Difference between revisions of "User:Gumprecht"

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= Wikipage of Jan Gumprecht =
 
= Wikipage of Jan Gumprecht =
  
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== About myself ==
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== About Myself ==
  
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I am a student in Computer Engineering from Germany with a specification in Optoelectronics. At the moment I am writing my diploma thesis on "3D-Ultrasound Integration in Slicer". My university back in Germany is University of Mannheim. From September 2006 to August 2007 I studied in Waterloo, On Canada.
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[[Image:Gumprecht Jan.jpg |thumb|Jan Gumprecht]]
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I am a student in Computer Engineering from the University of Mannheim, Germany with a specification in Optoelectronics. At the moment I am writing my diploma thesis on the project described below. This is not my first stay in North America. I studied already in Waterloo, On, Canada from September 2006 to August 2007 . You may find more information in my [[Media: Gumprecht-Jan-Resume.pdf | Resume]]
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== Contact Information ==
  
 
If you would like to contact me feel free to write me an e-mail.
 
If you would like to contact me feel free to write me an e-mail.
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E-mail: jgumprec (at sign) bwh.harvard.edu
 
E-mail: jgumprec (at sign) bwh.harvard.edu
  
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== What I am working on at the moment ==
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== Project - Development and Validation of an Open-Source Real-Time Freehand 3D Ultrasound Navigation System for Liver Surgery with GPGPU Acceleration==
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* Make 3D Volume Reconstruction of SynchroGrab work
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 +
In my project I developed an open-source navigation system with general purpose graphics unit (GPGPU) acceleration for real-time freehand 3D-Ultrasound using conventional hardware equipment.
 +
 
 +
The proposed software system consists of two distinct components (see graphic below). First, it records data of a tracked US-device and reconstructs volume data in real-time. Simultaneously, position and orientation data of a tracked instrument are acquired. Both the volumes and the spatial information about the tracked instrument are forwarded to the 3D simulation and navigation software [http://www.slicer.org Slicer3D].
  
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== Project - 3D-Ultrasound integration in Slicer ==
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[[Image:SystemStructure.png | 800px ]]
  
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The main part of the project will be the connection of [http://www.midasjournal.org/browse/publication/289 SynchroGrab] to Slicer via OpenIGTLink.
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=== Documentation of the System ===
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Synchrograb is an Open-Source software that generates 3D ultrasound volumes. In order create to create the 3D image it collects image data from an ultra sound device and combines them with the position data of tracking device. With the combination of images and position Synchrograb generates a 3D volume. At the end this 3D image is send to Slicer via OpenIGTLink.
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* Download a presentation of the system [[Media:Gumprecht_Jan-4DUltrasound.pdf | here]]
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* Download my thesis [[Media:Gumprecht_Jan-2009-Diploma_Thesis.pdf‎ |here]]
  
 
=== Technical Information ===
 
=== Technical Information ===
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All technical Information can be found here: [[Technical Information]]
 
All technical Information can be found here: [[Technical Information]]
  
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<br>
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=== Progress ===
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[[Image:SystemAufbau.png | 400px]]
 
  
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<br> <br>
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You can see the progress of my project [[4D Ultrasound Progress | here]]
  
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After discussing with Junichi I got a deeper understanding of how the technical solution might look like.
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=== Screenshots ===
  
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This will be the technical approach.
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[[Image:4DUltrasound-Screenshot-1.png | 600px]]
  
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[[Image:ProjectWorkflow.png]]
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[[Image:4DUltrasound-Screenshot-2.png | 600px]]
  
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== Steps to go ==
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[[Image:4DUltrasound-Screenshot-3.png | 600px]]
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{|border="0", cellpadding="5"
 
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|- bgcolor="silver"
 
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! colspan="2" | Create 3D volume with Synchrograb
 
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|-
 
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| align="center", width="70px" | || width="600px"|Create volume with data from the ultrasound device and the tracker
 
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|-
 
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| align="center" | || Create volume with mockup images and tracking information from the tracker
 
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|-
 
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| bgcolor="#009900" align="center" | DONE || Create volume with mockup images and mockup tracking information
 
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|- bgcolor="silver"
 
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! colspan="2" | Synchrograb
 
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|-
 
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| bgcolor="#009900" align="center" | DONE || Send 3D volume data via OpenIGTLink to Slicer and display data in Slicer
 
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|-
 
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| bgcolor="#009900" align="center" | DONE || Compile Synchrograb core i.d. uncomment unnecessary parts (Ultrasound, Tracker)
 
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|- bgcolor="silver"
 
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! colspan="2" | Preparation
 
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|-
 
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| bgcolor="#009900" align="center" | DONE || Display 3D volume data received via OpenIGTLink with the volume rendering module
 
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|-
 
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| bgcolor="#009900" align="center" | DONE || Create stand alone software to send volume data to Slicer via OpenIGTLink
 
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|-
 
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| bgcolor="#009900" align="center" | DONE || Compile and run Slicer with OpenIGTLink and volume rendering
 
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|-
 
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|}
 
  
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== Progress ==
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[[Image:4DUltrasound-Screenshot-4.png | 600px]]
  
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[[Image:4DUltrasound-Screenshot-5.png | 600px]]
  
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{| border="0" cellpadding="3" cellspacing=0
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[[Image:4DUltrasound-Screenshot-6.png | 600px]]
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|- bgcolor="#abcdef"
 
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! Month !! Week #  !! Start Date - End Date !! Done !! Date Done
 
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|-
 
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|height=10|
 
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|- bgcolor="#D0D0D0"
 
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! September !! Week 39 || 22.09 - 28.09 || ||
 
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|-
 
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|  || colspan="2" | Totally Understand GradientDiffusion Filter Module || align="center" | x || Thu Sep, 25th
 
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|-
 
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|  || colspan="2" | Set up Fedora 8 on th303_d4_6 || align="center" | x || Fri Sep, 26th
 
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|-
 
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| height="20px"|
 
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|- bgcolor="#D0D0D0"
 
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! October !!  Week 40 || 29.09 - 5.10 || ||
 
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|-
 
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| || colspan="2" |Set up CUDA driver on th303_d4_6 || align="center" | x || Tue Sep, 30th
 
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|-
 
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| || colspan="2" |Get CUDA Rendering Volume working in Slicer || align="center" |x || Wed Oct, 2nd
 
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|-
 
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| height="10px"|
 
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|- bgcolor="#E8E8E8"
 
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! bgcolor="#FFFFFF"| !! Week 41 || 06.10 - 12.10 || ||
 
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|-
 
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| || colspan="2" | Understand and Use OpenIGTLink || align="center" | x || Tue Oct, 7th
 
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|-
 
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| height="10px"|
 
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|- bgcolor="#E8E8E8"
 
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! bgcolor="#FFFFFF"| !! Week 42 || 13.10 - 19.10 || ||
 
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|-
 
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| || colspan="2" |Compile SynchroGrab (using latest OpenIGTLink Library) ||align="center" | x || Tue Oct, 14th
 
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|-
 
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| || colspan="2" |Send Volume Data via OpenIGTLink from SynchroGrab to Slicer ||align="center" | x || Tue Oct, 14th
 
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|-
 
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| height="10px"|
 
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|- bgcolor="#E8E8E8"
 
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! bgcolor="#FFFFFF"| !!  Week 43 || 20.10 - 26.10 || ||
 
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|-
 
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| || colspan="2" | Starting work on "Creating a 3D-Volume with Synchrograb"||align="center" |  ||
 
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|-
 
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| height="20px"|
 
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|- bgcolor="#D0D0D0"
 
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! November !!  | Week 44 || 27.10 - 02.11 || ||
 
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|-
 
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|height=5|
 
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|- bgcolor="#E8E8E8"
 
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! bgcolor="#FFFFFF"| !! Week 45 || 03.11 - 09.11 || ||
 
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|-
 
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| || colspan="2" | Video 4 Linux Video Source works ||align="center" | x || Tue Nov, 4th
 
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|-
 
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|height="10px" |
 
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|- bgcolor="#E8E8E8"
 
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!bgcolor="#FFFFFF"| !! Week 46 !! 10.11 - 16.11 || ||
 
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|-
 
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| || colspan="2" | Tracker Simulator works ||align="center" | x || Thu Nov, 13th
 
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|-
 
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|height="10px" |
 
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|- bgcolor="#E8E8E8"
 
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!bgcolor="#FFFFFF"| !! Week 47 !! 17.11 - 23.11 || ||
 
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|-
 
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| || colspan="2" | 3D Volume generated with mock-up images and mock-up tracking data  ||align="center" | x || Mon Nov, 17th
 
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|-
 
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|}
 
  
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== Other Stuff to do ==
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[[Image:4DUltrasound-Screenshot-7.png | 600px]]
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=== Find a new cart for the ultrasound unit ===
 
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* Infos in the intraweb
 
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* Figure out what hardware and how much space on the cart I need
 
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** CUDA Card
 
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** Capture Card
 
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** Ultrasound device
 
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** Tracker device
 
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** Uninterruptible power supply
 
  
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[[Image:4DUltrasound-Screenshot-8.png | 600px]]
  
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== General ==
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=== Images ===
  
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=== Infos on loadable Modules ===
 
  
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[http://www.slicer.org/slicerWiki/index.php/Slicer3:Loadable_Modules:HOWTO HowTo Loadable Module] <br>
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[[Image:4DUltrasound-Image-1.JPG | 600px]]
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[http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:How_to_implement_an_Interactive_Module_GUI HowToLoadable Module GUI]<br>
 
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[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation Infos about Executable Modules inSlicer] <br>
 
  
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=== Subscribe to different meetings ===
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[[Image:4DUltrasound-Image-2.JPG | 600px]]
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* Journal Club
 
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* 1st Monday Seminar
 
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* Office OPRC
 
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* Radiology Grand Rounds
 
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* Cimit Forum
 

Latest revision as of 17:50, 30 March 2011

Wikipage of Jan Gumprecht

About Myself

Jan Gumprecht

I am a student in Computer Engineering from the University of Mannheim, Germany with a specification in Optoelectronics. At the moment I am writing my diploma thesis on the project described below. This is not my first stay in North America. I studied already in Waterloo, On, Canada from September 2006 to August 2007 . You may find more information in my Resume

Contact Information

If you would like to contact me feel free to write me an e-mail.

E-mail: jgumprec (at sign) bwh.harvard.edu

Project - Development and Validation of an Open-Source Real-Time Freehand 3D Ultrasound Navigation System for Liver Surgery with GPGPU Acceleration

In my project I developed an open-source navigation system with general purpose graphics unit (GPGPU) acceleration for real-time freehand 3D-Ultrasound using conventional hardware equipment.

The proposed software system consists of two distinct components (see graphic below). First, it records data of a tracked US-device and reconstructs volume data in real-time. Simultaneously, position and orientation data of a tracked instrument are acquired. Both the volumes and the spatial information about the tracked instrument are forwarded to the 3D simulation and navigation software Slicer3D.

SystemStructure.png

Documentation of the System

  • Download a presentation of the system here
  • Download my thesis here

Technical Information

All technical Information can be found here: Technical Information

Progress

You can see the progress of my project here

Screenshots

4DUltrasound-Screenshot-1.png

4DUltrasound-Screenshot-2.png

4DUltrasound-Screenshot-3.png

4DUltrasound-Screenshot-4.png

4DUltrasound-Screenshot-5.png

4DUltrasound-Screenshot-6.png

4DUltrasound-Screenshot-7.png

4DUltrasound-Screenshot-8.png

Images

4DUltrasound-Image-1.JPG

4DUltrasound-Image-2.JPG

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