Difference between revisions of "User:Gumprecht"

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[[Image:Gumprecht Jan.jpg |thumb|Jan Gumprecht]]
 
[[Image:Gumprecht Jan.jpg |thumb|Jan Gumprecht]]
  
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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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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]]
  
 
== Contact Information ==
 
== Contact Information ==
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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==
 
== 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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In my project I am developing a Software for "Integrated Real-Time 3D Ultrasound Navigation" with the name ''4DUltrasound''. The program creates a 3D volume of recorded ultrasound frames in teal-time. The output of ''4DUltrasound'' is forwarded via [http://www.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] to [http://www.slicer.org Slicer3D].
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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.
  
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The main part of the project will be the connection of [http://www.midasjournal.org/browse/publication/289 SynchroGrab] to Slicer3D via OpenIGTLink.
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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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Synchrograb is an Open-Source software that generates 3D ultrasound volumes.
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[[Image:SystemStructure.png | 800px ]]
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=== Documentation of the System ===
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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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After discussing with Junichi I got a deeper understanding of how the technical solution might look like.
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You can see the progress of my project [[4D Ultrasound Progress | here]]
  
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This will be the technical approach.
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=== Screenshots ===
  
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[[Image:ProjectWorkflow.png]]
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[[Image:4DUltrasound-Screenshot-1.png | 600px]]
  
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== Steps to go ==
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[[Image:4DUltrasound-Screenshot-2.png | 600px]]
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{|border="0", cellpadding="5"
 
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|- bgcolor="silver"
 
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! colspan="2" | Slicer
 
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|-
 
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| align="center" bgcolor="#009900" | DONE || Implement slicer module to start Synchrograb from within Slicer
 
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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 ultrasound calibration matrix
 
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|-
 
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| align="center" width="70px", bgcolor="#009900" | DONE || width="600px"|Create 3D volume with data from the ultrasound device and the tracker
 
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|-
 
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| align="center" bgcolor="#009900" | DONE || Include options for turning on and off US/Tracker device in cmake
 
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|-
 
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| align="center" bgcolor="#009900" | DONE || Create 3D volume with mockup images and tracking information from the tracker
 
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|-
 
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| bgcolor="#009900" align="center" | DONE || Create 3D 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 - i.e. what I have done so far==
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[[Image:4DUltrasound-Screenshot-3.png | 600px]]
  
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[[Image:4DUltrasound-Screenshot-4.png | 600px]]
  
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{| border="0" cellpadding="3" cellspacing=0
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[[Image:4DUltrasound-Screenshot-5.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=5|
 
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|- bgcolor="#D0D0D0"
 
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!| February !! Week 05 !! 27.01 - 01.02 || ||
 
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|-
 
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|height="10px" |
 
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|-
 
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| || colspan="2" | Slices and tracker matrices are sended to Slicer in real-time  ||align="center" | x || Fri Jan, 16th
 
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|- bgcolor="#E8E8E8"
 
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!bgcolor="#FFFFFF"| !! Week 04 !! 19.01 - 26.01 || ||
 
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|-
 
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|height="10px" |
 
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|-
 
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| || colspan="2" | Literature research complete  ||align="center" | x || Thu Jan, 22th
 
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|- bgcolor="#E8E8E8"
 
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!bgcolor="#FFFFFF"| !! Week 03 !! 12.01 - 18.01 || ||
 
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|-
 
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|height="10px" |
 
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|-
 
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| || colspan="2" | -  ||align="center" |  ||
 
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|- bgcolor="#E8E8E8"
 
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!bgcolor="#FFFFFF"| !! Week 02 !! 05.01 - 11.01 || ||
 
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|-
 
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|height="10px" |
 
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|-
 
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| || colspan="2" | -  ||align="center" |  ||
 
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|- bgcolor="#D0D0D0"
 
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!| January !! Week 01 !! 29.12 - 04.01 || ||
 
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|-
 
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|height="20px" |
 
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|-
 
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| || colspan="2" | -  ||align="center" |  ||
 
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|- bgcolor="#E8E8E8"
 
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!bgcolor="#FFFFFF"| !! Week 52 !! 22.12 - 28.12 || ||
 
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|-
 
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|height="10px" |
 
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|-
 
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| || colspan="2" | Trilinear Interpolation works  ||align="center" | x || Wed Dec, 17th
 
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|-
 
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| || colspan="2" | Reconstructed Volume has correct depth  ||align="center" | x || Tue Dec, 16th
 
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|- bgcolor="#E8E8E8"
 
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!bgcolor="#FFFFFF"| !! Week 51 !! 15.12 - 21.12 || ||
 
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|-
 
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|height="10px" |
 
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|-
 
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| || colspan="2" | Created Slicer Module to start Synchrograb within Slicer  ||align="center" | x || Wed Dec, 10th
 
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|-
 
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| || colspan="2" | Ultrasound device module works  ||align="center" | x || Tue Dec, 9th
 
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|- bgcolor="#E8E8E8"
 
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!bgcolor="#FFFFFF"| !! Week 50 !! 08.12 - 14.12 || ||
 
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|-
 
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|height="10px" |
 
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|-
 
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| || colspan="2" | Fixed vtk3DPanoramicReconstructor together with Noby  ||align="center" | x || Fri Dec, 5th
 
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|-
 
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| || colspan="2" | NDI Tracker module works  ||align="center" | x || Wed Dec, 3rd
 
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|- bgcolor="#D0D0D0"
 
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!| December !! Week 49 !! 01.12 - 07.12 || ||
 
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|-
 
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| height="20px"|
 
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|-
 
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| || colspan="2" | - ||align="center" |  ||
 
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|- bgcolor="#E8E8E8"
 
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!bgcolor="#FFFFFF"| !! Week 48 !! 24.11 - 30.11 || ||
 
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|-
 
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|height="10px" |
 
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|-
 
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| || colspan="2" | vtkVideoSource works  ||align="center" | x || Mon Nov, 24th
 
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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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|height="10px" |
 
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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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|- bgcolor="#E8E8E8"
 
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!bgcolor="#FFFFFF"| !! Week 46 !! 10.11 - 16.11 || ||
 
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|-
 
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| height="10px"|
 
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|-
 
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| || colspan="2" | Tracker Simulator works ||align="center" | x || Thu Nov, 13th
 
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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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|height="10px" |
 
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|-
 
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| || colspan="2" | Ultrasound Simulator works ||align="center" | x || Tue Nov, 4th
 
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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="20px"|
 
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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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|- bgcolor="#E8E8E8"
 
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! bgcolor="#FFFFFF"| !!  Week 43 || 20.10 - 26.10 || ||
 
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|-
 
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| height="10px"|
 
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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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| || colspan="2" |Compile SynchroGrab (using latest OpenIGTLink Library) ||align="center" | x || Tue Oct, 14th
 
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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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| height="10px"|
 
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|-
 
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| || colspan="2" | Understand and Use OpenIGTLink || align="center" | x || Tue Oct, 7th
 
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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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|height=10|
 
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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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| || colspan="2" |Set up CUDA driver on th303_d4_6 || align="center" | x || Tue Sep, 30th
 
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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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| height="20px"|
 
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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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|  || colspan="2" | Totally Understand GradientDiffusion Filter Module || align="center" | x || Thu Sep, 25th
 
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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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|}
 
  
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== Other Stuff to do ==
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[[Image:4DUltrasound-Screenshot-6.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-7.png | 600px]]
  
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== General ==
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[[Image:4DUltrasound-Screenshot-8.png | 600px]]
  
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=== Links ===
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=== Images ===
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* [https://intweb/Sponsored_Staff_and_Volunteers  SPL Intraweb web for incoming staff]
 
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* [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:DocumentationWink Wink - Software for Video Documentation]
 
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* [http://bwhbri.partners.org/Editorial_Service/ BWH Editorial Service]
 
  
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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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