NAMIC Wiki - User contributions [en]

Project Week 25/SlicerCIP Bronchiectasis

2017-06-29T23:35:07Z

PietroNardelli:

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

==Key Investigators==

*Pietro Nardelli (Brigham and Women's Hospital, Harvard Medical School, USA)
*Jorge Onieva Onieva (Brigham and Women's Hospital, Harvard Medical School, USA)
*[https://lmi.med.harvard.edu/people/raul-san-jose-estepar Raúl San José Estépar] (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;"
|
The goal of this project is to create a new semi-automated tool for SlicerCIP that allows to define bronchiectasis by means of the airway to vessel ratio. If ratio > 1, then there is bronchiectasis.

|
* Implement a customized Slicer editor module to select the region of interest (airway + vessel)
* Implement a tool to compute the airway to vessel ratio
* Use SlicerCIP template to save results

|
* Customized Slicer module to measure airways and vessels by means of rulers created
* AV ratio is computed and shown to the user
* The SlicerCIP template is used save results and create PDF report
* Next step: use circular rulers for better measurement
|}

==Illustrations==

[[File:BronchiectasisModuleExample.png|thumb|center|upright=2.0]]

==Background and References==

*[https://github.com/acil-bwh/SlicerCIP SlicerCIP]

Project Week 25/SlicerCIP Bronchiectasis

2017-06-29T23:34:35Z

PietroNardelli:

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

==Key Investigators==

*Pietro Nardelli (Brigham and Women's Hospital, Harvard Medical School, USA)
*Jorge Onieva Onieva (Brigham and Women's Hospital, Harvard Medical School, USA)
*[https://lmi.med.harvard.edu/people/raul-san-jose-estepar Raúl San José Estépar] (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;"
|
The goal of this project is to create a new semi-automated tool for SlicerCIP that allows to define bronchiectasis by means of the airway to vessel ratio. If ratio > 1, then there is bronchiectasis.

|
* Implement a customized Slicer editor module to select the region of interest (airway + vessel)
* Implement a tool to compute the airway to vessel ratio
* Use SlicerCIP template to save results

|
* Customized Slicer module to measure airways and vessels by means of rulers created
* AV ratio is computed and shown to the user
* The SlicerCIP template is used save results and create PDF report
* Next step: use circular rulers for better measurement
|}

==Illustrations==

[[File:BronchiectasisModuleExample.png|thumb|center]]

==Background and References==

*[https://github.com/acil-bwh/SlicerCIP SlicerCIP]

Project Week 25/SlicerCIP ReportsTool

2017-06-29T23:31:41Z

PietroNardelli:

__NOTOC__

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

==Key Investigators==

*Pietro Nardelli (Brigham and Women's Hospital, Harvard Medical School, USA)
*Jorge Onieva Onieva (Brigham and Women's Hospital, Harvard Medical School, USA)
*[https://lmi.med.harvard.edu/people/raul-san-jose-estepar Raúl San José Estépar] (Brigham and Women's Hospital, Harvard Medical School, USA)
* [https://fedorov.github.io Andrey Fedorov] (remote) (Brigham and Women's Hospital, Harvard Medical School, USA)
* Christian Herz, (remote) (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;"
|
*The goal of this project is to create a new tool for SlicerCIP that allows the creation of a PDF report that summarize and illustrate quantitive analysis.

|
* Implement a HTML template for quantitative analysis report
* Implement a new module that fills the HTML with images and data

|

* New HTML template for quantitative analysis report created
* The HTML template can be filled with images and data for specific purposes
|}

==Illustrations==

[[File:PDFReportForEmphysema.png|thumb|center]]
[[File:PDFReportForAVRatioModule.png|thumb|center]]

==Background and References==

*[https://github.com/acil-bwh/SlicerCIP SlicerCIP]

[https://wiki.qt.io/Exporting_a_document_to_PDF Using QPrinter] should be possible.

Project Week 25/SlicerCIP ReportsTool

2017-06-29T23:31:18Z

PietroNardelli:

__NOTOC__

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

==Key Investigators==

*Pietro Nardelli (Brigham and Women's Hospital, Harvard Medical School, USA)
*Jorge Onieva Onieva (Brigham and Women's Hospital, Harvard Medical School, USA)
*[https://lmi.med.harvard.edu/people/raul-san-jose-estepar Raúl San José Estépar] (Brigham and Women's Hospital, Harvard Medical School, USA)
* [https://fedorov.github.io Andrey Fedorov] (remote) (Brigham and Women's Hospital, Harvard Medical School, USA)
* Christian Herz, (remote) (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;"
|
*The goal of this project is to create a new tool for SlicerCIP that allows the creation of a PDF report that summarize and illustrate quantitive analysis.

|
* Implement a HTML template for quantitative analysis report
* Implement a new module that fills the HTML with images and data

|

* New HTML template for quantitative analysis report created
* The HTML template can be filled with images and data for specific purposes
|}

==Illustrations==

[[File:PDFReportForEmphysema.png|thumb|center|upright=2.0]]
[[File:PDFReportForAVRatioModule.png|thumb|center|upright=2.0]]

==Background and References==

*[https://github.com/acil-bwh/SlicerCIP SlicerCIP]

[https://wiki.qt.io/Exporting_a_document_to_PDF Using QPrinter] should be possible.

Project Week 25/SlicerCIP ReportsTool

2017-06-29T23:29:28Z

PietroNardelli:

__NOTOC__

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

==Key Investigators==

*Pietro Nardelli (Brigham and Women's Hospital, Harvard Medical School, USA)
*Jorge Onieva Onieva (Brigham and Women's Hospital, Harvard Medical School, USA)
*[https://lmi.med.harvard.edu/people/raul-san-jose-estepar Raúl San José Estépar] (Brigham and Women's Hospital, Harvard Medical School, USA)
* [https://fedorov.github.io Andrey Fedorov] (remote) (Brigham and Women's Hospital, Harvard Medical School, USA)
* Christian Herz, (remote) (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;"
|
*The goal of this project is to create a new tool for SlicerCIP that allows the creation of a PDF report that summarize and illustrate quantitive analysis.

|
* Implement a HTML template for quantitative analysis report
* Implement a new module that fills the HTML with images and data

|

* New HTML template for quantitative analysis report created
* The HTML template can be filled with images and data for specific purposes
|}

==Illustrations==

[[File:PDFReportForEmphysema.png|thumb|center]]
[[File:PDFReportForAVRatioModule.png|thumb|center]]

==Background and References==

*[https://github.com/acil-bwh/SlicerCIP SlicerCIP]

[https://wiki.qt.io/Exporting_a_document_to_PDF Using QPrinter] should be possible.

File:PDFReportForEmphysema.png

2017-06-29T23:29:07Z

PietroNardelli:

PDFReportForEmphysema

Project Week 25/SlicerCIP ReportsTool

2017-06-29T23:27:11Z

PietroNardelli:

__NOTOC__

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

==Key Investigators==

*Pietro Nardelli (Brigham and Women's Hospital, Harvard Medical School, USA)
*Jorge Onieva Onieva (Brigham and Women's Hospital, Harvard Medical School, USA)
*[https://lmi.med.harvard.edu/people/raul-san-jose-estepar Raúl San José Estépar] (Brigham and Women's Hospital, Harvard Medical School, USA)
* [https://fedorov.github.io Andrey Fedorov] (remote) (Brigham and Women's Hospital, Harvard Medical School, USA)
* Christian Herz, (remote) (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;"
|
*The goal of this project is to create a new tool for SlicerCIP that allows the creation of a PDF report that summarize and illustrate quantitive analysis.

|
* Implement a HTML template for quantitative analysis report
* Implement a new module that fills the HTML with images and data

|

* New HTML template for quantitative analysis report created
* The HTML template can be filled with images and data for specific purposes
|}

==Illustrations==
[[File:EmphysemaReport.pdf|thumb]]

[[File:PDFReportForAVRatioModule.png|thumb]]

==Background and References==

*[https://github.com/acil-bwh/SlicerCIP SlicerCIP]

[https://wiki.qt.io/Exporting_a_document_to_PDF Using QPrinter] should be possible.

File:PDFReportForAVRatioModule.png

2017-06-29T23:26:58Z

PietroNardelli:

PDF report for AV Ratio module in SlicerCIP

File:EmphysemaReport.pdf

2017-06-29T23:25:41Z

PietroNardelli:

Report for emphysema analysis

Project Week 25/SlicerCIP ReportsTool

2017-06-29T23:24:35Z

PietroNardelli:

__NOTOC__

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

==Key Investigators==

*Pietro Nardelli (Brigham and Women's Hospital, Harvard Medical School, USA)
*Jorge Onieva Onieva (Brigham and Women's Hospital, Harvard Medical School, USA)
*[https://lmi.med.harvard.edu/people/raul-san-jose-estepar Raúl San José Estépar] (Brigham and Women's Hospital, Harvard Medical School, USA)
* [https://fedorov.github.io Andrey Fedorov] (remote) (Brigham and Women's Hospital, Harvard Medical School, USA)
* Christian Herz, (remote) (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;"
|
*The goal of this project is to create a new tool for SlicerCIP that allows the creation of a PDF report that summarize and illustrate quantitive analysis.

|
* Implement a HTML template for quantitative analysis report
* Implement a new module that fills the HTML with images and data

|

* New HTML template for quantitative analysis report created
* The HTML template can be filled with images and data for specific purposes
|}

==Illustrations==

==Background and References==

*[https://github.com/acil-bwh/SlicerCIP SlicerCIP]

[https://wiki.qt.io/Exporting_a_document_to_PDF Using QPrinter] should be possible.

File:BronchiectasisModuleExample.png

2017-06-29T23:11:51Z

PietroNardelli:

Example of usage of bronchiectasis module

Project Week 25/SlicerCIP Bronchiectasis

2017-06-29T23:06:48Z

PietroNardelli:

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

==Key Investigators==

*Pietro Nardelli (Brigham and Women's Hospital, Harvard Medical School, USA)
*Jorge Onieva Onieva (Brigham and Women's Hospital, Harvard Medical School, USA)
*[https://lmi.med.harvard.edu/people/raul-san-jose-estepar Raúl San José Estépar] (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;"
|
The goal of this project is to create a new semi-automated tool for SlicerCIP that allows to define bronchiectasis by means of the airway to vessel ratio. If ratio > 1, then there is bronchiectasis.

|
* Implement a customized Slicer editor module to select the region of interest (airway + vessel)
* Implement a tool to compute the airway to vessel ratio
* Use SlicerCIP template to save results

|
* Customized Slicer module to measure airways and vessels by means of rulers created
* AV ratio is computed and shown to the user
* The SlicerCIP template is used save results and create PDF report
* Next step: use circular rulers for better measurement
|}

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

*[https://github.com/acil-bwh/SlicerCIP SlicerCIP]

Project Week 25/SlicerCIP Bronchiectasis

2017-06-13T09:30:50Z

PietroNardelli:

__NOTOC__

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

==Key Investigators==

*Pietro Nardelli (Brigham and Women's Hospital, Harvard Medical School, USA)
*Jorge Onieva Onieva (Brigham and Women's Hospital, Harvard Medical School, USA)
*Raúl San José Estépar (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;"
|
The goal of this project is to create a new semi-automated tool for SlicerCIP that allows to define bronchiectasis by means of the airway to vessel ratio. If ratio > 1, then there is bronchiectasis.

|
* Implement a customized Slicer editor module to select the region of interest (airway + vessel)
* Implement a tool to compute the airway to vessel ratio
* Use SlicerCIP template to save results

|

|}

==Illustrations==

==Background and References==

SlicerCIP: https://github.com/acil-bwh/SlicerCIP

Project Week 25

2017-06-13T09:25:18Z

PietroNardelli: /* 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]]
<br>

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

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

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

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

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/879371330 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
#(TBD) Hangout #11: June 14: Review of Project Pages
#(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 | Deep Learning: Data Augmentation for Prostate Segmentation]]
#DICOM Segmentation Support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#[[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]]
#Steerable Catheters Path Planner Extension for Brain Surgery Applications (Alberto Favaro, Marlene Pinzi)
#[[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]]
#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/Slice-to-Volume Registration to Support MRI guided Interventions | Slice-to-Volume Registration to Support MRI guided Interventions ]] (Gino Gulamhussene)
#[[Project_Week_25/SALT_Spatiotemporal_Modeling: | Slicer SALT Validation: Spatiotemporal Modeling of Subcortical Structures ]] (James Fishbaugh, Guido Gerig)
#[[Project_Week_25/Wrist_Kinematics: | Kinematic Analysis of the Wrist from Dynamic MRI]] (James Fishbaugh, Guido Gerig)
#[[Project_Week_25/SlicerCIP_Bronchiectasis | SlicerCIP: Tool for Quantitative Analysis of Bronchiectasis]] (Pietro Nardelli, Jorge Onieva, Raúl San José Estépar)
#[[Project_Week_25/SlicerCIP_ReportsTool | SlicerCIP: Tool for Creation of Reports for Quantitive Analysis]] (Pietro Nardelli, Jorge Onieva, Raúl San José Estépar)
#[[Project_Week_25/Multimodal: | Multimodal, Multiresolution, Multivolume Data]] (Guido Gerig)

=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, University of Groningen, The Nederlands
# 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
# Jorge Quintero Nehrkorn :: Canary Islands, Spain

Project Week 25

2017-06-13T09:23:21Z

PietroNardelli: /* 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]]
<br>

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

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

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

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

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/879371330 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
#(TBD) Hangout #11: June 14: Review of Project Pages
#(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 | Deep Learning: Data Augmentation for Prostate Segmentation]]
#DICOM Segmentation Support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#[[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]]
#Steerable Catheters Path Planner Extension for Brain Surgery Applications (Alberto Favaro, Marlene Pinzi)
#[[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]]
#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/Slice-to-Volume Registration to Support MRI guided Interventions | Slice-to-Volume Registration to Support MRI guided Interventions ]] (Gino Gulamhussene)
#[[Project_Week_25/SALT_Spatiotemporal_Modeling: | Slicer SALT Validation: Spatiotemporal Modeling of Subcortical Structures ]] (James Fishbaugh, Guido Gerig)
#[[Project_Week_25/Wrist_Kinematics: | Kinematic Analysis of the Wrist from Dynamic MRI]] (James Fishbaugh, Guido Gerig)
#[[Project_Week_25/SlicerCIP_Bronchiectasis | SlicerCIP: Tool for Quantitative Analysis of Bronchiectasis]] (Pietro Nardelli, Jorge Onieva, Raúl San José Estépar)
#[[Project_Week_25/SlicerCIP_ReportsTool | SlicerCIP: Tool for Creation of Reports for Quantitive Analysis]]
(Pietro Nardelli, Jorge Onieva, Raúl San José Estépar)
#[[Project_Week_25/Multimodal: | Multimodal, Multiresolution, Multivolume Data]] (Guido Gerig)

=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, University of Groningen, The Nederlands
# 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
# Jorge Quintero Nehrkorn :: Canary Islands, Spain

Project Week 25/SlicerCIP ReportsTool

2017-06-13T09:21:55Z

PietroNardelli: Created page with "__NOTOC__ Back to Projects List ==Key Investigators==  *Pietro Nardelli (Brigham and Women's Hospital, H..."

Project Week 25

2017-06-13T09:14:58Z

PietroNardelli: /* 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]]
<br>

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

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

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

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

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/879371330 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
#(TBD) Hangout #11: June 14: Review of Project Pages
#(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 | Deep Learning: Data Augmentation for Prostate Segmentation]]
#DICOM Segmentation Support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#[[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]]
#Steerable Catheters Path Planner Extension for Brain Surgery Applications (Alberto Favaro, Marlene Pinzi)
#[[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]]
#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/Slice-to-Volume Registration to Support MRI guided Interventions | Slice-to-Volume Registration to Support MRI guided Interventions ]] (Gino Gulamhussene)
#[[Project_Week_25/SALT_Spatiotemporal_Modeling: | Slicer SALT Validation: Spatiotemporal Modeling of Subcortical Structures ]] (James Fishbaugh, Guido Gerig)
#[[Project_Week_25/Wrist_Kinematics: | Kinematic Analysis of the Wrist from Dynamic MRI]] (James Fishbaugh, Guido Gerig)
#[[Project_Week_25/SlicerCIP_Bronchiectasis | SlicerCIP: Tool for Quantitative Analysis of Bronchiectasis]](Pietro Nardelli, Jorge Onieva, Raúl San José Estépar)
#[[Project_Week_25/SlicerCIP_ReportsTool | SlicerCIP: Tool for Creation of Reports for Quantitive Analysis]](Pietro Nardelli, Jorge Onieva, Raúl San José Estépar)
#[[Project_Week_25/Multimodal: | Multimodal, Multiresolution, Multivolume Data]] (Guido Gerig)

=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, University of Groningen, The Nederlands
# 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
# Jorge Quintero Nehrkorn :: Canary Islands, Spain

Project Week 25

2017-06-12T14:59:14Z

PietroNardelli: /* 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]]
<br>

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

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

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

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

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/879371330 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
#(TBD) Hangout #11: June 14: Review of Project Pages
#(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 | Deep Learning: Data Augmentation for Prostate Segmentation]]
#DICOM Segmentation Support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#[[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]]
#Steerable Catheters Path Planner Extension for Brain Surgery Applications (Alberto Favaro, Marlene Pinzi)
#[[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]]
#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)
#2D Slice to 3D Volume Registration to Support Radiologic Interventions (Gino Gulamhussene)
#[[Project_Week_25/SALT_Spatiotemporal_Modeling: | Slicer SALT Validation: Spatiotemporal Modeling of Subcortical Structures ]] (James Fishbaugh, Guido Gerig)
#[[Project_Week_25/Wrist_Kinematics: | Kinematic Analysis of the Wrist from Dynamic MRI]] (James Fishbaugh, Guido Gerig)
#[[Project_Week_25/SlicerCIP_Bronchiectasis | SlicerCIP: Tool for Interactive Bronchiectasis Identification and Measurement]](Pietro Nardelli, Jorge Onieva, Raúl San José Estépar)
#[[Project_Week_25/Multimodal: | Multimodal, Multiresolution, Multivolume Data]] (Guido Gerig)

=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, University of Groningen, The Nederlands
# 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
# Jorge Quintero Nehrkorn :: Canary Islands, Spain

Project Week 25

2017-06-12T14:56:38Z

PietroNardelli: /* 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]]
<br>

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

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

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

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

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/879371330 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
#(TBD) Hangout #11: June 14: Review of Project Pages
#(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 | Deep Learning: Data Augmentation for Prostate Segmentation]]
#DICOM Segmentation Support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#[[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]]
#Steerable Catheters Path Planner Extension for Brain Surgery Applications (Alberto Favaro, Marlene Pinzi)
#[[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]]
#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)
#2D Slice to 3D Volume Registration to Support Radiologic Interventions (Gino Gulamhussene)
#[[Project_Week_25/SALT_Spatiotemporal_Modeling: | Slicer SALT Validation: Spatiotemporal Modeling of Subcortical Structures ]] (James Fishbaugh, Guido Gerig)
#[[Project_Week_25/Wrist_Kinematics: | Kinematic Analysis of the Wrist from Dynamic MRI]] (James Fishbaugh, Guido Gerig)
#[[Project_Week_25/SlicerCIP_Bronchiectasis | SlicerCIP: Tool for Interactive Bronchiectasis Identification and Measurement]]
#[[Project_Week_25/Multimodal: | Multimodal, Multiresolution, Multivolume Data]] (Guido Gerig)

=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, University of Groningen, The Nederlands
# 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
# Jorge Quintero Nehrkorn :: Canary Islands, Spain

Project Week 25/SlicerCIP Bronchiectasis

2017-06-12T14:53:00Z

PietroNardelli:

__NOTOC__

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

==Key Investigators==

*Pietro Nardelli (Brigham and Women's Hospital, Harvard Medical School, USA)
*Jorge Onieva Onieva (Brigham and Women's Hospital, Harvard Medical School, USA)
*Raúl San José Estépar (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;"
|
The goal of this project is to create a new tool for SlicerCIP that allows to identify bronchiectatic airways on chest CT images in a manual or semi-automatic basis with the help of a customized Slicer Editor module. The tool should allow to compute different measures of the specified airway (area, std dev, mean, etc.) and save them into an xml file along with airway location.

|
* Implement a customized Slicer editor module
* Implement a tool to compute a set of measures on the identified airway (area, mean, std. dev., etc.)
* Test with different CT images

|

|}

==Illustrations==

==Background and References==

SlicerCIP: https://github.com/acil-bwh/SlicerCIP

Project Week 25

2017-06-12T14:09:02Z

PietroNardelli: /* 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]]
<br>

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

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

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

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

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/879371330 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
#(TBD) Hangout #11: June 14: Review of Project Pages
#(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 | Deep Learning: Data Augmentation for Prostate Segmentation]]
#DICOM Segmentation Support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#[[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]]
#Steerable Catheters Path Planner Extension for Brain Surgery Applications (Alberto Favaro, Marlene Pinzi)
#[[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]]
#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)
#2D Slice to 3D Volume Registration to Support Radiologic Interventions (Gino Gulamhussene)
#[[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 Interactive Bronchiectasis Definition and Measurement]]

=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, University of Groningen, The Nederlands
# 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
# Jorge Quintero Nehrkorn :: Canary Islands, Spain

Project Week 25

2017-06-12T11:38:36Z

PietroNardelli:

__NOTOC__
Back to [[Events]]

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

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

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

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

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

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

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/879371330 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
#(TBD) Hangout #11: June 14: Review of Project Pages
#(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 | Deep Learning: Data Augmentation for Prostate Segmentation]]
#DICOM Segmentation Support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#[[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]]
#Steerable Catheters Path Planner Extension for Brain Surgery Applications (Alberto Favaro, Marlene Pinzi)
#[[Project_Week_25/Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification | Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification]] (Simon Drouin, Christian Hansen, David Black)
#[[Project_Week_25/DICOM_for_Quantitative_Imaging_and_Integration_with_Processing_Applications|DICOM for Quantitative Imaging and Integration with Processing Applications]]
#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)
#2D Slice to 3D Volume Registration to Support Radiologic Interventions (Gino Gulamhussene)
#[[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: Interactive Bronchiectasis Definition]]

=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, University of Groningen, The Nederlands
# 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
# Jorge Quintero Nehrkorn :: Canary Islands, Spain

Project Week 25

2017-06-12T11:36:34Z

PietroNardelli:

__NOTOC__
Back to [[Events]]

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

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

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

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

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

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

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/879371330 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
#(TBD) Hangout #11: June 14: Review of Project Pages
#(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 | Deep Learning: Data Augmentation for Prostate Segmentation]]
#DICOM Segmentation Support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#[[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]]
#Steerable Catheters Path Planner Extension for Brain Surgery Applications (Alberto Favaro, Marlene Pinzi)
#[[Project_Week_25/Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification | Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification]] (Simon Drouin, Christian Hansen, David Black)
#[[Project_Week_25/DICOM_for_Quantitative_Imaging_and_Integration_with_Processing_Applications|DICOM for Quantitative Imaging and Integration with Processing Applications]]
#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)
#2D Slice to 3D Volume Registration to Support Radiologic Interventions (Gino Gulamhussene)
#[[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: Interactive Bronchiectasis Definition]]

=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, University of Groningen, The Nederlands
# 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
# Jorge Quintero Nehrkorn :: Canary Islands, Spain

Project Week 25/SlicerCIP Bronchiectasis

2017-06-12T11:33:04Z

PietroNardelli: Created page with "__NOTOC__ Back to Projects List ==Key Investigators==  *Pietro Nardelli (Brigham and Women's Hospital, H..."

Project Week 25

2017-06-12T09:58:24Z

PietroNardelli:

__NOTOC__
Back to [[Events]]

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

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

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

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

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

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

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/879371330 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
#(TBD) Hangout #11: June 14: Review of Project Pages
#(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 | Deep Learning: Data Augmentation for Prostate Segmentation]]
#DICOM Segmentation Support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#[[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]]
#Steerable Catheters Path Planner Extension for Brain Surgery Applications (Alberto Favaro, Marlene Pinzi)
#[[Project_Week_25/Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification | 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)
#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)
#2D Slice to 3D Volume Registration to Support Radiologic Interventions (Gino Gulamhussene)
#[[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]]
#SlicerCIP: Interactive Bronchiectasis Definition (Pietro Nardelli, Raúl San José Estépar)

=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, University of Groningen, The Nederlands
# 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
# Jorge Quintero Nehrkorn :: Canary Islands, Spain

Project Week 25

2017-06-12T09:56:57Z

PietroNardelli:

__NOTOC__
Back to [[Events]]

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

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

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

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

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

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

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/879371330 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
#(TBD) Hangout #11: June 14: Review of Project Pages
#(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 | Deep Learning: Data Augmentation for Prostate Segmentation]]
#DICOM Segmentation Support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#[[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]]
#Steerable Catheters Path Planner Extension for Brain Surgery Applications (Alberto Favaro, Marlene Pinzi)
#[[Project_Week_25/Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification | 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)
#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)
#2D Slice to 3D Volume Registration to Support Radiologic Interventions (Gino Gulamhussene)
#[[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]]
#SlicerCIP: interactive bronchiectasis definition (Pietro Nardelli, Raúl San José Estépar)

=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, University of Groningen, The Nederlands
# 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
# Jorge Quintero Nehrkorn :: Canary Islands, Spain

2014 Summer Project Week:Multiscale Non Local Means filter (NLM) for chest CT images

2014-06-27T03:56:20Z

PietroNardelli:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:NoisyChestCTImage.png|Chest CT image affected by Gaussian noise (sigma = 100)
Image:FilteredChestCTImage.png|Chest CT image filtered using a multi-scale NLM filter
</gallery>

==Key Investigators==
* Pietro Nardelli
* Raul San Jose Estepar

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*Improving the quality of CT images is important due to the increased use of these images for diagnostic purposes and the need to reduce dose. We have inspected possible methods for improving image quality while preserving important information. We are thus interested in developing a modified NLM formulation based on quadratic approximation of distances. Our idea is to exploit a multi-scale approach in order to better compute salient features that will be used in the approximation of local patches centered on pixels under comparison. The quadratic approximation of local intensities is very suitable in modalities like CT where tubular and sheet-like structures are visible. Our interest is focused mainly on chest CT images, as the filter would be used combined with an airway segmentation module. Our goal is thus to develop a NLM filter to be integrated within Slicer. The filter should also be tested on different noisy images.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*A first version of a modified NLM filter has been already developed as a standalone module using ITK classes. However, it is still not working properly. Therefore, the module needs to be improved first in order to obtain good results.
*The module will be then integrated within Slicer as CLI/Scripted module.
*A new Slicer interface will be created in order to make the module more user-friendly
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Small issues have been fixed.
* The filter has been tested on a few chest CT images
* More improvements and new tests will be necessary.
</div>
</div>

File:FilteredChestCTImage.png

2014-06-27T03:52:11Z

PietroNardelli: Chest CT Image filtered using a multiscale NLM filter

Chest CT Image filtered using a multiscale NLM filter

File:NoisyChestCTImage.png

2014-06-27T03:51:12Z

PietroNardelli: Chest CT Image with Gaussian noise (sigma 100)

Chest CT Image with Gaussian noise (sigma 100)

2014 Summer Project Week

2014-06-23T12:44:17Z

PietroNardelli: /* Chronic Obstructive Pulmonary Disease, Lung, Chest */

__NOTOC__

[[image:PW-MIT2014.png|300px]]

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 23
!style="width:18%" |Tuesday, June 24
!style="width:18%" |Wednesday, June 25
!style="width:18%" |Thursday, June 26
!style="width:18%" |Friday, June 27
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)
<br>
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Neuro|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) <br>
[[MIT_Project_Week_Rooms#Star|Star]]

<br>----------------------------------------<br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Prostate|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Noby Hata)
[[MIT_Project_Week_Rooms#Star|Star]]
<br>----------------------------------------<br>
|
|-
|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
|
|}

== '''Background''' ==

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

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

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==Huntington's Disease==
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)

==Head and Neck Cancer==
*[[2014_Summer_Project_Week:Interactive_DIR| Interactive DIR]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp)
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)

==TBI==
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Stroke==
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)

==Image-Guided Therapy==

* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata)
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras)
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)
* [[2014_Summer_Project_Week:Image To Mesh Conversion for Brain MRI | Image To Mesh Conversion for Brain MRI]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift | An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer(WPI), Nirav Patel(WPI), Nobuhiko Hata (BWH) )
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
*[[2014_Summer_Project_Week:Intraoperative_Registration_of_preoperative_CT_and_C-arm_CT_of_the_lung | Intraoperative Registration of preoperative CT and C-arm CT of the lung]] (Katharina Breininger, Jay Jagadeesan)

==Chronic Obstructive Pulmonary Disease, Lung, Chest ==

*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Multiscale_Non_Local_Means_filter_(NLM)_for_chest_CT_images | Multiscale Non Local Means filter (NLM) for chest CT images]] (Pietro Nardelli, Raul San Jose)

==[http://qiicr.org QIICR]==
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})
* [[2014_Summer_Project_Week: DICOM SEG conversion to support archival of QIN Grand challenges results|DICOM SEG conversion to support archival of QIN Grand challenges results]] (Jayashree, Andrey, Steve, {David remotely})

==Feature Extraction==
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)

==Brain==
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*[[2014_Summer_Project_Week:Slicer_LDDMM_Shape_Analysis | Slicer Interface to LDDMM shape anlaysis]] (Saurabh Jain, JHU; Steve Pieper, Isomics; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders | CAD Toolbox for Neurological Disorders]] (Sidong Liu, Siqi Liu, Fan Zhang, Yang Song, Weidong Cai, Sonia Pujol, Ron Kikinis)
*[[2014_Summer_Project_Week:Longitudinal_patient_specific_DTI_analysis | Longitudinal patient-specific DTI analysis using Slicer for neonatal asphyxia]] (Anuja Sharma, SCI, Utah; Francois Budin, UNC; Martin Styner, UNC; Guido Gerig, SCI, Utah)
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Kevin Wang, Andras Lasso)
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)
*[[2014_Summer_Project_Week:DRAMMS_Slicer| Integrating DRAMMS deformable registration into Slicer]] (Yangming Ou, Steve Pieper, Andriy Fedorov, Tina Kapur, Christos Davatzikos, Ron Kikinis, Randy Gollub, Jayashree Kalpathy-Cramer)

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)

== '''Logistics''' ==

*'''Dates:''' June 23-27, 2014.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' https://www.regonline.com/namic2014summerprojectweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2014summerprojectweek Please click here to register.])

#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Saskia Camps, SPL, saskiacamps@gmail.com
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Adrian Dalca, MIT CSAIL, adalca@mit.edu
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu
#Polina Golland, MIT CSAIL, polina@csail.mit.edu
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu
#Franklin King, Queen's University, franklin.king@queensu.ca
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu
#Robin Kouver, BWH/SPL, r.kouver@gmail.com
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca
#Yangming Li, University of Washington, ymli81@uw.edu
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu
#Jim Miller, GE Research, millerjv@ge.com
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu
#Danielle Pace, MIT CSAIL, dfpace@mit.edu
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org
#Nirav Patel, WPI, napatel@wpi.edu
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu
#Adam Rankin, Queen's University, rankin@queensu.ca
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
#Tamas Ungi, Queen's University, ungi@queensu.ca
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca
#David Welch, University of Iowa, david-welch@uiowa.edu
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Summer Project Week:Multiscale Non Local Means filter (NLM) for chest CT images

2014-06-23T12:43:22Z

PietroNardelli: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Pietro Nardelli
* Raul San Jose Estepar

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*Improving the quality of CT images is important due to the increased use of these images for diagnostic purposes and the need to reduce dose. We have inspected possible methods for improving image quality while preserving important information. We are thus interested in developing a modified NLM formulation based on quadratic approximation of distances. Our idea is to exploit a multi-scale approach in order to better compute salient features that will be used in the approximation of local patches centered on pixels under comparison. The quadratic approximation of local intensities is very suitable in modalities like CT where tubular and sheet-like structures are visible. Our interest is focused mainly on chest CT images, as the filter would be used combined with an airway segmentation module. Our goal is thus to develop a NLM filter to be integrated within Slicer. The filter should also be tested on different noisy images.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*A first version of a modified NLM filter has been already developed as a standalone module using ITK classes. However, it is still not working properly. Therefore, the module needs to be improved first in order to obtain good results.
*The module will be then integrated within Slicer as CLI/Scripted module.
*A new Slicer interface will be created in order to make the module more user-friendly
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Project Week Template

2014-06-11T14:37:36Z

PietroNardelli:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Summer Project Week:Multiscale Non Local Means filter (NLM) for chest CT images

2014-06-11T14:36:26Z

PietroNardelli:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Pietro Nardelli

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*Improving the quality of CT images is important due to the increased use of these images for diagnostic purposes and the need to reduce dose. We have inspected possible methods for improving image quality while preserving important information. We are thus interested in developing a modified NLM formulation based on quadratic approximation of distances. Our idea is to exploit a multi-scale approach in order to better compute salient features that will be used in the approximation of local patches centered on pixels under comparison. The quadratic approximation of local intensities is very suitable in modalities like CT where tubular and sheet-like structures are visible. Our interest is focused mainly on chest CT images, as the filter would be used combined with an airway segmentation module. Our goal is thus to develop a NLM filter to be integrated within Slicer. The filter should also be tested on different noisy images.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*A first version of a modified NLM filter has been already developed as a standalone module using ITK classes. However, it is still not working properly. Therefore, the module needs to be improved first in order to obtain good results.
*The module will be then integrated within Slicer as CLI/Scripted module.
*A new Slicer interface will be created in order to make the module more user-friendly
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Project Week Template

2014-06-11T14:34:14Z

PietroNardelli:

2014 Project Week Template

2014-06-10T17:55:31Z

PietroNardelli:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Pietro Nardelli

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*Improving the quality of CT images is important due to the increased use of these images for diagnostic purposes and the need to reduce dose. We have inspected possible methods for improving image quality while preserving important information. We are thus interested in developing a modified NLM formulation based on quadratic approximation of distances. Our idea is to exploit a multi-scale approach in order to better compute salient features that will be used in the approximation of local patches centered on pixels under comparison. The quadratic approximation of local intensities is very suitable in modalities like CT where tubular and sheet-like structures are visible. Our interest is focused mainly on chest CT images, as the filter would be used combined with an airway segmentation module. Our goal is thus to develop a NLM filter to be integrated within Slicer. The filter should also be tested on different noisy images.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*A first version of a modified NLM filter has been already developed as a standalone module using ITK classes. However, it is still not working properly. Therefore, the module needs first to be improved in order to obtain good results.
*The module will be then integrated within Slicer as CLI/ module.
*A new Slicer interface will be created in order to make the module more user-friendly
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Summer Project Week:Multiscale Non Local Means filter (NLM) for chest CT images

2014-06-10T17:17:24Z

PietroNardelli: Created page with '__NOTOC__ <gallery> Image:PW-MIT2014.png|Projects List </gallery> ==Key Investigators== ==Project Description== <div style="margin: 20px…'

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Summer Project Week

2014-06-10T17:16:42Z

PietroNardelli: /* Other */

2014 Winter Project Week:Slicer CIP Slicer MRML

2014-01-10T06:59:35Z

PietroNardelli:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:Cattura.JPG|[[Chest labelmap]]
Image:Cattura1.JPG|[[Chest labelmap after user selection]]
</gallery>

==Key Investigators==
Pietro Nardelli, Raul San Jose
==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a library of tools (Chest Imaging Platform) for the processing and the analysis of chest images. The main objective is to create new MRML nodes able to manage our chest labelmap to employ a Region/Type scheme. In particular, we want to allow the user to show only the selected region/type of a chest labelmap.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* A new vtkMRMLRegionTypeNode which inherits from vtkMRMLScalarVolumeNode will be created. This node will be used within a loadable module to handle our chest labelmap and allow the user to show only a selected region/type-
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Private github repository: https://github.com/acil-bwh/SlicerCIP
* New vtkMRMLRegionTypeNode created
* New loadable module allowing the user to show only selected region and type developed
* Still a bit slow. Need to speed it up!
* A new specific chest lookup table needs to be developed!

File:Cattura1.JPG

2014-01-10T06:52:00Z

PietroNardelli: Chest labelmap after user selection

Chest labelmap after user selection

File:Cattura.JPG

2014-01-10T06:51:11Z

PietroNardelli: Chest labelmap

Chest labelmap

2014 Winter Project Week:Slicer CIP Slicer MRML

2014-01-06T04:34:19Z

PietroNardelli:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Pietro Nardelli, Raul San Jose
==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a library of tools (Chest Imaging Platform) for the processing and the analysis of chest images. The main objective is to create new MRML nodes able to manage our chest labelmap to employ a Region/Type scheme. In particular, we want to allow the user to show only the selected region/type of a chest labelmap.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* A new vtkMRMLRegionTypeNode which inherits from vtkMRMLScalarVolumeNode will be created. This node will be used within a loadable module to handle our chest labelmap and allow the user to show only a selected region/type-
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

2012 Summer Project Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets

2012-06-22T13:47:43Z

PietroNardelli: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Airway_Segmentation.png|Airway Segmentation
Image:Comparison.png|Comparison of the Case_30 of the EXACT '09 dataset
</gallery>

==Key Investigators==
* University College Cork: Padraig Cantillon-Murphy, Pietro Nardelli
* HMS/HSDM: Raul San Jose Estepar

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are currently developing a system for endoscopic lung biopsy which would allow access to peripheral nodules using electromagnetic steering by means of external coils. The goal of the project is to steer a catheter inside the lung using an electromagnetic field (provided by 3 electromagnetic coils) and to couple this electromagnetic navigation system with real-time image registration so that the physician can see a 3D reconstruction of where he is in the airway by means of a virtual endoscopy system (registered to a prior CT).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

For the virtual endoscopy system we are using 3D Slicer to implement a new tool that should allow the physician to have a fast 3D reconstruction of the airway and to move inside it following the catheter.
The idea for the tool is to firstly develop an element of semi-automatic segmentation improving the already available Slicer’s Simple Region Growing Module in order to obtain a new Adaptive Threshold Region Growing Module capable of automatic increment. Then, by choosing the right threshold to reconstruct the airway as well as possible and to avoid leakage problems: for this purpose, we are planning to follow the Kiraly’s method [1], which seems a good trade-off between complexity and segmentation’s capability. In this way, we think to be able to obtain a first non-complete but sufficient for the most of the times segmentation and reconstruction of the airway,
Once the airway has been firstly segmented and reconstructed with the method above, the goal is to allow the physician to select the Region of Interest (ROI) (s)he wants to reach (such as a nodule inside a peripheral branch), and to implement a centerline extraction of the reconstructed airway, followed by a path decision, in order to obtain the right way to get the ROI: in this case, the Centerline Extraction Module developed by Estepar et al. for Airway Inspector (based on Slicer 2.8) [2] might be very helpful and we think to extend it to the new Slicer 4.
As the last segmentation part, we are planning to add (if possible) some new method to the Editor module in order to allow the physician, if necessary, to add and see new or existing branches of the airway, which the automatic segmentation can miss. The idea here is to allow the physician to improve the automatic segmentation described above for the purposes of having an optimized path to get to ROIs in deepest part of the lung.
Once the airway’s segmentation has been obtained and the lung has been reconstructed, we are planning to use (and possibly improve) the Slicer's Endoscopy and IGT Modules in order to move through the airway and to recognize and follow the catheter inside the lung.
We have a very nice collaboration in Cork with some interventional pulmonologists in the area of guidance for lung biopsy in cancer patients and the datasets we are using were generated by a 64-GE MEDICAL SYSTEM scanner at Cork University Hospital, with 2mm of slice thickness and a standard convolution kernel. We have also available the CT datasets which were used during EXACT 2009 and are freely available, as a benchmark for our approach against others existing .

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
CLI Module for Airway Segmentation created, with quite good results (comparable with other team's results)

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in - No
##Extension -- commandline - Yes
##Extension -- loadable
#Other (Please specify)

==References==

1. Kiraly AP, Higgings WE, McLennan G, Hoffman EA, McLennan G, Reinhardt JM. Three-dimensional human airway segmentation methods for clinical virtual bronchoscopy. ''Acad Radiol'' 2002;9:1153-1168.

2. San Jose Estepar R, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin CF. Airway inspector: An open source application for lung morphometry. In First International Workshop on Pulmonary Image Processing. New York City, USA, 2008;293-302.
</div>

2012 Summer Project Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets

2012-06-22T12:54:02Z

PietroNardelli:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Airway_Segmentation.png|Airway Segmentation
Image:Comparison.png|Comparison of the Case_30 of the EXACT '09 dataset
</gallery>

==Key Investigators==
* University College Cork: Padraig Cantillon-Murphy, Pietro Nardelli
* HMS/HSDM: Raul San Jose Estepar

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are currently developing a system for endoscopic lung biopsy which would allow access to peripheral nodules using electromagnetic steering by means of external coils. The goal of the project is to steer a catheter inside the lung using an electromagnetic field (provided by 3 electromagnetic coils) and to couple this electromagnetic navigation system with real-time image registration so that the physician can see a 3D reconstruction of where he is in the airway by means of a virtual endoscopy system (registered to a prior CT).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

For the virtual endoscopy system we are using 3D Slicer to implement a new tool that should allow the physician to have a fast 3D reconstruction of the airway and to move inside it following the catheter.
The idea for the tool is to firstly develop an element of semi-automatic segmentation improving the already available Slicer’s Simple Region Growing Module in order to obtain a new Adaptive Threshold Region Growing Module capable of automatic increment. Then, by choosing the right threshold to reconstruct the airway as well as possible and to avoid leakage problems: for this purpose, we are planning to follow the Kiraly’s method [1], which seems a good trade-off between complexity and segmentation’s capability. In this way, we think to be able to obtain a first non-complete but sufficient for the most of the times segmentation and reconstruction of the airway,
Once the airway has been firstly segmented and reconstructed with the method above, the goal is to allow the physician to select the Region of Interest (ROI) (s)he wants to reach (such as a nodule inside a peripheral branch), and to implement a centerline extraction of the reconstructed airway, followed by a path decision, in order to obtain the right way to get the ROI: in this case, the Centerline Extraction Module developed by Estepar et al. for Airway Inspector (based on Slicer 2.8) [2] might be very helpful and we think to extend it to the new Slicer 4.
As the last segmentation part, we are planning to add (if possible) some new method to the Editor module in order to allow the physician, if necessary, to add and see new or existing branches of the airway, which the automatic segmentation can miss. The idea here is to allow the physician to improve the automatic segmentation described above for the purposes of having an optimized path to get to ROIs in deepest part of the lung.
Once the airway’s segmentation has been obtained and the lung has been reconstructed, we are planning to use (and possibly improve) the Slicer's Endoscopy and IGT Modules in order to move through the airway and to recognize and follow the catheter inside the lung.
We have a very nice collaboration in Cork with some interventional pulmonologists in the area of guidance for lung biopsy in cancer patients and the datasets we are using were generated by a 64-GE MEDICAL SYSTEM scanner at Cork University Hospital, with 2mm of slice thickness and a standard convolution kernel. We have also available the CT datasets which were used during EXACT 2009 and are freely available, as a benchmark for our approach against others existing .

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in - No
##Extension -- commandline - Yes
##Extension -- loadable
#Other (Please specify)

==References==

1. Kiraly AP, Higgings WE, McLennan G, Hoffman EA, McLennan G, Reinhardt JM. Three-dimensional human airway segmentation methods for clinical virtual bronchoscopy. ''Acad Radiol'' 2002;9:1153-1168.

2. San Jose Estepar R, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin CF. Airway inspector: An open source application for lung morphometry. In First International Workshop on Pulmonary Image Processing. New York City, USA, 2008;293-302.
</div>

File:Comparison.png

2012-06-22T12:50:42Z

PietroNardelli:

2012 Summer Project Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets

2012-06-22T12:49:18Z

PietroNardelli:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Airway_Segmentation.png|Airway Segmentation
</gallery>

==Key Investigators==
* University College Cork: Padraig Cantillon-Murphy, Pietro Nardelli
* HMS/HSDM: Raul San Jose Estepar

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are currently developing a system for endoscopic lung biopsy which would allow access to peripheral nodules using electromagnetic steering by means of external coils. The goal of the project is to steer a catheter inside the lung using an electromagnetic field (provided by 3 electromagnetic coils) and to couple this electromagnetic navigation system with real-time image registration so that the physician can see a 3D reconstruction of where he is in the airway by means of a virtual endoscopy system (registered to a prior CT).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

For the virtual endoscopy system we are using 3D Slicer to implement a new tool that should allow the physician to have a fast 3D reconstruction of the airway and to move inside it following the catheter.
The idea for the tool is to firstly develop an element of semi-automatic segmentation improving the already available Slicer’s Simple Region Growing Module in order to obtain a new Adaptive Threshold Region Growing Module capable of automatic increment. Then, by choosing the right threshold to reconstruct the airway as well as possible and to avoid leakage problems: for this purpose, we are planning to follow the Kiraly’s method [1], which seems a good trade-off between complexity and segmentation’s capability. In this way, we think to be able to obtain a first non-complete but sufficient for the most of the times segmentation and reconstruction of the airway,
Once the airway has been firstly segmented and reconstructed with the method above, the goal is to allow the physician to select the Region of Interest (ROI) (s)he wants to reach (such as a nodule inside a peripheral branch), and to implement a centerline extraction of the reconstructed airway, followed by a path decision, in order to obtain the right way to get the ROI: in this case, the Centerline Extraction Module developed by Estepar et al. for Airway Inspector (based on Slicer 2.8) [2] might be very helpful and we think to extend it to the new Slicer 4.
As the last segmentation part, we are planning to add (if possible) some new method to the Editor module in order to allow the physician, if necessary, to add and see new or existing branches of the airway, which the automatic segmentation can miss. The idea here is to allow the physician to improve the automatic segmentation described above for the purposes of having an optimized path to get to ROIs in deepest part of the lung.
Once the airway’s segmentation has been obtained and the lung has been reconstructed, we are planning to use (and possibly improve) the Slicer's Endoscopy and IGT Modules in order to move through the airway and to recognize and follow the catheter inside the lung.
We have a very nice collaboration in Cork with some interventional pulmonologists in the area of guidance for lung biopsy in cancer patients and the datasets we are using were generated by a 64-GE MEDICAL SYSTEM scanner at Cork University Hospital, with 2mm of slice thickness and a standard convolution kernel. We have also available the CT datasets which were used during EXACT 2009 and are freely available, as a benchmark for our approach against others existing .

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in - No
##Extension -- commandline - Yes
##Extension -- loadable
#Other (Please specify)

==References==

1. Kiraly AP, Higgings WE, McLennan G, Hoffman EA, McLennan G, Reinhardt JM. Three-dimensional human airway segmentation methods for clinical virtual bronchoscopy. ''Acad Radiol'' 2002;9:1153-1168.

2. San Jose Estepar R, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin CF. Airway inspector: An open source application for lung morphometry. In First International Workshop on Pulmonary Image Processing. New York City, USA, 2008;293-302.
</div>

2012 Summer Project Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets

2012-06-22T12:47:54Z

PietroNardelli:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* University College Cork: Padraig Cantillon-Murphy, Pietro Nardelli
* HMS/HSDM: Raul San Jose Estepar

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are currently developing a system for endoscopic lung biopsy which would allow access to peripheral nodules using electromagnetic steering by means of external coils. The goal of the project is to steer a catheter inside the lung using an electromagnetic field (provided by 3 electromagnetic coils) and to couple this electromagnetic navigation system with real-time image registration so that the physician can see a 3D reconstruction of where he is in the airway by means of a virtual endoscopy system (registered to a prior CT).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

For the virtual endoscopy system we are using 3D Slicer to implement a new tool that should allow the physician to have a fast 3D reconstruction of the airway and to move inside it following the catheter.
The idea for the tool is to firstly develop an element of semi-automatic segmentation improving the already available Slicer’s Simple Region Growing Module in order to obtain a new Adaptive Threshold Region Growing Module capable of automatic increment. Then, by choosing the right threshold to reconstruct the airway as well as possible and to avoid leakage problems: for this purpose, we are planning to follow the Kiraly’s method [1], which seems a good trade-off between complexity and segmentation’s capability. In this way, we think to be able to obtain a first non-complete but sufficient for the most of the times segmentation and reconstruction of the airway,
Once the airway has been firstly segmented and reconstructed with the method above, the goal is to allow the physician to select the Region of Interest (ROI) (s)he wants to reach (such as a nodule inside a peripheral branch), and to implement a centerline extraction of the reconstructed airway, followed by a path decision, in order to obtain the right way to get the ROI: in this case, the Centerline Extraction Module developed by Estepar et al. for Airway Inspector (based on Slicer 2.8) [2] might be very helpful and we think to extend it to the new Slicer 4.
As the last segmentation part, we are planning to add (if possible) some new method to the Editor module in order to allow the physician, if necessary, to add and see new or existing branches of the airway, which the automatic segmentation can miss. The idea here is to allow the physician to improve the automatic segmentation described above for the purposes of having an optimized path to get to ROIs in deepest part of the lung.
Once the airway’s segmentation has been obtained and the lung has been reconstructed, we are planning to use (and possibly improve) the Slicer's Endoscopy and IGT Modules in order to move through the airway and to recognize and follow the catheter inside the lung.
We have a very nice collaboration in Cork with some interventional pulmonologists in the area of guidance for lung biopsy in cancer patients and the datasets we are using were generated by a 64-GE MEDICAL SYSTEM scanner at Cork University Hospital, with 2mm of slice thickness and a standard convolution kernel. We have also available the CT datasets which were used during EXACT 2009 and are freely available, as a benchmark for our approach against others existing .

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in - No
##Extension -- commandline - Yes
##Extension -- loadable
#Other (Please specify)

==References==

1. Kiraly AP, Higgings WE, McLennan G, Hoffman EA, McLennan G, Reinhardt JM. Three-dimensional human airway segmentation methods for clinical virtual bronchoscopy. ''Acad Radiol'' 2002;9:1153-1168.

2. San Jose Estepar R, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin CF. Airway inspector: An open source application for lung morphometry. In First International Workshop on Pulmonary Image Processing. New York City, USA, 2008;293-302.
</div>

2012 Summer Project Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets

2012-06-22T12:47:12Z

PietroNardelli: /* Key Investigators */

__NOTOC__
<gallery>
</gallery>

<image>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</image>

==Key Investigators==
* University College Cork: Padraig Cantillon-Murphy, Pietro Nardelli
* HMS/HSDM: Raul San Jose Estepar

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are currently developing a system for endoscopic lung biopsy which would allow access to peripheral nodules using electromagnetic steering by means of external coils. The goal of the project is to steer a catheter inside the lung using an electromagnetic field (provided by 3 electromagnetic coils) and to couple this electromagnetic navigation system with real-time image registration so that the physician can see a 3D reconstruction of where he is in the airway by means of a virtual endoscopy system (registered to a prior CT).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

For the virtual endoscopy system we are using 3D Slicer to implement a new tool that should allow the physician to have a fast 3D reconstruction of the airway and to move inside it following the catheter.
The idea for the tool is to firstly develop an element of semi-automatic segmentation improving the already available Slicer’s Simple Region Growing Module in order to obtain a new Adaptive Threshold Region Growing Module capable of automatic increment. Then, by choosing the right threshold to reconstruct the airway as well as possible and to avoid leakage problems: for this purpose, we are planning to follow the Kiraly’s method [1], which seems a good trade-off between complexity and segmentation’s capability. In this way, we think to be able to obtain a first non-complete but sufficient for the most of the times segmentation and reconstruction of the airway,
Once the airway has been firstly segmented and reconstructed with the method above, the goal is to allow the physician to select the Region of Interest (ROI) (s)he wants to reach (such as a nodule inside a peripheral branch), and to implement a centerline extraction of the reconstructed airway, followed by a path decision, in order to obtain the right way to get the ROI: in this case, the Centerline Extraction Module developed by Estepar et al. for Airway Inspector (based on Slicer 2.8) [2] might be very helpful and we think to extend it to the new Slicer 4.
As the last segmentation part, we are planning to add (if possible) some new method to the Editor module in order to allow the physician, if necessary, to add and see new or existing branches of the airway, which the automatic segmentation can miss. The idea here is to allow the physician to improve the automatic segmentation described above for the purposes of having an optimized path to get to ROIs in deepest part of the lung.
Once the airway’s segmentation has been obtained and the lung has been reconstructed, we are planning to use (and possibly improve) the Slicer's Endoscopy and IGT Modules in order to move through the airway and to recognize and follow the catheter inside the lung.
We have a very nice collaboration in Cork with some interventional pulmonologists in the area of guidance for lung biopsy in cancer patients and the datasets we are using were generated by a 64-GE MEDICAL SYSTEM scanner at Cork University Hospital, with 2mm of slice thickness and a standard convolution kernel. We have also available the CT datasets which were used during EXACT 2009 and are freely available, as a benchmark for our approach against others existing .

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in - No
##Extension -- commandline - Yes
##Extension -- loadable
#Other (Please specify)

==References==

1. Kiraly AP, Higgings WE, McLennan G, Hoffman EA, McLennan G, Reinhardt JM. Three-dimensional human airway segmentation methods for clinical virtual bronchoscopy. ''Acad Radiol'' 2002;9:1153-1168.

2. San Jose Estepar R, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin CF. Airway inspector: An open source application for lung morphometry. In First International Workshop on Pulmonary Image Processing. New York City, USA, 2008;293-302.
</div>

2012 Summer Project Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets

2012-06-22T12:45:25Z

PietroNardelli:

__NOTOC__
<gallery>
</gallery>

==Key Investigators==
* University College Cork: Padraig Cantillon-Murphy, Pietro Nardelli
* HMS/HSDM: Raul San Jose Estepar

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are currently developing a system for endoscopic lung biopsy which would allow access to peripheral nodules using electromagnetic steering by means of external coils. The goal of the project is to steer a catheter inside the lung using an electromagnetic field (provided by 3 electromagnetic coils) and to couple this electromagnetic navigation system with real-time image registration so that the physician can see a 3D reconstruction of where he is in the airway by means of a virtual endoscopy system (registered to a prior CT).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

For the virtual endoscopy system we are using 3D Slicer to implement a new tool that should allow the physician to have a fast 3D reconstruction of the airway and to move inside it following the catheter.
The idea for the tool is to firstly develop an element of semi-automatic segmentation improving the already available Slicer’s Simple Region Growing Module in order to obtain a new Adaptive Threshold Region Growing Module capable of automatic increment. Then, by choosing the right threshold to reconstruct the airway as well as possible and to avoid leakage problems: for this purpose, we are planning to follow the Kiraly’s method [1], which seems a good trade-off between complexity and segmentation’s capability. In this way, we think to be able to obtain a first non-complete but sufficient for the most of the times segmentation and reconstruction of the airway,
Once the airway has been firstly segmented and reconstructed with the method above, the goal is to allow the physician to select the Region of Interest (ROI) (s)he wants to reach (such as a nodule inside a peripheral branch), and to implement a centerline extraction of the reconstructed airway, followed by a path decision, in order to obtain the right way to get the ROI: in this case, the Centerline Extraction Module developed by Estepar et al. for Airway Inspector (based on Slicer 2.8) [2] might be very helpful and we think to extend it to the new Slicer 4.
As the last segmentation part, we are planning to add (if possible) some new method to the Editor module in order to allow the physician, if necessary, to add and see new or existing branches of the airway, which the automatic segmentation can miss. The idea here is to allow the physician to improve the automatic segmentation described above for the purposes of having an optimized path to get to ROIs in deepest part of the lung.
Once the airway’s segmentation has been obtained and the lung has been reconstructed, we are planning to use (and possibly improve) the Slicer's Endoscopy and IGT Modules in order to move through the airway and to recognize and follow the catheter inside the lung.
We have a very nice collaboration in Cork with some interventional pulmonologists in the area of guidance for lung biopsy in cancer patients and the datasets we are using were generated by a 64-GE MEDICAL SYSTEM scanner at Cork University Hospital, with 2mm of slice thickness and a standard convolution kernel. We have also available the CT datasets which were used during EXACT 2009 and are freely available, as a benchmark for our approach against others existing .

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in - No
##Extension -- commandline - Yes
##Extension -- loadable
#Other (Please specify)

==References==

1. Kiraly AP, Higgings WE, McLennan G, Hoffman EA, McLennan G, Reinhardt JM. Three-dimensional human airway segmentation methods for clinical virtual bronchoscopy. ''Acad Radiol'' 2002;9:1153-1168.

2. San Jose Estepar R, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin CF. Airway inspector: An open source application for lung morphometry. In First International Workshop on Pulmonary Image Processing. New York City, USA, 2008;293-302.
</div>

2012 Summer Project Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets

2012-06-22T12:45:00Z

PietroNardelli:

__NOTOC__
<gallery>
Airway_Segmentation.png
</gallery>

==Key Investigators==
* University College Cork: Padraig Cantillon-Murphy, Pietro Nardelli
* HMS/HSDM: Raul San Jose Estepar

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are currently developing a system for endoscopic lung biopsy which would allow access to peripheral nodules using electromagnetic steering by means of external coils. The goal of the project is to steer a catheter inside the lung using an electromagnetic field (provided by 3 electromagnetic coils) and to couple this electromagnetic navigation system with real-time image registration so that the physician can see a 3D reconstruction of where he is in the airway by means of a virtual endoscopy system (registered to a prior CT).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

For the virtual endoscopy system we are using 3D Slicer to implement a new tool that should allow the physician to have a fast 3D reconstruction of the airway and to move inside it following the catheter.
The idea for the tool is to firstly develop an element of semi-automatic segmentation improving the already available Slicer’s Simple Region Growing Module in order to obtain a new Adaptive Threshold Region Growing Module capable of automatic increment. Then, by choosing the right threshold to reconstruct the airway as well as possible and to avoid leakage problems: for this purpose, we are planning to follow the Kiraly’s method [1], which seems a good trade-off between complexity and segmentation’s capability. In this way, we think to be able to obtain a first non-complete but sufficient for the most of the times segmentation and reconstruction of the airway,
Once the airway has been firstly segmented and reconstructed with the method above, the goal is to allow the physician to select the Region of Interest (ROI) (s)he wants to reach (such as a nodule inside a peripheral branch), and to implement a centerline extraction of the reconstructed airway, followed by a path decision, in order to obtain the right way to get the ROI: in this case, the Centerline Extraction Module developed by Estepar et al. for Airway Inspector (based on Slicer 2.8) [2] might be very helpful and we think to extend it to the new Slicer 4.
As the last segmentation part, we are planning to add (if possible) some new method to the Editor module in order to allow the physician, if necessary, to add and see new or existing branches of the airway, which the automatic segmentation can miss. The idea here is to allow the physician to improve the automatic segmentation described above for the purposes of having an optimized path to get to ROIs in deepest part of the lung.
Once the airway’s segmentation has been obtained and the lung has been reconstructed, we are planning to use (and possibly improve) the Slicer's Endoscopy and IGT Modules in order to move through the airway and to recognize and follow the catheter inside the lung.
We have a very nice collaboration in Cork with some interventional pulmonologists in the area of guidance for lung biopsy in cancer patients and the datasets we are using were generated by a 64-GE MEDICAL SYSTEM scanner at Cork University Hospital, with 2mm of slice thickness and a standard convolution kernel. We have also available the CT datasets which were used during EXACT 2009 and are freely available, as a benchmark for our approach against others existing .

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in - No
##Extension -- commandline - Yes
##Extension -- loadable
#Other (Please specify)

==References==

1. Kiraly AP, Higgings WE, McLennan G, Hoffman EA, McLennan G, Reinhardt JM. Three-dimensional human airway segmentation methods for clinical virtual bronchoscopy. ''Acad Radiol'' 2002;9:1153-1168.

2. San Jose Estepar R, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin CF. Airway inspector: An open source application for lung morphometry. In First International Workshop on Pulmonary Image Processing. New York City, USA, 2008;293-302.
</div>

File:Airway Segmentation.png

2012-06-22T12:44:12Z

PietroNardelli: