Summer Project Week/VRPN Integration | VRPN Integration]] (Dženan Zukić)
* [[2016 Summer Project Week/AR with a tablet device in the surgical room | AR with a Tablet Device in the Surgical Room]] (David García, Javier Pascau)
* [[2016 Summer Project Week/Auditory Display | Auditory Display Integration]] (David Black, Sarah Frisken, Christian Hansen, Longquan Chen)

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

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

=== Tutorial===
* [[2016 Summer Project Week/SlicerDMRIDocumentation | Tutorials and Documentations in SlicerDMRI]] (Lauren J. O'Donnell, Fan Zhang, Isaiah Norton)
* [[2016 Summer Project Week/CameraTutorial | How to use Basler Cameras for Medical Applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)
* [[2016 Summer Project Week/UniversityCourse | Create the basics of a university course about medical image computing]] (Attila Nagy)

= '''Registrants''' =

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

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

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

2016 Summer Project Week

2016-06-22T19:45:23Z

Lasso: /* Agenda */

__NOTOC__

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

='''Logistics'''=
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
*'''Location:''' Heidelberg, Germany.
**'''Getting to Heidelberg:''' Most will fly into Frankfurt Main International (FRA). At the airport look for "long distance trains". There you can buy a ticket from the machine to Heidelberg Hauptbahnhof (main station), around EUR 25. It usually takes less than an hour, with a change in Mannheim to a regional train. https://www.bahn.de . If you arrive on Sunday you can take a bus from the station to the Old Town or where your hotel is. Heidelberg is pretty small, look for directions on Google Maps. If you arrive on Monday see below on how to get to DKFZ directly.
**'''Monday''' at German Cancer Research Center - DKFZ
*** Enter through the main lobby ( just north of https://goo.gl/maps/e3ZbcsM5KC82, you can't miss it, it's the tallest building on campus with a big "dkfz." on top). The meeting room is on the 8th floor (H824, "Glaskasten", "glass box"). We will leave some instructions how to get there at the reception. The meeting time in the lobby will be 8:45am for those who wish to be at the meeting room by 9am. Official activities will start at noon with lunch.
*** To get to DKFZ in the morning you can use the Google Maps link above, public transport information is available there. For people staying in the Old Town, near Bismarckplatz or coming from the station it will be most likely Bus #32, exit at stop "Chirurgische Klinik", which is the second one after crossing the Neckar river. More detailed timetables at [http://fahrplanauskunft.vrn.de/vrn/XSLT_TRIP_REQUEST2?language=en the local transportation services VRN]. If you are up early there is also a nice [https://goo.gl/maps/SRRG6x7KDNU2 walk along the river].
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
***Suggested place for meetings is the Marstall student center ([https://www.google.de/maps/place/Zeughaus-Mensa+im+Marstall/@49.4124525,8.7056926,349m/data=!3m1!1e3!4m5!3m4!1s0x0000000000000000:0x8fd41be2e27fc36e!8m2!3d49.412919!4d8.7044381 map])
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
*Preparatory Conference Calls:
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

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

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

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

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

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

An introduction and summary of all previous Project Events is available [[Project_Events|here]].

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

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

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

='''Equipment'''=
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)
*[[2016_Summer_Project_Week:Equipment_Requests|Specialized equipment that people would like to have]] '''Updated June 16 2016'''

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

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

=== Infrastructure ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)
* [[2016 Summer Project Week/3D Lasso Selection | Implementation and Testing Performance of 3-D Lasso Selection within the Segmentation Editor Infrastructure ]] (Davide Punzo, Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2016 Summer Project Week/Segmentations Integration | Integration of Segmentations Infrastructure and Related Modules to Slicer Core]] (Csaba Pinter, Andras Lasso)
* [[2016 Summer Project Week/DICOM Tractography Results | Finalizing DICOM Tractography Results Implementation in DCMTK for BWH Project]] (Lauren O'Donnell, Isaiah Norton, Michael Onken)
* [[2016 Summer Project Week/Feedback for Project Week | Measuring the Impact of Project Weeks]] (Tina Kapur)
* [[2016 Summer Project WEB and 3D DICOM viewer to the rest of us]] (Koji Kobayashi)

=== Augmented Reality ===
* [[2016 Summer Project Week/OpenVR_integration | OpenVR Integration]] (Adam Rankin, Andras Lasso)
* [[2016 Summer Project Week/VRPN Integration | VRPN Integration]] (Dženan Zukić)
* [[2016 Summer Project Week/AR with a tablet device in the surgical room | AR with a Tablet Device in the Surgical Room]] (David García, Javier Pascau)
* [[2016 Summer Project Week/Auditory Display | Auditory Display Integration]] (David Black, Sarah Frisken, Christian Hansen, Longquan Chen)

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

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

=== Tutorial===
* [[2016 Summer Project Week/SlicerDMRIDocumentation | Tutorials and Documentations in SlicerDMRI]] (Lauren J. O'Donnell, Fan Zhang, Isaiah Norton)
* [[2016 Summer Project Week/CameraTutorial | How to use Basler Cameras for Medical Applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)
* [[2016 Summer Project Week/UniversityCourse | Create the basics of a university course about medical image computing]] (Attila Nagy)

= '''Registrants''' =

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

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

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

2016 Summer Project Week/Workshop on Shared Software Platform for Ultrasound-Guided Medical Interventions

2016-06-22T09:48:33Z

Lasso: /* Participants */

= Introduction =

Several groups have developed ultrasound-guided intervention systems in the last two decades but until recently these groups have worked mostly in parallel, independently from each other. The Image Guided Systems Inter-Operability (IGSIO) group was founded in 2016 January after lengthy discussions regarding the standardization of tracked ultrasound communication to work towards improving the interoperability between industrial products and research software platforms. See more information about this effort at http://igsio.github.io/.

The goal of this workshop is to promote the concept and practice of a shared software platform for ultrasound-guided interventions. Participants will learn, in practice, to build clinical applications using software platform tools.

= Tentative agenda (keep checking this page for more details) =

* 9-10am: Introduction of existing open-source infrastructure for building ultrasound-guided intervention systems
** [[Media:Slicelets2016.pdf|Plus/SlicerIGT/3DSlicer (Andras Lasso)]]
** CustusX
** IBIS
* 10.30am-12pm: Bring your own problem - discussion of implementation options for specific clinical procedures using open-source platforms.
** EM needle guidance in breast brachytherapy (Thomas Vaughan)
** Tracked ultrasound guided lumpectomy (Tamas Ungi)
** <add your name and clinical application here>
* Afternoon: Hands-on session for setting up prototype systems for ultrasound guidance and tool navigation.

= Registration =

No registration is required, just add your name to the participant list below or send an email to Andras Lasso (lasso@queensu.ca).

= Participants =
* Christian Askeland
* Janne Beate Bakeng
* David Black
* Longquan Chen
* Lauren O'Donnell
* Simon Drouin
* Jon Eiesland
* Sarah Frisken
* Mónica García-Sevilla
* Verónica García-Vazquez
* Thomas Kirchner
* Bojan Kocev
* Ines Machado
* David García-Mato
* Hans Meine
* Javier Pascau
* Steve Pieper
* Csaba Pinter
* Adam Rankin
* Ole Vegard Solberg
* Yannick Suter
* Junichi Tokuda
* Tamas Ungi
* Rocío Lopez-Velazco

2016 Summer Project Week/Workshop on Shared Software Platform for Ultrasound-Guided Medical Interventions

2016-06-22T08:48:17Z

Lasso: /* Participants */

= Introduction =

Several groups have developed ultrasound-guided intervention systems in the last two decades but until recently these groups have worked mostly in parallel, independently from each other. The Image Guided Systems Inter-Operability (IGSIO) group was founded in 2016 January after lengthy discussions regarding the standardization of tracked ultrasound communication to work towards improving the interoperability between industrial products and research software platforms. See more information about this effort at http://igsio.github.io/.

The goal of this workshop is to promote the concept and practice of a shared software platform for ultrasound-guided interventions. Participants will learn, in practice, to build clinical applications using software platform tools.

= Tentative agenda (keep checking this page for more details) =

* 9-10am: Introduction of existing open-source infrastructure for building ultrasound-guided intervention systems
** [[Media:Slicelets2016.pdf|Plus/SlicerIGT/3DSlicer (Andras Lasso)]]
** CustusX
** IBIS
* 10.30am-12pm: Bring your own problem - discussion of implementation options for specific clinical procedures using open-source platforms.
** EM needle guidance in breast brachytherapy (Thomas Vaughan)
** Tracked ultrasound guided lumpectomy (Tamas Ungi)
** <add your name and clinical application here>
* Afternoon: Hands-on session for setting up prototype systems for ultrasound guidance and tool navigation.

= Registration =

No registration is required, just add your name to the participant list below or send an email to Andras Lasso (lasso@queensu.ca).

= Participants =
* Christian Askeland
* Janne Beate Bakeng
* Longquan Chen
* Simon Drouin
* Jon Eiesland
* Thomas Kirchner
* Adam Rankin
* Ole Vegard Solberg
* Junichi Tokuda
* Sarah Frisken
* Bojan Kocev
* Ines Machado
* Tamas Ungi
* David Black
* Lauren O'Donnell
* Yannick Suter
* Hans Meine
* David García-Mato
* Javier Pascau
* Rocío Lopez-Velazco
* Mónica García-Sevilla
* Verónica García-Vazquez
* Steve Pieper

2016 Summer Project Week/Workshop on Shared Software Platform for Ultrasound-Guided Medical Interventions

2016-06-22T08:38:51Z

Lasso: /* Tentative agenda (keep checking this page for more details) */

= Introduction =

Several groups have developed ultrasound-guided intervention systems in the last two decades but until recently these groups have worked mostly in parallel, independently from each other. The Image Guided Systems Inter-Operability (IGSIO) group was founded in 2016 January after lengthy discussions regarding the standardization of tracked ultrasound communication to work towards improving the interoperability between industrial products and research software platforms. See more information about this effort at http://igsio.github.io/.

The goal of this workshop is to promote the concept and practice of a shared software platform for ultrasound-guided interventions. Participants will learn, in practice, to build clinical applications using software platform tools.

= Tentative agenda (keep checking this page for more details) =

* 9-10am: Introduction of existing open-source infrastructure for building ultrasound-guided intervention systems
** [[Media:Slicelets2016.pdf|Plus/SlicerIGT/3DSlicer (Andras Lasso)]]
** CustusX
** IBIS
* 10.30am-12pm: Bring your own problem - discussion of implementation options for specific clinical procedures using open-source platforms.
** EM needle guidance in breast brachytherapy (Thomas Vaughan)
** Tracked ultrasound guided lumpectomy (Tamas Ungi)
** <add your name and clinical application here>
* Afternoon: Hands-on session for setting up prototype systems for ultrasound guidance and tool navigation.

= Registration =

No registration is required, just add your name to the participant list below or send an email to Andras Lasso (lasso@queensu.ca).

= Participants =
* Christian Askeland
* Janne Beate Bakeng
* Longquan Chen
* Simon Drouin
* Jon Eiesland
* Thomas Kirchner
* Adam Rankin
* Ole Vegard Solberg
* Junichi Tokuda
* Sarah Frisken
* Bojan Kocev
* Ines Machado
* Tamas Ungi
* David Black
* Lauren O'Donnell
* Yannick Suter
* Hans Meine
* David García-Mato
* Javier Pascau
* Rocío Lopez-Velazco
* Mónica García-Sevilla
* Verónica García-Vazquez

File:Slicelets2016.pdf

2016-06-22T08:37:26Z

Lasso: Overview presentation about how 3D Slicer can be customized for implementing complete application workflows.

Overview presentation about how 3D Slicer can be customized for implementing complete application workflows.

2016 Summer Project Week/Segmentations Integration

2016-06-20T12:09:01Z

Lasso:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:SegmentationHighlights01s.png|Highlights of segmentations 1
Image:SegmentationHighlights02s.png|Highlights of segmentations 2
Image:20160526_SegmentationObject.PNG|Segmentation object
Image:20160526_ConversionGraph.PNG|Conversion graph for automated conversions
Image:20160526_SegmentationsArchitecture.png|Segmentations architecture
Image:ContourRepresentations_201507.png|Representations
</gallery>

==Key Investigators==
* Csaba Pinter
* Andras Lasso
* Steve Pieper
* Jean-Christophe Fillion-Robin (to be consulted remotely)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Integration of the Segmentation infrastructure into Slicer core
* The infrastructure contains the following components:
** SegmentationCore: Pure VTK implementation of the segmentation object, oriented VTK image data and utilities, and the automated conversion mechanism
** Segmentation MRML: Segmentation MRML node, display node, storage node, displayable managers
** Segmentations module: Slicer module for handling segmentation nodes, various re-usable widgets, and subject hierarchy plugins
** Segment Editor: Slicer module for editing segmentation nodes directly. Similar to Editor, but has a C++ core, and extended functionality that makes use of the advanced Segmentations features
** Segment Morphology: Slicer module for performing expand/shrink and logical operations (union, intersection, subtraction) on segments. Its logic can be used in Segment Editor effects
** Segment Registration (?): Distance map based registration of segmentations (from SlicerProstate::DistanceMapBasedRegistration, integration TBD)
* [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx Presentation slides] explaining the motivation, features, and details of the infrastructure
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Move classes into Slicer core
** Convert to Slicer core coding conventions (curly brackets in line with the contained block)
** vtkSegmentationCore -> vtkAddon'''?'''
** Segmentations/MRML -> Libs/MRML/Core
** Segmentations/MRMLDM -> Libs/MRML/DisplayableManager
** Segmentations/Widgets -> MRML/Widgets'''?'''
** Segmentations/EditorEffects -> '''?'''
** Segmentations -> Modules/Loadable
** SegmentEditor -> Modules/Scripted
* Discuss possible integration vtkOrientedImageData to VTK core
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2016 Summer Project Week/Segmentations Integration

2016-06-20T12:03:05Z

Lasso:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:20160526_SegmentationObject.PNG|Segmentation object
Image:20160526_ConversionGraph.PNG|Conversion graph for automated conversions
Image:20160526_SegmentationsArchitecture.png|Segmentations architecture
Image:ContourRepresentations_201507.png|Representations
Image:SegmentationHighlights01s.png|Highlights of segmentations 1
Image:SegmentationHighlights02s.png|Highlights of segmentations 2
</gallery>

==Key Investigators==
* Csaba Pinter
* Andras Lasso
* Steve Pieper
* Jean-Christophe Fillion-Robin (to be consulted remotely)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Integration of the Segmentation infrastructure into Slicer core
* The infrastructure contains the following components:
** SegmentationCore: Pure VTK implementation of the segmentation object, oriented VTK image data and utilities, and the automated conversion mechanism
** Segmentation MRML: Segmentation MRML node, display node, storage node, displayable managers
** Segmentations module: Slicer module for handling segmentation nodes, various re-usable widgets, and subject hierarchy plugins
** Segment Editor: Slicer module for editing segmentation nodes directly. Similar to Editor, but has a C++ core, and extended functionality that makes use of the advanced Segmentations features
** Segment Morphology: Slicer module for performing expand/shrink and logical operations (union, intersection, subtraction) on segments. Its logic can be used in Segment Editor effects
** Segment Registration (?): Distance map based registration of segmentations (from SlicerProstate::DistanceMapBasedRegistration, integration TBD)
* [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx Presentation slides] explaining the motivation, features, and details of the infrastructure
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Move classes into Slicer core
** Convert to Slicer core coding conventions (curly brackets in line with the contained block)
** vtkSegmentationCore -> vtkAddon'''?'''
** Segmentations/MRML -> Libs/MRML/Core
** Segmentations/MRMLDM -> Libs/MRML/DisplayableManager
** Segmentations/Widgets -> MRML/Widgets'''?'''
** Segmentations/EditorEffects -> '''?'''
** Segmentations -> Modules/Loadable
** SegmentEditor -> Modules/Scripted
* Discuss possible integration vtkOrientedImageData to VTK core
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2016 Summer Project Week/Segmentations Integration

2016-06-20T12:02:20Z

Lasso:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:20160526_SegmentationObject.PNG|Segmentation object
Image:20160526_ConversionGraph.PNG|Conversion graph for automated conversions
Image:20160526_SegmentationsArchitecture.png|Segmentations architecture
Image:ContourRepresentations_201507.png|Representations
Image:SegmentationHighlights01s.png|Highlights of segmentations and segmentation editor 1
Image:SegmentationHighlights02s.png|Highlights of segmentations and segmentation editor 2
</gallery>

==Key Investigators==
* Csaba Pinter
* Andras Lasso
* Steve Pieper
* Jean-Christophe Fillion-Robin (to be consulted remotely)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Integration of the Segmentation infrastructure into Slicer core
* The infrastructure contains the following components:
** SegmentationCore: Pure VTK implementation of the segmentation object, oriented VTK image data and utilities, and the automated conversion mechanism
** Segmentation MRML: Segmentation MRML node, display node, storage node, displayable managers
** Segmentations module: Slicer module for handling segmentation nodes, various re-usable widgets, and subject hierarchy plugins
** Segment Editor: Slicer module for editing segmentation nodes directly. Similar to Editor, but has a C++ core, and extended functionality that makes use of the advanced Segmentations features
** Segment Morphology: Slicer module for performing expand/shrink and logical operations (union, intersection, subtraction) on segments. Its logic can be used in Segment Editor effects
** Segment Registration (?): Distance map based registration of segmentations (from SlicerProstate::DistanceMapBasedRegistration, integration TBD)
* [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx Presentation slides] explaining the motivation, features, and details of the infrastructure
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Move classes into Slicer core
** Convert to Slicer core coding conventions (curly brackets in line with the contained block)
** vtkSegmentationCore -> vtkAddon'''?'''
** Segmentations/MRML -> Libs/MRML/Core
** Segmentations/MRMLDM -> Libs/MRML/DisplayableManager
** Segmentations/Widgets -> MRML/Widgets'''?'''
** Segmentations/EditorEffects -> '''?'''
** Segmentations -> Modules/Loadable
** SegmentEditor -> Modules/Scripted
* Discuss possible integration vtkOrientedImageData to VTK core
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

File:SegmentationHighlights02s.png

2016-06-20T12:01:48Z

Lasso:

2016 Summer Project Week/Segmentations Integration

2016-06-20T12:01:29Z

Lasso:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:20160526_SegmentationObject.PNG|Segmentation object
Image:20160526_ConversionGraph.PNG|Conversion graph for automated conversions
Image:20160526_SegmentationsArchitecture.png|Segmentations architecture
Image:ContourRepresentations_201507.png|Representations
Image:SegmentationHighlights01s.png|Hightlights 1
</gallery>

==Key Investigators==
* Csaba Pinter
* Andras Lasso
* Steve Pieper
* Jean-Christophe Fillion-Robin (to be consulted remotely)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Integration of the Segmentation infrastructure into Slicer core
* The infrastructure contains the following components:
** SegmentationCore: Pure VTK implementation of the segmentation object, oriented VTK image data and utilities, and the automated conversion mechanism
** Segmentation MRML: Segmentation MRML node, display node, storage node, displayable managers
** Segmentations module: Slicer module for handling segmentation nodes, various re-usable widgets, and subject hierarchy plugins
** Segment Editor: Slicer module for editing segmentation nodes directly. Similar to Editor, but has a C++ core, and extended functionality that makes use of the advanced Segmentations features
** Segment Morphology: Slicer module for performing expand/shrink and logical operations (union, intersection, subtraction) on segments. Its logic can be used in Segment Editor effects
** Segment Registration (?): Distance map based registration of segmentations (from SlicerProstate::DistanceMapBasedRegistration, integration TBD)
* [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx Presentation slides] explaining the motivation, features, and details of the infrastructure
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Move classes into Slicer core
** Convert to Slicer core coding conventions (curly brackets in line with the contained block)
** vtkSegmentationCore -> vtkAddon'''?'''
** Segmentations/MRML -> Libs/MRML/Core
** Segmentations/MRMLDM -> Libs/MRML/DisplayableManager
** Segmentations/Widgets -> MRML/Widgets'''?'''
** Segmentations/EditorEffects -> '''?'''
** Segmentations -> Modules/Loadable
** SegmentEditor -> Modules/Scripted
* Discuss possible integration vtkOrientedImageData to VTK core
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>