NAMIC Wiki - User contributions [en]

Project Week 25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation

2017-06-30T09:56:31Z

Jennifer Nitsch: /* Project Description */

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

==Key Investigators==
*[http://www.mic.uni-bremen.de/jennifer-nitsch/ Jennifer Nitsch] (University of Bremen, Germany)
*[http://www.mic.uni-bremen.de/cmt-management-team/scheherazade-kras/ Scheherazade Kraß] (University of Bremen, Germany)
*[http://campar.in.tum.de/Main/JuliaRackerseder Julia Rackerseder] (Technical University of Munich, 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;"
|

*Segmented multiple anatomical structures/landmarks in both MRI and Ultrasound (US) images, using machine learning algorithms (applicability of Deep Learning algorithms is currently tested, DL for US-images, data augmentation...).

*The next step would be to analyze the improvement of registration quality with different segmentations/generated landmarks in order to adapt the segmentation algorithms.

*(Kuka LWR project, Shery) Using advanced segmentation and registration features for iterative robot control. The respective status of the Kuka LWR iiwa (position, configuration) is simulated and visualized as 3-D model in MeVisLab. Medical data sets including target pose (position and path towards it) can be send and received via the OpenIGTLink network protocol as well.

|

*Starting from multi-modal image segmentation in preopertive MRI and intraoperative Ultrasound images,
it would be to discuss in which "form" one or multiple segmented structures should influence the registration result.
*Get data from public data archive of US and MRI images and segment anatomical structures in both modalities.

*Discussion: Benefit of additional information of multiple segmentations for registration.

|

*Working with the public RESECT dataset [http://sintef.no/projectweb/usigt-en/data/]
*Using segmentations to register MRI with US (algorithms are not overfitted on previously used data)
*Locally refine with image based registration
*Plastimatch B-spline deformable registration module works well for image based registration [https://www.slicer.org/wiki/Documentation/4.6/Modules/PlmBSplineDeformableRegistration]

TODO:
*Implement LC2 norm to improve image based registration between US and MRI (Wein, Wolfgang, et al. "Global registration of ultrasound to mri using the LC2 metric for enabling neurosurgical guidance." International Conference on Medical Image Computing and Computer-Assisted Intervention. Springer, Berlin, Heidelberg, 2013.)
*Create module to load RESECT dataset including landmarks for ground truth

(Kuka LWR project, Shery)
*1.) Plus setup config file adapted to communicate via OpenIGTLink module in MeVisLab.
*2.) Further development of project controlling the Kuka lwr: New marker-based point selection, that could be used to simulate needle placement in MRI images.

|}

==Illustrations==
[[image:RegistrationInNeuroNavigationSystem.png|500px]]

Using segmented structures as guiding frame for multi-modal image registration:

[[image:MultimodalImageSegmentation3.png|500px]]

LWR Robot simulation in MeVisLab:

[[image:Picture 2016-12-19 13 55 31.png|500px]]
[[image:Picture 2017-06-26 11 04 59.png|500px]]

==Background and References==

In glioma surgery neuronavigation systems assist in determining the tumor's location and estimating its extent. However, the intraoperative situation diverges seriously from the preoperative situation in the MRI scan
displayed on the navigation system. The movement of brain tissue during surgery, i.e., caused by brainshift
and tissue removal, must be considered mentally by the surgeon. A task that gets more challenging in later
phases of the tumor resection.

Besides, it is an exhaustive issue and the shift of cerebral structures must be
expected being non-uniform and that it implies a deformation of the image data. This makes it especially hard
to mentally predict and model.

Thus, intraoperative imaging modalities are used to visualize the current intraoperative situation. IUS,
for instance, is easy to use intraoperatively, offers real-time information, is widely available at low cost and
causes no radiation. These are important advantages when iUS is compared with iCT or iMRI. However, in
image-guided surgery precise image registration of iUS and preMRI and the thereon-based image fusion is still
an unsolved problem. The different representations of cerebral structures in both modalities as well as
artifacts within the iUS, hinder direct fusion of both modalities.

Project Week 25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation

2017-06-29T08:35:41Z

Jennifer Nitsch: /* Project Description */

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

==Key Investigators==
*[http://www.mic.uni-bremen.de/jennifer-nitsch/ Jennifer Nitsch] (University of Bremen, Germany)
*[http://www.mic.uni-bremen.de/cmt-management-team/scheherazade-kras/ Scheherazade Kraß] (University of Bremen, Germany)
*[http://campar.in.tum.de/Main/JuliaRackerseder Julia Rackerseder] (Technical University of Munich, 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;"
|

*Segmented multiple anatomical structures/landmarks in both MRI and Ultrasound (US) images, using machine learning algorithms (applicability of Deep Learning algorithms is currently tested, DL for US-images, data augmentation...).

*The next step would be to analyze the improvement of registration quality with different segmentations/generated landmarks in order to adapt the segmentation algorithms.

*Using advanced segmentation and registration features for iterative robot control. The respective status of the Kuka LWR iiwa (position, configuration) is simulated and visualized as 3-D model in MeVisLab. Medical data sets including target pose (position and path towards it) can be send and received via the OpenIGTLink network protocol as well.

|

*Starting from multi-modal image segmentation in preopertive MRI and intraoperative Ultrasound images,
it would be to discuss in which "form" one or multiple segmented structures should influence the registration result.
*Get data from public data archive of US and MRI images and segment anatomical structures in both modalities.

*Discussion: Benefit of additional information of multiple segmentations for registration.

|

*Working with the public RESECT dataset [http://sintef.no/projectweb/usigt-en/data/]
*Using segmentations to register MRI with US (algorithms are not overfitted on previously used data)
*Locally refine with image based registration
*Plastimatch B-spline deformable registration module works well for image based registration [https://www.slicer.org/wiki/Documentation/4.6/Modules/PlmBSplineDeformableRegistration]

TODO:
*Implement LC2 norm to improve image based registration between US and MRI (Wein, Wolfgang, et al. "Global registration of ultrasound to mri using the LC2 metric for enabling neurosurgical guidance." International Conference on Medical Image Computing and Computer-Assisted Intervention. Springer, Berlin, Heidelberg, 2013.)
*Create module to load RESECT dataset including landmarks for ground truth
|}

==Illustrations==
[[image:RegistrationInNeuroNavigationSystem.png|500px]]

Using segmented structures as guiding frame for multi-modal image registration:

[[image:MultimodalImageSegmentation3.png|500px]]

LWR Robot simulation in MeVisLab:

[[image:Picture 2016-12-19 13 55 31.png|500px]]
[[image:Picture 2017-06-26 11 04 59.png|500px]]

==Background and References==

In glioma surgery neuronavigation systems assist in determining the tumor's location and estimating its extent. However, the intraoperative situation diverges seriously from the preoperative situation in the MRI scan
displayed on the navigation system. The movement of brain tissue during surgery, i.e., caused by brainshift
and tissue removal, must be considered mentally by the surgeon. A task that gets more challenging in later
phases of the tumor resection.

Besides, it is an exhaustive issue and the shift of cerebral structures must be
expected being non-uniform and that it implies a deformation of the image data. This makes it especially hard
to mentally predict and model.

Thus, intraoperative imaging modalities are used to visualize the current intraoperative situation. IUS,
for instance, is easy to use intraoperatively, offers real-time information, is widely available at low cost and
causes no radiation. These are important advantages when iUS is compared with iCT or iMRI. However, in
image-guided surgery precise image registration of iUS and preMRI and the thereon-based image fusion is still
an unsolved problem. The different representations of cerebral structures in both modalities as well as
artifacts within the iUS, hinder direct fusion of both modalities.

Project Week 25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation

2017-06-29T08:32:09Z

Jennifer Nitsch: /* Project Description */

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

==Key Investigators==
*[http://www.mic.uni-bremen.de/jennifer-nitsch/ Jennifer Nitsch] (University of Bremen, Germany)
*[http://www.mic.uni-bremen.de/cmt-management-team/scheherazade-kras/ Scheherazade Kraß] (University of Bremen, Germany)
*[http://campar.in.tum.de/Main/JuliaRackerseder Julia Rackerseder] (Technical University of Munich, 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;"
|

*Segmented multiple anatomical structures/landmarks in both MRI and Ultrasound (US) images, using machine learning algorithms (applicability of Deep Learning algorithms is currently tested, DL for US-images, data augmentation...).

*The next step would be to analyze the improvement of registration quality with different segmentations/generated landmarks in order to adapt the segmentation algorithms.

*Using advanced segmentation and registration features for iterative robot control. The respective status of the Kuka LWR iiwa (position, configuration) is simulated and visualized as 3-D model in MeVisLab. Medical data sets including target pose (position and path towards it) can be send and received via the OpenIGTLink network protocol as well.

|

*Starting from multi-modal image segmentation in preopertive MRI and intraoperative Ultrasound images,
it would be to discuss in which "form" one or multiple segmented structures should influence the registration result.
*Get data from public data archive of US and MRI images and segment anatomical structures in both modalities.
|

*Working with the public RESECT dataset [http://sintef.no/projectweb/usigt-en/data/]
*Using segmentations to register MRI with US (algorithms are not overfitted on previously used data)
*Locally refine with image based registration
*Plastimatch B-spline deformable registration module works well for image based registration [https://www.slicer.org/wiki/Documentation/4.6/Modules/PlmBSplineDeformableRegistration]

TODO:
*Implement LC2 norm to improve image based registration between US and MRI (Wein, Wolfgang, et al. "Global registration of ultrasound to mri using the LC2 metric for enabling neurosurgical guidance." International Conference on Medical Image Computing and Computer-Assisted Intervention. Springer, Berlin, Heidelberg, 2013.)
*Create module to load RESECT dataset including landmarks for ground truth
|}

==Illustrations==
[[image:RegistrationInNeuroNavigationSystem.png|500px]]

Using segmented structures as guiding frame for multi-modal image registration:

[[image:MultimodalImageSegmentation3.png|500px]]

LWR Robot simulation in MeVisLab:

[[image:Picture 2016-12-19 13 55 31.png|500px]]
[[image:Picture 2017-06-26 11 04 59.png|500px]]

==Background and References==

In glioma surgery neuronavigation systems assist in determining the tumor's location and estimating its extent. However, the intraoperative situation diverges seriously from the preoperative situation in the MRI scan
displayed on the navigation system. The movement of brain tissue during surgery, i.e., caused by brainshift
and tissue removal, must be considered mentally by the surgeon. A task that gets more challenging in later
phases of the tumor resection.

Besides, it is an exhaustive issue and the shift of cerebral structures must be
expected being non-uniform and that it implies a deformation of the image data. This makes it especially hard
to mentally predict and model.

Thus, intraoperative imaging modalities are used to visualize the current intraoperative situation. IUS,
for instance, is easy to use intraoperatively, offers real-time information, is widely available at low cost and
causes no radiation. These are important advantages when iUS is compared with iCT or iMRI. However, in
image-guided surgery precise image registration of iUS and preMRI and the thereon-based image fusion is still
an unsolved problem. The different representations of cerebral structures in both modalities as well as
artifacts within the iUS, hinder direct fusion of both modalities.

Project Week 25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation

2017-06-26T10:52:23Z

Jennifer Nitsch: /* Key Investigators */

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

==Key Investigators==
*[http://www.mic.uni-bremen.de/jennifer-nitsch/ Jennifer Nitsch] (University of Bremen, Germany)
*[http://www.mic.uni-bremen.de/cmt-management-team/scheherazade-kras/ Scheherazade Kraß] (University of Bremen, Germany)
* Rackerseder, Julia (Technical University of Munich, 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;"
|

*Segmented multiple anatomical structures/landmarks in both MRI and Ultrasound (US) images, using machine learning algorithms (applicability of Deep Learning algorithms is currently tested, DL for US-images, data augmentation...).

*The next step would be to analyze the improvement of registration quality with different segmentations/generated landmarks in order to adapt the segmentation algorithms.

*Using advanced segmentation and registration features for iterative robot control. The respective status of the Kuka LWR iiwa (position, configuration) is simulated and visualized as 3-D model in MeVisLab. Medical data sets in-cluding target pose (position and path towards it) can be send and received via the OpenIGTLink network protocol as well.

|

*Starting from multi-modal image segmentation in preopertive MRI and intraoperative Ultrasound images,
it would be to discuss in which "form" one or multiple segmented structures should influence the registration result.
|

|}

==Illustrations==
[[image:RegistrationInNeuroNavigationSystem.png|500px]]

Using segmented structures as guiding frame for multi-modal image registration:

[[image:MultimodalImageSegmentation3.png|500px]]

LWR Robot simulation in MeVisLab:

[[image:Picture 2016-12-19 13 55 31.png|500px]]
[[image:Picture 2017-06-26 11 04 59.png|500px]]

==Background and References==

In glioma surgery neuronavigation systems assist in determining the tumor's location and estimating its extent. However, the intraoperative situation diverges seriously from the preoperative situation in the MRI scan
displayed on the navigation system. The movement of brain tissue during surgery, i.e., caused by brainshift
and tissue removal, must be considered mentally by the surgeon. A task that gets more challenging in later
phases of the tumor resection.

Besides, it is an exhaustive issue and the shift of cerebral structures must be
expected being non-uniform and that it implies a deformation of the image data. This makes it especially hard
to mentally predict and model.

Thus, intraoperative imaging modalities are used to visualize the current intraoperative situation. IUS,
for instance, is easy to use intraoperatively, offers real-time information, is widely available at low cost and
causes no radiation. These are important advantages when iUS is compared with iCT or iMRI. However, in
image-guided surgery precise image registration of iUS and preMRI and the thereon-based image fusion is still
an unsolved problem. The different representations of cerebral structures in both modalities as well as
artifacts within the iUS, hinder direct fusion of both modalities.

Project Week 25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation

2017-06-26T09:01:07Z

Jennifer Nitsch: /* Illustrations */

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

==Key Investigators==
*[http://www.mic.uni-bremen.de/jennifer-nitsch/ Jennifer Nitsch] (University of Bremen, Germany)
*[http://www.mic.uni-bremen.de/cmt-management-team/scheherazade-kras/ Scheherazade Kraß] (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;"
|

*Segmented multiple anatomical structures/landmarks in both MRI and Ultrasound (US) images, using machine learning algorithms (applicability of Deep Learning algorithms is currently tested, DL for US-images, data augmentation...).

*The next step would be to analyze the improvement of registration quality with different segmentations/generated landmarks in order to adapt the segmentation algorithms.

*Using advanced segmentation and registration features for iterative robot control. The respective status of the Kuka LWR iiwa (position, configuration) is simulated and visualized as 3-D model in MeVisLab. Medical data sets in-cluding target pose (position and path towards it) can be send and received via the OpenIGTLink network protocol as well.

|

*Starting from multi-modal image segmentation in preopertive MRI and intraoperative Ultrasound images,
it would be to discuss in which "form" one or multiple segmented structures should influence the registration result.
|

|}

==Illustrations==
[[image:RegistrationInNeuroNavigationSystem.png|500px]]

Using segmented structures as guiding frame for multi-modal image registration:

[[image:MultimodalImageSegmentation3.png|500px]]

LWR Robot simulation in MeVisLab:

[[image:Picture 2016-12-19 13 55 31.png|50px MeVisLab-Kuka]]

==Background and References==

In glioma surgery neuronavigation systems assist in determining the tumor's location and estimating its extent. However, the intraoperative situation diverges seriously from the preoperative situation in the MRI scan
displayed on the navigation system. The movement of brain tissue during surgery, i.e., caused by brainshift
and tissue removal, must be considered mentally by the surgeon. A task that gets more challenging in later
phases of the tumor resection.

Besides, it is an exhaustive issue and the shift of cerebral structures must be
expected being non-uniform and that it implies a deformation of the image data. This makes it especially hard
to mentally predict and model.

Thus, intraoperative imaging modalities are used to visualize the current intraoperative situation. IUS,
for instance, is easy to use intraoperatively, offers real-time information, is widely available at low cost and
causes no radiation. These are important advantages when iUS is compared with iCT or iMRI. However, in
image-guided surgery precise image registration of iUS and preMRI and the thereon-based image fusion is still
an unsolved problem. The different representations of cerebral structures in both modalities as well as
artifacts within the iUS, hinder direct fusion of both modalities.

Project Week 25/CNN for multi-plane prostate segmentation

2017-06-26T08:41:31Z

Jennifer Nitsch:

__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;"
|

* 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/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation

2017-06-23T10:55:46Z

Jennifer Nitsch: /* Background and References */

Project Week 25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation

2017-06-23T10:40:09Z

Jennifer Nitsch: /* Project Description */

Project Week 25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation

2017-06-21T11:50:29Z

Jennifer Nitsch: /* Project Description */

Project Week 25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation

2017-06-15T14:08:04Z

Jennifer Nitsch:

Project Week 25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation

2017-06-15T13:16:27Z

Jennifer Nitsch: /* Illustrations */

File:MultimodalImageSegmentation3.png

2017-06-15T13:14:51Z

Jennifer Nitsch:

Segmentation for Improving Registration.

File:MultimodalImageSegmentation2.png

2017-06-15T13:07:31Z

Jennifer Nitsch:

Segmentation for Improving Registration.

Project Week 25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation

2017-06-15T09:59:19Z

Jennifer Nitsch: /* Illustrations */

File:MultimodalImageSegmentation.png

2017-06-15T09:58:09Z

Jennifer Nitsch:

Illustration Segmentation and Registration.

File:RegistrationInNeuroNavigationSystem.png

2017-06-15T09:51:45Z

Jennifer Nitsch:

Accuracy on neuronavigation systems.

Project Week 25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation

2017-06-07T14:35:33Z

Jennifer Nitsch: Created page with "__NOTOC__ Back to Projects List ==Key Investigators== {| |- | [http://www.mic.uni-bremen.de/jennifer-nitsch/ Jennifer Nitsch] || [http://www.m..."

__NOTOC__

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

==Key Investigators==
{|
|-
| [http://www.mic.uni-bremen.de/jennifer-nitsch/ Jennifer Nitsch] || [http://www.mic.uni-bremen.de/cmt-management-team/scheherazade-kras/ Scheherazade Kraß]
|-
| Investigator 4 || Investigator 5 || Investigator 6
|}

==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;"
|

Please start each sentence in a new line.

Like this.
|

Please start each sentence in a new line.

|

Please start each sentence in a new line.

|}

==Illustrations==

==Background and References==

Project Week 25

2017-06-07T14:25:55Z

Jennifer Nitsch: /* 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].

==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

#Needle segmentation Project 1 (Guillaume Pernelle, Tina Kapur, Paolo Zaffino, Salvatore Scaramuzzino, Francesca Spadea)
#Needle segmentation Project 2 (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)
#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,)
#Deep Learning: Data augmentation for prostate segmentation (Anneke Meyer, Christian Hansen, 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

Project Week 25

2017-05-24T13:06:34Z

Jennifer Nitsch:

__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]]
 

=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
#(TBD) Hangout #10: Wednesday June 7, 2017, 9am EDT (GMT-4) TBD
#(TBD) Hangout #11: Wednesday June 14, 2017, 9am EDT (GMT-4) TBD
#(Francesca Spadea) Hangout #12: Wednesday June 21, 2017, 9am EDT (GMT-4) 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 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==

'''''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.''''' 

{{#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

=Projects=

Please put a brief preliminary title for your project here with some names in parenthesis for potential team members

#Needle segmentation Project 1 (Guillaume Pernelle, Tina Kapur, Paolo Zaffino, Salvatore Scaramuzzino, Francesca Spadea)
#Needle segmentation Project 2 (Paolo Zaffino, Salvatore Scaramuzzino, Francesca Spadea, Guillaume Pernelle, Tina Kapur)
#DICOM Segmentation support for Cornerstone / OHIF Viewer (Erik Ziegler)
#Conversion of DICOM single frame MR to Enhanced Multiframe (Michael Onken, Steve Pieper)
#Human-Computer Interaction under sterile conditions (Christian Hansen, Julian Hettig, Benjamin Hatscher, David Black)
#Development and evaluation of new AR visualization technniques to support radiological interventions (Christian Hansen, Florian Heinrich, Andrè Mewes)
#Interactive manipulation of plots and graphs: i) panning; ii) click and drag; iii) data selection (Davide Punzo, Steve Pieper)
#Next generation of volume rendering in VTK (Simon Drouin, Steve Pieper, Ole Vegard Solberg)
#Tracked Ultrasound Standardization IV: Controlling US acquisition (Simon Drouin, Ole Vegard Solberg, Andras Lasso, 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)
#Tissue deformation estimation based on dense points cloud reconstruction using stereo images (Sara Moccia)
#Segmentation for improving image registration of preoperative MRI/intraoperative ultrasound images for neuro-navigation (Jennifer Nitsch, Scheherazade Kraß)

=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

Project Week 25

2017-05-24T13:05:52Z

Jennifer Nitsch:

__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]]
 

=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
#(TBD) Hangout #10: Wednesday June 7, 2017, 9am EDT (GMT-4) TBD
#(TBD) Hangout #11: Wednesday June 14, 2017, 9am EDT (GMT-4) TBD
#(Francesca Spadea) Hangout #12: Wednesday June 21, 2017, 9am EDT (GMT-4) 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 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==

'''''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.''''' 

{{#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

=Projects=

Please put a brief preliminary title for your project here with some names in parenthesis for potential team members

#Needle segmentation Project 1 (Guillaume Pernelle, Tina Kapur, Paolo Zaffino, Salvatore Scaramuzzino, Francesca Spadea)
#Needle segmentation Project 2 (Paolo Zaffino, Salvatore Scaramuzzino, Francesca Spadea, Guillaume Pernelle, Tina Kapur)
#DICOM Segmentation support for Cornerstone / OHIF Viewer (Erik Ziegler)
#Conversion of DICOM single frame MR to Enhanced Multiframe (Michael Onken, Steve Pieper)
#Human-Computer Interaction under sterile conditions (Christian Hansen, Julian Hettig, Benjamin Hatscher, David Black)
#Development and evaluation of new AR visualization technniques to support radiological interventions (Christian Hansen, Florian Heinrich, Andrè Mewes)
#Interactive manipulation of plots and graphs: i) panning; ii) click and drag; iii) data selection (Davide Punzo, Steve Pieper)
#Next generation of volume rendering in VTK (Simon Drouin, Steve Pieper, Ole Vegard Solberg)
#Tracked Ultrasound Standardization IV: Controlling US acquisition (Simon Drouin, Ole Vegard Solberg, Andras Lasso, 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)
#Tissue deformation estimation based on dense points cloud reconstruction using stereo images (Sara Moccia)
#Segmentation for improving image registration of preoperative MRI/intraoperative ultrasound images for neuro-navigation(Jennifer Nitsch, Scheherazade Kraß)

=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

2017 Winter Project Week/2017 NVIDIA Demo Contest

2017-02-22T16:44:58Z

Jennifer Nitsch:

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

</gallery>

==Key Investigators==

*Abdul Halabi, NVIDIA
*Abel Brown, NVIDIA

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

* To identify a Deep Learning that is appropriate for adding to NVIDIA's demo suite
|

* Observe the projects in progress here, and award a TitanX card on Friday morning
|

|}

==Background and References==

Links to competition entries:
* Prostate Gland Segmentation with Fully Convolutional Neural Networks: (Alireza Mehrtash, Mehran Pesteie, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)
** Youtube Link: https://youtu.be/5lvY0cZ4qfk
* [[2017 Winter Project Week/Knee Cartilage Segmentation | Knee Cartilage Segmentation]] (Hans Meine)
* [[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch, Hans Meine)
* [[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Paolo Zaffino, Ziyang Wang, Guillaume Pernelle, Tina Kapur)
*[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)
*
*'''Winner NVIDIA Demo Contest'''
* [[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch, Hans Meine)

2017 Winter Project Week/2017 NVIDIA Demo Contest

2017-01-17T15:01:31Z

Jennifer Nitsch: /* Background and References */

2017 Winter Project Week

2017-01-16T14:40:34Z

Jennifer Nitsch: /* 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]] (Paolo Zaffino, Ziyang Wang, Guillaume Pernelle, Tina Kapur)
#[[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/Population Based Image Imputation | Population Based Image Imputation]] (Adrian Dalca, Katie Bouman, Mert Sabuncu, Polina Golland)
#[[2017 Winter Project Week/Knee Cartilage Segmentation | Knee Cartilage Segmentation]] (Hans Meine)

== 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, Satra Ghosh)
#[[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)
#[[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, 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)
#[[2017 Winter Project Week/Integrative_Intraoperative_Interface | Integrative Interface for Intraoperative Software Applications ]] (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, Johan Andruejol, JC Fillon-Robin, James Fishbaugh, Priscille de Dumast)
#[[2017 Winter Project Week/MandibularRegression | Mandibular and maxillary Shape Regression ]] (Beatriz Paniagua, Clement Mirabel, Priscille de Dumast, James Fishbaugh, Lucia Cevidanes, Daniella Garib)
#[[2017 Winter Project Week/Slicer_VR | Slicer + VR = <3]] (Adam Rankin, Andras Lasso, Ryan D'Souza (NDI), Matthew Jolley (Children's Hospital of Philadelphia), Kitware+Slicer dev (JC,JFinet,etc...)
#[[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,)
#[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov, Alireza Mehrtash, Christian Hansen, Teodora Szasz)
#[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch, Hans Meine)
#[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Jakub Kaczmarzyk, 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 | Plastimatch multi-planar and multi-metric registration ]] (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/Organizations | Slicer* Community Topics, Projects, Flavors: The SLICERVERSE ]] (Beatriz Paniagua, Lauren O'Donnell, Isaiah Norton, Gregory Sharp, Louise Oram)

==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)
#[[2017 Winter Project Week/2017 Winter Project Week Surgery|Project Week Survey]] (Krisztina Fischer, Tina Kapur)
#[[2017 Winter Project Week/Next project week| Next project week: PW#25]] (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
# Chen, Longquan :: Surgical Planning Lab
# 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
# Mousavi, Parvin :: Brigham and Women's Hospital
# Nitsch, Jennifer :: University of Bremen
# Norton, Isaiah :: Brigham and Women's Hospital
# O'Donnell, Lauren :: Brigham and Women's Hospital
# Onieva, Jorge :: 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
# Pienaar, Rudolph :: Boston Children'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
# Ross, James :: Brigham and Women's Hospital
# Szczepankiewicz, Filip :: Lund University
# Sharp, Gregory :: Massachusetts General Hospital
# Sridharan, Patmaa :: University of Pennsylvania-CBICA
# Szasz, Teodora :: University of Chicago
# Tokuda, Junichi :: Brigham and Women's Hospital
# 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
# Woo, Jonghye :: Massachusetts General Hospital
# 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, Hongtao :: Hebei General 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/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery

2017-01-16T14:37:53Z

Jennifer Nitsch:

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

File:USandMRIimagesMLSegmentation.png|Several structures of the brain segmented from US- and MR images.
File:Dnn.png
File:SkullStrip.tcsproj.mp4
</gallery>

==Key Investigators==

* Jennifer Nitsch, University of Bremen (Germany)
* Hans Meine, 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;"
|

* Multi-Modual Image Segmentation of preoperative MR- and intraoperative Ultrasound(US)-images for multi-modual image registration.
* Segmentation of the following anatomical structures: Falx cerebri, tentorium cerebelli, white matter, gray matter, CSF (ventricles), blood vessels.
* Testing applicability of Deep Learing on current data
|

* Generation/ Refinement of ground truth data
* Generation/Creation/Refinement of characteristic (anatomical) landmarks (e.g. charactersitic representation of cerebellum, insula cortex (lateral sulcus), choroid plexus.
* Prepare images for Deep Learning and seeting up Deep learning infrastructure.
|

*Trained a DNN for skull stripping on 18 data sets from a public database, also segmented in GM, WM, CSF
*There a a lot of databases for T1-weighted brain images, but good reference data is rare...
|}

==Background and References==

2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery

2017-01-13T15:49:34Z

Jennifer Nitsch:

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

File:USandMRIimagesMLSegmentation.png|Several structures of the brain segmented from US- and MR images.
File:Dnn.png
File:SkullStrip.tcsproj.mp4
</gallery>

==Key Investigators==

* 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;"
|

* Multi-Modual Image Segmentation of preoperative MR- and intraoperative Ultrasound(US)-images for multi-modual image registration.
* Segmentation of the following anatomical structures: Falx cerebri, tentorium cerebelli, white matter, gray matter, CSF (ventricles), blood vessels.
* Testing applicability of Deep Learing on current data
|

* Generation/ Refinement of ground truth data
* Generation/Creation/Refinement of characteristic (anatomical) landmarks (e.g. charactersitic representation of cerebellum, insula cortex (lateral sulcus), choroid plexus.
* Prepare images for Deep Learning and seeting up Deep learning infrastructure.
|

*Trained a DNN for skull stripping on 18 data sets from a public database, also segmented in GM, WM, CSF
*There a a lot of databases for T1-weighted brain images, but good reference data is rare...
|}

==Background and References==

File:SkullStrip.tcsproj.mp4

2017-01-13T15:48:37Z

Jennifer Nitsch:

2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery

2017-01-13T15:26:46Z

Jennifer Nitsch:

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

File:USandMRIimagesMLSegmentation.png|Several structures of the brain segmented from US- and MR images.
File:Dnn.png
</gallery>

==Key Investigators==

* 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;"
|

* Multi-Modual Image Segmentation of preoperative MR- and intraoperative Ultrasound(US)-images for multi-modual image registration.
* Segmentation of the following anatomical structures: Falx cerebri, tentorium cerebelli, white matter, gray matter, CSF (ventricles), blood vessels.
* Testing applicability of Deep Learing on current data
|

* Generation/ Refinement of ground truth data
* Generation/Creation/Refinement of characteristic (anatomical) landmarks (e.g. charactersitic representation of cerebellum, insula cortex (lateral sulcus), choroid plexus.
* Prepare images for Deep Learning and seeting up Deep learning infrastructure.
|

*Trained a DNN for skull stripping on 18 data sets from a public database, also segmented in GM, WM, CSF
*There a a lot of databases for T1-weighted brain images, but good reference data is rare...
|}

==Background and References==

File:Dnn.png

2017-01-13T15:20:35Z

Jennifer Nitsch:

2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery

2017-01-13T13:32:55Z

Jennifer Nitsch:

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

File:USandMRIimagesMLSegmentation.png|Several structures of the brain segmented from US- and MR images.
</gallery>

==Key Investigators==

* 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;"
|

* Multi-Modual Image Segmentation of preoperative MR- and intraoperative Ultrasound(US)-images for multi-modual image registration.
* Segmentation of the following anatomical structures: Falx cerebri, tentorium cerebelli, white matter, gray matter, CSF (ventricles), blood vessels.
* Testing applicability of Deep Learing on current data
|

* Generation/ Refinement of ground truth data
* Generation/Creation/Refinement of characteristic (anatomical) landmarks (e.g. charactersitic representation of cerebellum, insula cortex (lateral sulcus), choroid plexus.
* Prepare images for Deep Learning and seeting up Deep learning infrastructure.
|

*Trained a DNN for skull stripping on 18 data sets from a public database, also segmented in GM, WM, CSF
*There a a lot of databases for T1-weighted brain images, but good reference data is rare...
|}

==Background and References==

2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery

2017-01-09T18:12:51Z

Jennifer Nitsch:

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

File:USandMRIimagesMLSegmentation.png|Several structures of the brain segmented from US- and MR images.
</gallery>

==Key Investigators==

* 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;"
|

* Multi-Modual Image Segmentation of preoperative MR- and intraoperative Ultrasound(US)-images for multi-modual image registration.
* Segmentation of the following anatomical structures: Falx cerebri, tentorium cerebelli, white matter, gray matter, CSF (ventricles), blood vessels.
* Testing applicability of Deep Learing on current data
|

* Generation/ Refinement of ground truth data
* Generation/Creation/Refinement of characteristic (anatomical) landmarks (e.g. charactersitic representation of cerebellum, insula cortex (lateral sulcus), choroid plexus.
* Prepare images for Deep Learning and seeting up Deep learning infrastructure.
|

*
|}

==Background and References==

2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery

2017-01-09T16:48:49Z

Jennifer Nitsch:

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

File:USandMRIimagesMLSegmentation.png|Several structures of the brain segmented from US- and MR images.
</gallery>

==Key Investigators==

* 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;"
|

* Multi-Modual Image Segmentation of preoperative MR- and intraoperative Ultrasound(US)-images
* Segmentation of the following anatomical structures: Falx cerebri, tentorium cerebelli, white matter, gray matter, CSF (ventricles), blood vessels.
* Testing applicability of Deep Learing on current data
|

* Generation/ Refinement of ground truth data
* Generation/Creation/Refinement of characteristic (anatomical) landmarks (e.g. charactersitic representation of cerebellum, insula cortex (lateral sulcus), choroid plexus.
* Prepare images for Deep Learning and seeting up Deep learning infrastructure.
|

*
|}

==Background and References==

2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery

2017-01-09T16:42:09Z

Jennifer Nitsch:

File:USandMRIimagesMLSegmentation.png

2017-01-09T16:37:52Z

Jennifer Nitsch:

2017 Winter Project Week/Dinner

2017-01-07T14:12:50Z

Jennifer Nitsch:

==Dinner Specs==

*Date and Time: Thursday, January 12, 6pm
*Location: Desi Dhaba, 401 Massachusetts Ave, Cambridge (about 10 minute walk from MIT)
*Food: Indian. (Goat curry, chicken tikka masala, chana masala (vegan), saag paneer, 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

2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery

2017-01-03T10:03:29Z

Jennifer Nitsch: 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..."

2017 Winter Project Week

2017-01-03T09:52:30Z

Jennifer Nitsch: /* IGT: Navigation, Robotics, Surgical Planning */