NAMIC Wiki - User contributions [en]

Project Week 25/CNN for multi-plane prostate segmentation

2017-06-30T10:20:09Z

Ameyer: /* Illustrations */

__NOTOC__

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

==Key Investigators==
*[http://isgwww.cs.uni-magdeburg.de/isg/meyer.html Anneke Meyer] (University of Magdeburg, Germany)
*[http://www.spl.harvard.edu/pages/People/mehrtash Alireza Mehrtash] (Brigham and Women's Hospital, Harvard Medical School, USA)
*[http://isgwww.cs.uni-magdeburg.de/cas/ Christian Hansen] (University of Magdeburg, Germany)
*[http://www.spl.harvard.edu/pages/People/fedorov Andrey Fedorov] (Brigham and Women's Hospital, Harvard Medical School, USA)
*[http://www.mic.uni-bremen.de/jennifer-nitsch/ Jennifer Nitsch] (University of Bremen, Germany)

==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;"
|

For prostate lesion assessment, MRI volumes in sagittal, coronal and axial orientation are acquired. The goal is to segment the prostate in these volumes and fuse the segmentations in order to obtain better accuracy, especially in the apex and base regions (compared to segmentations obtained only on axial volumes).
|

* Work done:
**created training data for different orientations
** Automatic segmentation of each plane with Encoder-Decoder Network
* Work ahead:
** Explore, discuss and investigate different approaches for fusion of the segmentations, e.g. simple majority voting, suface reconstruction from point cloud, ...

|

* built framework for predicting and fusing the segmentations
* tested simple majority voting in isotropic voxel volumes
* Future Work:
** weighted voting depending on location and plane
** Surface extraction from point clouds

|}

==Illustrations==
[[File:MRIImage.png|thumb|MRIs of the prostate (axial, sagittal and coronal volume)]]
[[File:Segmentation2.png|thumb|example segmentation (apex, mid-gland and base slices).]]

==Background and References==

File:Segmentation2.png

2017-06-30T10:19:54Z

Ameyer:

example segmentation

Project Week 25/CNN for multi-plane prostate segmentation

2017-06-30T10:16:52Z

Ameyer: /* Illustrations */

__NOTOC__

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

==Key Investigators==
*[http://isgwww.cs.uni-magdeburg.de/isg/meyer.html Anneke Meyer] (University of Magdeburg, Germany)
*[http://www.spl.harvard.edu/pages/People/mehrtash Alireza Mehrtash] (Brigham and Women's Hospital, Harvard Medical School, USA)
*[http://isgwww.cs.uni-magdeburg.de/cas/ Christian Hansen] (University of Magdeburg, Germany)
*[http://www.spl.harvard.edu/pages/People/fedorov Andrey Fedorov] (Brigham and Women's Hospital, Harvard Medical School, USA)
*[http://www.mic.uni-bremen.de/jennifer-nitsch/ Jennifer Nitsch] (University of Bremen, Germany)

==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;"
|

For prostate lesion assessment, MRI volumes in sagittal, coronal and axial orientation are acquired. The goal is to segment the prostate in these volumes and fuse the segmentations in order to obtain better accuracy, especially in the apex and base regions (compared to segmentations obtained only on axial volumes).
|

* Work done:
**created training data for different orientations
** Automatic segmentation of each plane with Encoder-Decoder Network
* Work ahead:
** Explore, discuss and investigate different approaches for fusion of the segmentations, e.g. simple majority voting, suface reconstruction from point cloud, ...

|

* built framework for predicting and fusing the segmentations
* tested simple majority voting in isotropic voxel volumes
* Future Work:
** weighted voting depending on location and plane
** Surface extraction from point clouds

|}

==Illustrations==
[[File:MRIImage.png|thumb|MRIs of the prostate (axial, sagittal and coronal volume)]]

==Background and References==

File:MRIImage.png

2017-06-30T10:13:35Z

Ameyer:

MRIs of the prostate (axial, sagittal and coronal view)

Project Week 25/CNN for multi-plane prostate segmentation

2017-06-30T09:42:23Z

Ameyer: /* Project Description */

__NOTOC__

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

==Key Investigators==
*[http://isgwww.cs.uni-magdeburg.de/isg/meyer.html Anneke Meyer] (University of Magdeburg, Germany)
*[http://www.spl.harvard.edu/pages/People/mehrtash Alireza Mehrtash] (Brigham and Women's Hospital, Harvard Medical School, USA)
*[http://isgwww.cs.uni-magdeburg.de/cas/ Christian Hansen] (University of Magdeburg, Germany)
*[http://www.spl.harvard.edu/pages/People/fedorov Andrey Fedorov] (Brigham and Women's Hospital, Harvard Medical School, USA)
*[http://www.mic.uni-bremen.de/jennifer-nitsch/ Jennifer Nitsch] (University of Bremen, Germany)

==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;"
|

For prostate lesion assessment, MRI volumes in sagittal, coronal and axial orientation are acquired. The goal is to segment the prostate in these volumes and fuse the segmentations in order to obtain better accuracy, especially in the apex and base regions (compared to segmentations obtained only on axial volumes).
|

* Work done:
**created training data for different orientations
** Automatic segmentation of each plane with Encoder-Decoder Network
* Work ahead:
** Explore, discuss and investigate different approaches for fusion of the segmentations, e.g. simple majority voting, suface reconstruction from point cloud, ...

|

* built framework for predicting and fusing the segmentations
* tested simple majority voting in isotropic voxel volumes
* Future Work:
** weighted voting depending on location and plane
** Surface extraction from point clouds

|}

==Illustrations==
==Background and References==

Project Week 25

2017-06-21T15:19:33Z

Ameyer: /* Projects */

__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]]
 

=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].

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/725310144 click here] to join the videoconference (zoom is the tool as of May 31)

#(Tina Kapur) Hangout #1: April 5 ([[PW25 Hangouts Notes|Notes]])
#(Steve Pieper) Hangout #2: April 12: Web browser based computing: Dockerized Slicer with remote computing and GPU computing; Cornerstone/LesionTracker OHIF; XTK->AMI (threejs); ePad; vtk.js; QWebEngine;
#(Andras Lasso) Hangout #3: April 19: Connecting devices such as surgical navigation, ultrasound, 3D Slicer, PLUS, OpenIGTLink, Augmented reality;
#(Tina Kapur) Hangout #4: April 26: Deep Learning for Detection of Cancer and Instruments;
#(Simon Drouin) Hangout #5: May 3: Volume Rendering, Augmented Reality, and Virtual Reality. [https://docs.google.com/document/d/1UwdSzjnDm1yEeQ44OEhXWbH6V83Uo1Cd4KngxoyrRdI/edit Notes];
#(Tina Kapur) Hangout #6: May 10: For new participants: What is project week and how to get the most out of participating in it?
#(Andrey Fedorov) Hangout #7: May 17:DICOM for Quantitative Imaging and integration with processing applications. ([http://bit.ly/2017NSPW-DICOM notes])
#(Tina Kapur) Hangout #8: May 24:Discussion of Projects and teams that have been provided on the wiki page by participants, internationalization strategy for Slicer.
#(Francesca Spadea) Hangout #9: May 31: Review of local logistics -- all registered attendees should join
#(Tina Kapur) Hangout #10: June 7: Discussion of Projects, Project Pages
#(Francesca Spadea, Tina Kapur) Hangout #11: June 14: Review of Project Pages and Logistics
#(Francesca Spadea) Hangout #12: June 21: Review of local logistics -- all registered attendees with questions should join

==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 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 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 [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

=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

#[[Project_Week_25/NeedleSegmentation | Needle Segmentation]]
#[[Project_Week_25/Human-Computer_Interaction_under_sterile_conditions |Human-Computer Interaction under Sterile Conditions]]
# [[Project_Week_25/Next_Generation_GPU_Volume_Rendering | Next Generation of Volume Rendering in VTK ]]
# [[Project_Week_25/Tracked-Ultrasound-Standardization-IV | Tracked Ultrasound Standardization IV: Controlling US Acquisition]]
#[[Project_Week_25/Intra-operative deformable_registration_based_on_dense_point_cloud_reconstruction |Intra-operative Deformable Registration Based on Dense Point Cloud Reconstruction]]
#[[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]]
#[[Project_Week_25/CNN_for_multi-plane_prostate_segmentation | CNN for multi-plane prostate segmentation]]
#[[Project_Week_25/Conversion of DICOM Single Frame MR to Enhanced Multiframe | Conversion of DICOM Single Frame MR to Enhanced Multiframe]]
#[[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/Interactive_Manipulation_of_Plots_and_Graphs | Interactive Manipulation of Plots and Graphs]]
#[[Project_Week_25/Steerable Catheters Path Planner Extension for Brain Surgery Applications | Steerable Catheters Path Planner Extension for Brain Surgery Applications]]
#[[Project_Week_25/Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification | Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification]]
#[[Project_Week_25/DICOM_for_Quantitative_Imaging_and_Integration_with_Processing_Applications|DICOM for Quantitative Imaging and Integration with Processing Applications]]
#[[Project_Week_25/CNN for PseudoCT Generation from T1T2 MR|CNN for PseudoCT Generation from T1/T2 MRI]]
#[[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/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]]
#[[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]]
#[[Project_Week_25/Multimodal: | Multimodal, Multiresolution, Multivolume Data]]
#[[Project_Week_25/DICOM Segmentation Support for Cornerstone and OHIF Viewer | DICOM Segmentation Support for Cornerstone/ OHIF Viewer]]
#Slicer Export to VR (Juan Ruiz Alzola, Mike Halle)

=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

Project Week 25/CNN for multi-plane prostate segmentation

2017-06-21T15:19:29Z

Ameyer: Created page with "__NOTOC__ Back to Projects List ==Key Investigators== *[http://isgwww.cs.uni-magdeburg.de/isg/meyer.html Anneke Meyer] (University of Magdeburg,..."

__NOTOC__

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

==Key Investigators==
*[http://isgwww.cs.uni-magdeburg.de/isg/meyer.html Anneke Meyer] (University of Magdeburg, Germany)
*[http://www.spl.harvard.edu/pages/People/mehrtash Alireza Mehrtash] (Brigham and Women's Hospital, Harvard Medical School, USA)
*[http://isgwww.cs.uni-magdeburg.de/cas/ Christian Hansen] (University of Magdeburg, Germany)
*[http://www.spl.harvard.edu/pages/People/fedorov Andrey Fedorov] (Brigham and Women's Hospital, Harvard Medical School, USA)

==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;"
|

* Fusion of multi-plane segmentations of the prostate in order to obtain better accuracy, especially in the apex and base regions.
* Investigate multiple ways of fusing the segmentation of three network outputs.
|

* Work done:
**created training data for different orientations
** Automatic segmentation of each plane with Encoder-Decoder Network
* Work ahead:
** Explore, discuss and investigate different approaches for fusion of the segmentations, e.g. simple majority voting, suface reconstruction from point cloud, ...

|

|}

==Illustrations==
==Background and References==

Project Week 25

2017-06-21T15:12:54Z

Ameyer:

__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]]
 

=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].

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/725310144 click here] to join the videoconference (zoom is the tool as of May 31)

#(Tina Kapur) Hangout #1: April 5 ([[PW25 Hangouts Notes|Notes]])
#(Steve Pieper) Hangout #2: April 12: Web browser based computing: Dockerized Slicer with remote computing and GPU computing; Cornerstone/LesionTracker OHIF; XTK->AMI (threejs); ePad; vtk.js; QWebEngine;
#(Andras Lasso) Hangout #3: April 19: Connecting devices such as surgical navigation, ultrasound, 3D Slicer, PLUS, OpenIGTLink, Augmented reality;
#(Tina Kapur) Hangout #4: April 26: Deep Learning for Detection of Cancer and Instruments;
#(Simon Drouin) Hangout #5: May 3: Volume Rendering, Augmented Reality, and Virtual Reality. [https://docs.google.com/document/d/1UwdSzjnDm1yEeQ44OEhXWbH6V83Uo1Cd4KngxoyrRdI/edit Notes];
#(Tina Kapur) Hangout #6: May 10: For new participants: What is project week and how to get the most out of participating in it?
#(Andrey Fedorov) Hangout #7: May 17:DICOM for Quantitative Imaging and integration with processing applications. ([http://bit.ly/2017NSPW-DICOM notes])
#(Tina Kapur) Hangout #8: May 24:Discussion of Projects and teams that have been provided on the wiki page by participants, internationalization strategy for Slicer.
#(Francesca Spadea) Hangout #9: May 31: Review of local logistics -- all registered attendees should join
#(Tina Kapur) Hangout #10: June 7: Discussion of Projects, Project Pages
#(Francesca Spadea, Tina Kapur) Hangout #11: June 14: Review of Project Pages and Logistics
#(Francesca Spadea) Hangout #12: June 21: Review of local logistics -- all registered attendees with questions should join

==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 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 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 [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

=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

#[[Project_Week_25/NeedleSegmentation | Needle Segmentation]]
#[[Project_Week_25/Human-Computer_Interaction_under_sterile_conditions |Human-Computer Interaction under Sterile Conditions]]
# [[Project_Week_25/Next_Generation_GPU_Volume_Rendering | Next Generation of Volume Rendering in VTK ]]
# [[Project_Week_25/Tracked-Ultrasound-Standardization-IV | Tracked Ultrasound Standardization IV: Controlling US Acquisition]]
#[[Project_Week_25/Intra-operative deformable_registration_based_on_dense_point_cloud_reconstruction |Intra-operative Deformable Registration Based on Dense Point Cloud Reconstruction]]
#[[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]]
#[[Project_Week_25/Deep_Learning_Data_augmentation_for_prostate_segmentation | CNN for multi-plane prostate segmentation]]
#[[Project_Week_25/Conversion of DICOM Single Frame MR to Enhanced Multiframe | Conversion of DICOM Single Frame MR to Enhanced Multiframe]]
#[[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/Interactive_Manipulation_of_Plots_and_Graphs | Interactive Manipulation of Plots and Graphs]]
#[[Project_Week_25/Steerable Catheters Path Planner Extension for Brain Surgery Applications | Steerable Catheters Path Planner Extension for Brain Surgery Applications]]
#[[Project_Week_25/Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification | Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification]]
#[[Project_Week_25/DICOM_for_Quantitative_Imaging_and_Integration_with_Processing_Applications|DICOM for Quantitative Imaging and Integration with Processing Applications]]
#[[Project_Week_25/CNN for PseudoCT Generation from T1T2 MR|CNN for PseudoCT Generation from T1/T2 MRI]]
#[[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/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]]
#[[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]]
#[[Project_Week_25/Multimodal: | Multimodal, Multiresolution, Multivolume Data]]
#[[Project_Week_25/DICOM Segmentation Support for Cornerstone and OHIF Viewer | DICOM Segmentation Support for Cornerstone/ OHIF Viewer]]
#Slicer Export to VR (Juan Ruiz Alzola, Mike Halle)

=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

Project Week 25

2017-06-08T11:33:22Z

Ameyer:

__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]]
 

=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)Volume Rendering, Augmented Reality, and Virtual Reality. [https://docs.google.com/document/d/1UwdSzjnDm1yEeQ44OEhXWbH6V83Uo1Cd4KngxoyrRdI/edit Notes];[https://plus.google.com/hangouts/_/kitware.com/pw-25?hceid=a2l0d2FyZS5jb21fc2IwN2kxNzFvbGFjOWFhdmg0NmlyNDk1YzRAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ.fffs75fitbu0mvpl3vvmrcqf3s&authuser=0 hangout page]
#(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? [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page]
#(Andrey Fedorov) Hangout #7: Wednesday May 17, 2017, 9am EDT (GMT-4) DICOM for Quantitative Imaging and integration with processing applications. [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page] ([http://bit.ly/2017NSPW-DICOM notes])
#(Tina Kapur) Hangout #8: Wednesday May 24, 2017, 9am EDT (GMT-4) Review of Projects and teams that have been provided on the wiki page by participants, internationalization strategy for Slicer. [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page]
#(Francesca Spadea) Hangout #9: Wednesday May 31, 2017, 9am EDT (GMT-4) Review of local logistics -- all registered attendees should join [https://zoom.us/j/879371330 zoom "hangout" page]
#(Tina Kapur) Hangout #10: Wednesday June 7, 2017, 9am EDT (GMT-4) Review of Projects, Project Pages [https://zoom.us/j/879371330 zoom "hangout" page]
#(TBD) Hangout #11: Wednesday June 14, 2017, 9am EDT (GMT-4) TBD [https://zoom.us/j/879371330 zoom "hangout" page]
#(Francesca Spadea) Hangout #12: Wednesday June 21, 2017, 9am EDT (GMT-4) Review of local logistics -- all registered attendees with questions should join [https://zoom.us/j/879371330 zoom "hangout" page]

==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 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 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==

{{#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

=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

#[[Project_Week_25/NeedleSegmentation | Needle segmentation]] (Paolo Zaffino, Salvatore Scaramuzzino, Francesca Spadea, Guillaume Pernelle, Tina Kapur)
#DICOM Segmentation support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#Conversion of DICOM single frame MR to Enhanced Multiframe (Michael Onken, Steve Pieper, Andras Lasso, Csaba Pinter)
#[[Project_Week_25/Human-Computer_Interaction_under_sterile_conditions |Human-Computer Interaction under sterile conditions]] (Christian Hansen, Julian Hettig, Benjamin Hatscher, David Black, Marco Nolden, Juan Ruiz)
#Development and evaluation of new AR visualization techniques to support radiological interventions (Christian Hansen, Florian Heinrich, Andrè Mewes, Juan Ruiz, Marco Nolden)
#Interactive manipulation of plots and graphs: i) panning; ii) click and drag; iii) data selection (Davide Punzo, Steve Pieper, Jean-Christophe Fillion-Robin)
# [[Project_Week_25/Next_Generation_GPU_Volume_Rendering | Next generation of volume rendering in VTK ]] (Simon Drouin, Steve Pieper, Ole Vegard Solberg, Andras Lasso)
# [[Project_Week_25/Tracked-Ultrasound-Standardization-IV | Tracked Ultrasound Standardization IV: Controlling US acquisition]] (Simon Drouin, Ole Vegard Solberg, Csaba Pinter, Andras Lasso [electronically: Longquan Chen, Adam Rankin])
#Steerable catheters path planner extension for brain surgery applications (Alberto Favaro, Marlene Pinzi)
#Improving depth perception in interventional Augmented Reality visualization/(+sonification?) (Simon Drouin, Christian Hansen, David Black)
#DICOM for Quantitative Imaging and integration with processing applications (Jasmin Metzger, Marco Nolden, Steve Pieper)
#[[Project_Week_25/Intra-operative deformable_registration_based_on_dense_point_cloud_reconstruction |Intra-operative deformable registration based on dense point cloud reconstruction]] (Sara Moccia, Andre Mewes, Gino Gulamhussene, Florian Heinrich)
#[[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]] (Jennifer Nitsch, Scheherazade Kraß,)
#CNN for pseudoCT generation from T1/T2 MRI (Giampaolo Pileggi, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea, Gino Gulamhussene, Anneke Meyer)
#Internationalizing Slicer modules (Juan Ruiz Alzola, )
#Interfacing Slicer to mobile phone-controlled sensors (Juan Ruiz Alzola, )
#Slicer and 3D Printing (Juan Ruiz Alzola, Mike Halle, Christian Hansen)
#Slicer export to VR (Juan Ruiz Alzola, Mike Halle,)
#[[Project_Week_25/Deep_Learning_Data_augmentation_for_prostate_segmentation | Deep Learning: Data augmentation for prostate segmentation]] (Anneke Meyer, Christian Hansen, Alireza Mehrtash, Andrey Federov)
#2D Slice to 3D volume registration to support radiologic interventions (Gino Gulamhussene,)

=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
# Kraß, Scheherazade :: University of Bremen, Germany
# Gerig, Guido :: NYU Tandon School of Engineering, USA
# Punzo, Davide :: Kapteyn Astronomical Institute, 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 :: Universität Magdeburg, Germany
# Vegard Solberg, Ole :: Norway
# Heinrich, Florian :: Universität Magdeburg, Germany
# Mewes, André :: Universität Magdeburg, Germany
# Hatscher, Benjamin :: Universität Magdeburg, Germany
# Hettig, Julian :: Universität Magdeburg, Germany
# Meyer, Anneke :: Universität Magdeburg, Germany
# Gulamhussene, Gino :: Universität Magdeburg, Germany
# Cassetta, Roberto :: Politecnico di Milano, Italy
# Fillion-Robin, Jean-Christophe :: Kitware, USA
# Metzger, Jasmin :: DKFZ, Germany
# Fishbaugh, James :: NYU Tandon School of Engineering, USA
# Nolden, Marco :: DKFZ, Germany

2017 Winter Project Week/ProstateSectorSegmentation

2017-01-13T15:52:14Z

Ameyer: /* Project Description */

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

File:Prostate_MRI.PNG|Transversal slice of Prostate MRI.
File:SectorMap_Prostate.PNG|Sector Map according to PI-RADS v2.
File:ManualSegmentations.PNG|Manual Segmentation on transversal slices.
</gallery>

==Key Investigators==

* Anneke Meyer, University of Magdeburg (Germany)
* Andrey Fedorov, BWH
* Alireza Mehrtash, BWH
* Christian Hansen, University of Magdeburg (Germany)
* Teodora Szasz, University of Chicago

==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;"
|

* Segmentation of prostate and its sectors
* Specifically, segmentation of the following prostate sectors: peripheral zones, transition zones, central zone, anterior fibromuscular stroma and urethral sphincter
|

* Generation/ Refinement of ground truth data
* Creation of a 3D sector model
* Test with ProstateX challenge dataset (where zones of findings are given) to predict the zone with Deep Learning
* if more training data is available: deep learning for an automatic sector segmentation
* Try atlas-based segmentation approach to map zone segmentations on more datasets

|

* Creation of 3 zone segmentations of the prostate (different volumes)
* Prediction of zones for specific locations in ProstateX dataset with Deep Learning is in progress
* Next Steps: Create 3D model with higher resolution. Atlas based segmentation on more publicly available data.
|}

==Background and References==

2017 Winter Project Week/ProstateSectorSegmentation

2017-01-13T15:51:25Z

Ameyer: /* Project Description */

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

File:Prostate_MRI.PNG|Transversal slice of Prostate MRI.
File:SectorMap_Prostate.PNG|Sector Map according to PI-RADS v2.
File:ManualSegmentations.PNG|Manual Segmentation on transversal slices.
</gallery>

==Key Investigators==

* Anneke Meyer, University of Magdeburg (Germany)
* Andrey Fedorov, BWH
* Alireza Mehrtash, BWH
* Christian Hansen, University of Magdeburg (Germany)
* Teodora Szasz, University of Chicago

==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;"
|

* Segmentation of prostate and its sectors
* Specifically, segmentation of the following prostate sectors: peripheral zones, transition zones, central zone, anterior fibromuscular stroma and urethral sphincter
|

* Generation/ Refinement of ground truth data
* Creation of a 3D sector model
* Test with ProstateX challenge dataset (where zones of findings are given) to predict the zone with Deep Learning
* if more training data is available: deep learning for an automatic sector segmentation
* Try atlas-based segmentation approach to map zone segmentations on more datasets

|

* Creation of 3 zone segmentations of the prostate (different volumes)
* Prediction of zones for specific locations in ProstateX challenge with Deep Learning is in progress
* Next Steps: Create 3D model with higher resolution. Atlas based segmentation on more publicly available data.
|}

==Background and References==

2017 Winter Project Week/ProstateSectorSegmentation

2017-01-13T15:49:31Z

Ameyer: /* Project Description */

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

File:Prostate_MRI.PNG|Transversal slice of Prostate MRI.
File:SectorMap_Prostate.PNG|Sector Map according to PI-RADS v2.
File:ManualSegmentations.PNG|Manual Segmentation on transversal slices.
</gallery>

==Key Investigators==

* Anneke Meyer, University of Magdeburg (Germany)
* Andrey Fedorov, BWH
* Alireza Mehrtash, BWH
* Christian Hansen, University of Magdeburg (Germany)
* Teodora Szasz, University of Chicago

==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;"
|

* Segmentation of prostate and its sectors
* Specifically, segmentation of the following prostate sectors: peripheral zones, transition zones, central zone, anterior fibromuscular stroma and urethral sphincter
|

* Generation/ Refinement of ground truth data
* Creation of a 3D sector model
* Test with ProstateX challenge dataset (where zones of findings are given) to predict the zone with Deep Learning
* if more training data is available: deep learning for an automatic sector segmentation
* Try atlas-based segmentation approach to map zone segmentations on more datasets

|

* Creation of 3 zone segmentations of the prostate (different volumes)
* Prediction of zones in ProstateX challenge with Deep Learning is in progress
* Next Steps: Create 3D model with higher resolution. Atlas based segmentation on more publicly available data.
|}

==Background and References==

2017 Winter Project Week/ProstateSectorSegmentation

2017-01-13T15:45:33Z

Ameyer:

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

File:Prostate_MRI.PNG|Transversal slice of Prostate MRI.
File:SectorMap_Prostate.PNG|Sector Map according to PI-RADS v2.
File:ManualSegmentations.PNG|Manual Segmentation on transversal slices.
</gallery>

==Key Investigators==

* Anneke Meyer, University of Magdeburg (Germany)
* Andrey Fedorov, BWH
* Alireza Mehrtash, BWH
* Christian Hansen, University of Magdeburg (Germany)
* Teodora Szasz, University of Chicago

==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;"
|

* Segmentation of prostate and its sectors
* Specifically, segmentation of the following prostate sectors: peripheral zones, transition zones, central zone, anterior fibromuscular stroma and urethral sphincter
|

* Generation/ Refinement of ground truth data
* Creation of a 3D sector model
* Test with ProstateX challenge dataset (where zones of findings are given) to predict the zone with Deep Learning
* if more training data is available: deep learning for an automatic sector segmentation
* (Try (model-based) segmentation approach (costs for segmentation optimization can be derived for example from supervised classification of the gland tissue). The shape of individual sector models could be used as segmentation prior)

|

* Creation of 3 zone segmentations of the prostate (different volumes)
* Prediction of zones in ProstateX challenge with Deep Learning is in progress
|}

==Background and References==

File:ManualSegmentations.PNG

2017-01-13T15:44:02Z

Ameyer:

2017 Winter Project Week/ProstateSectorSegmentation

2017-01-13T14:33:48Z

Ameyer: /* Project Description */

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

File:Prostate_MRI.PNG|Transversal slice of Prostate MRI.
File:SectorMap_Prostate.PNG|Sector Map according to PI-RADS v2.
</gallery>

==Key Investigators==

* Anneke Meyer, University of Magdeburg (Germany)
* Andrey Fedorov, BWH
* Alireza Mehrtash, BWH
* Christian Hansen, University of Magdeburg (Germany)
* Teodora Szasz, University of Chicago

==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;"
|

* Segmentation of prostate and its sectors
* Specifically, segmentation of the following prostate sectors: peripheral zones, transition zones, central zone, anterior fibromuscular stroma and urethral sphincter
|

* Generation/ Refinement of ground truth data
* Creation of a 3D sector model
* Test with ProstateX challenge dataset (where zones of findings are given) to predict the zone with Deep Learning
* if more training data is available: deep learning for an automatic sector segmentation
* (Try (model-based) segmentation approach (costs for segmentation optimization can be derived for example from supervised classification of the gland tissue). The shape of individual sector models could be used as segmentation prior)

|

* Creation of 3 zone segmentations of the prostate (different volumes)
* Prediction of zones in ProstateX challenge with Deep Learning is in progress
|}

==Background and References==

2017 Winter Project Week

2017-01-09T18:02:13Z

Ameyer: /* Shape Analysis, Segmentation */

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

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

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

==Logistics==

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

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

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

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

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

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

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

==Conference Calls for Preparation==

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

==Calendar==

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

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

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

='''Projects'''=

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

== 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)
# [[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, 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, Julian Smith, Warren Rozen, David Hunter-Smith)
#[[2017 Winter Project Week/Intraoperative_Functional_Visualization | Visualization Concept for Intraoperative Use of Functional Mapping Data ]] (Rebekka Lauer, Anna Roethe, 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 | 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/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
#[[2017 Winter Project Week/UpdatingCommunityForums | Updating Community Forums (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)
#[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
#[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)
#[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)
#[[2017 Winter Project Week/Integrative_Intraoperative_Interface | Integrative Interface for Intraoperative Software Applications ]] (Rebekka Lauer, Anna Roethe, 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)

= '''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/ProstateSectorSegmentation

2017-01-09T18:00:13Z

Ameyer: /* Key Investigators */

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

File:Prostate_MRI.PNG|Transversal slice of Prostate MRI.
File:SectorMap_Prostate.PNG|Sector Map according to PI-RADS v2.
</gallery>

==Key Investigators==

* Anneke Meyer, University of Magdeburg (Germany)
* Andrey Fedorov, BWH
* Alireza Mehrtash, BWH
* Christian Hansen, University of Magdeburg (Germany)

==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;"
|

* Segmentation of prostate and its sectors
* Specifically, segmentation of the following prostate sectors: peripheral zones, transition zones, central zone, anterior fibromuscular stroma and urethral sphincter
|

* Generation/ Refinement of ground truth data
* Creation of a 3D sector model
* Initialization of segmentation with user interaction or atlas-based segmentation (in order to decrease search space)
* Try (model-based) segmentation approach (costs for segmentation optimization can be derived for example from supervised classification of the gland tissue). The shape of individual sector models could be used as segmentation prior
* if more training data is available: deep learning for a better cost generation or for an automatic sector segmentation

|

*
|}

==Background and References==

2017 Winter Project Week/ProstateSectorSegmentation

2017-01-08T15:22:31Z

Ameyer:

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

File:Prostate_MRI.PNG|Transversal slice of Prostate MRI.
File:SectorMap_Prostate.PNG|Sector Map according to PI-RADS v2.
</gallery>

==Key Investigators==

* Anneke Meyer, University of Magdeburg (Germany)
* Andrey Fedorov, BWH

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

* Segmentation of prostate and its sectors
* Specifically, segmentation of the following prostate sectors: peripheral zones, transition zones, central zone, anterior fibromuscular stroma and urethral sphincter
|

* Generation/ Refinement of ground truth data
* Creation of a 3D sector model
* Initialization of segmentation with user interaction or atlas-based segmentation (in order to decrease search space)
* Try (model-based) segmentation approach (costs for segmentation optimization can be derived for example from supervised classification of the gland tissue). The shape of individual sector models could be used as segmentation prior
* if more training data is available: deep learning for a better cost generation or for an automatic sector segmentation

|

*
|}

==Background and References==

File:SectorMap Prostate.PNG

2017-01-08T15:21:11Z

Ameyer: Sector map of prostate according to PI-RADS v2.

Sector map of prostate according to PI-RADS v2.

File:Prostate MRI.PNG

2017-01-08T15:15:16Z

Ameyer: MRI of prostate gland.

MRI of prostate gland.

2017 Winter Project Week/Dinner

2017-01-08T01:05:31Z

Ameyer: /* 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. Menu: Goat curry, chicken tikka masala, chana masala (vegan), saag paneer (veg), naan, rice
*Cost: $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
# Ron Kikinis
# Zora Kikinis
# Brian Helba
# Jennifer Nitsch
# Jean-Christophe Fillion-Robin
# Anneke Meyer

2017 Winter Project Week/ProstateSectorSegmentation

2017-01-02T21:22:24Z

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

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

</gallery>

==Key Investigators==

* Anneke Meyer, University of Magdeburg (Germany)
* Andrey Fedorov, BWH

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

* Segmentation of prostate and its sectors
* Specifically, segmentation of the following prostate sectors: peripheral zones, transition zones, central zone, anterior fibromuscular stroma and urethral sphincter
|

* Generation/ Refinement of ground truth data
* Creation of a 3D sector model
* Initialization of segmentation with user interaction or atlas-based segmentation (in order to decrease search space)
* Try (model-based) segmentation approach (costs for segmentation optimization can be derived for example from supervised classification of the gland tissue). The shape of individual sector models could be used as segmentation prior
* if more training data is available: deep learning for a better cost generation or for an automatic sector segmentation

|

*
|}

==Background and References==

2017 Winter Project Week

2017-01-02T21:11:17Z

Ameyer: /* To be Categorized */

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

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

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

==Logistics==

*'''Dates:''' January 9-13, 2017.
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.

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

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

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

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

A summary of all previous Project Events is available [[Project_Events#Past_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]

==Conference Calls for Preparation==

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

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 9
!style="width:18%" |Tuesday, January 10
!style="width:18%" |Wednesday, January 11
!style="width:18%" |Thursday, January 12
!style="width:18%" |Friday, January 13
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#faedb6"| '''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|rowspan="2"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-10:30am'''
|bgcolor="#88aaae"|[http://www.spl.harvard.edu/pages/People/ctempany Clare Tempany] led Image-Guided Therapy Discussion
|bgcolor="#88aaae"|9:00am-10:00am: Shape Analysis Breakout ---- ---- ---- ---- ---- ---- 10:00am-12:00pm: Luis Ibanez TensorFlow Workshop
|bgcolor="#88aaae"|Fiona Fennessy led Quantitative Imaging for Prostate Cancer Discussion
|bgcolor="#88aaae"|
|-
|bgcolor="#ffffdd"|'''10:30am-12pm:'''
|'''[http://cmictig.cs.ucl.ac.uk/people/academic-staff/1-sourselin Sebastien Ourselin, PhD, UCL] Talk'''
|
|
|
|Project Reporting
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1:00-5:30pm'''
|'''1:00pm-2:30pm:''' Project Presentations
|
|
|'''2:00-3:30pm''' 2017 Tutorial Contest Review
|'''1:30-2:30pm:''' [[AMIGO_TourPW2017Winter|AMIGO Tour]]
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day [[2017_Winter_Project_Week/Dinner|Dinner on Thursday Night]] (Optional)
|
|}

==Calendar==

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

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

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

='''Projects'''=

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

== Learning and GPUs ==

* [[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Ziyang Wang, Guillaume Pernelle, Tina Kapur)
* [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei Wang (Vivian))

== Web Technologies ==
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer)

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

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

== Robotics in IGT ==
* [[2017 Winter Project Week/OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab | OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab ]] (Scheherazade Kraß (Shery), Junichi Tokuda, Longquan Chen, )

== Craniofacial ==
* [[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)

== Infrastructure ==
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)
* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)
* [[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
* [[2017 Winter Project Week/DiPy_in_Slicer | DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)

== DICOM ==
* [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)

==To be Categorized==

* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
* [[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
* [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua)
* [[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
* [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)
* [[2017 Winter Project Week/LORDWI | Density-based DMRI registration ]] (Henrik Groenholt Jensen, Lauren J. O'Donnell, Tina Kapur, Fan Zhang, Carl-Frederik Westin)
* [[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram)
* [[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)

= '''Registrants''' =

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

# A, Zeina :: SHBOUL
# Aerts, Hugo :: DFCI-Harvard
# Alam, Mahbubul :: Old Dominion University
# Anderson, Peter :: Retired
# Andruejol, Johan :: Kitware, Inc.
# Bakeng, Janne Beate :: SINTEF
# Beers, Andrew :: Massachusetts General Hospital
# Bernal Rusiel, Jorge Luis :: Boston Children's Hospital
# Bremer, Erich :: Stony Brook University
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital
# Chae, Michael :: Monash University
# Chauvin, Laurent :: ETS
# Dalca, Adrian :: Massachusetts Institute of Technology
# Fedorov, Andriy :: Brigham and Women's Hospital
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.
# Girault, Alexis :: Kitware, Inc.
# Golland, Polina :: Massachusetts Institute of Technology
# Gollub, Randy :: Massachusetts General Hospital
# Gong, Shun :: Brigham and Women's Hospital
# Guerrier de Dumast, Priscille :: University of Michigan
# Harris, Gordon :: Massachusetts General Hospital
# Herz, Christian :: Brigham and Women's Hospital
# Hong, Sungmin :: New York University
# Hosny, Ahmed :: Dana-Farber
# Jagadeesan, Jayender :: Brigham and Women's Hospital
# Kapur, Tina :: Brigham and Women's Hospital
# Kikinis, Ron :: Brigham and Women's Hospital
# Lisle, Curtis :: KnowledgeVis, LLC
# Mastrogiacomo, Katie :: Brigham and Women's Hospital
# Mateus, D. :: TUM
# Mehrtash, Alireza :: Brigham and Women's Hospital
# Meine, Hans :: University of Bremen
# Meyer, Anneke :: University of Magdeburg
# Miller, James :: GE Research
# Mirabel, Clement :: University of Michigan
# Nitsch, Jennifer :: University of Bremen
# Norton, Isaiah :: Brigham and Women's Hospital
# O'Donnell, Lauren :: Brigham and Women's Hospital
# Oram, Louise :: The Intervention Centre-Oslo University Hospital
# Paniagua, Beatriz :: Kitware, Inc.
# Parmar, Chintan :: DFCI-Harvard Medical School
# Peled, Sharon :: Brigham and Women's Hospital
# Pieper, Steve :: Isomics, Inc.
# Pinter, Csaba :: Queen's University
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School
# Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School
# Rankin, Adam :: Robarts Research Institute
# Rheault, Francois :: Université de Sherbrooke
# Sharp, Gregory :: Massachusetts General Hospital
# Sridharan, Patmaa :: University of Pennsylvania-CBICA
# Vidyaratne, Lasitha :: Old Dominion University
# Ye, Wu :: Brigham and Women's Hospital
# Zeleznik, Roman :: DFCI
# Zhang, Fan :: Brigham and Women's Hospital
# Zhang, Miaomiao :: Massachusetts Institute of Technology
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital