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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 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 in Waterloo, On, Canada from September 2006 to August 2007 . | + | 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 == | | == 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]. | + | 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. | + | 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]. |
− | 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]] |
| + | * Download my thesis [[Media:Gumprecht_Jan-2009-Diploma_Thesis.pdf |here]] |
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| === 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>
| + | === 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.
| + | You can see the progress of my project [[4D Ultrasound Progress | here]] |
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− | This will be the technical approach.
| + | === Screenshots === |
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− | [[Image:ProjectWorkflow.png]] | + | [[Image:4DUltrasound-Screenshot-1.png | 600px]] |
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− | == Steps to go ==
| + | [[Image:4DUltrasound-Screenshot-2.png | 600px]] |
− | {|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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− | | 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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− | | 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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− | | 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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− | | 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==
| + | [[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
| + | [[Image:4DUltrasound-Screenshot-5.png | 600px]] |
− | |- 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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− | |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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− | | || 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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− | |height="10px" |
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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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− | |height="10px" |
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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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− | |height="10px" |
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− | | || colspan="2" | Trilinear Interpolation works ||align="center" | x || Wed Dec, 17th
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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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− | |height="10px" |
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− | | || colspan="2" | Created Slicer Module to start Synchrograb within Slicer ||align="center" | x || Wed Dec, 10th
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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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− | |height="10px" |
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− | | || colspan="2" | Fixed vtk3DPanoramicReconstructor together with Noby ||align="center" | x || Fri Dec, 5th
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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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− | |height="10px" |
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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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− | |height="10px" |
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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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− | | height="10px"|
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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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− | |height="10px" |
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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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− | | height="20px"|
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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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− | | height="10px"|
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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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− | | height="10px"|
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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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− | |height=10|
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− | | || colspan="2" |Get CUDA Rendering Volume working in Slicer || align="center" |x || Wed Oct, 2nd
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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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− | | height="20px"|
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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 ==
| + | [[Image:4DUltrasound-Screenshot-6.png | 600px]] |
− | === 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 ==
| + | [[Image:4DUltrasound-Screenshot-8.png | 600px]] |
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− | === Links === | + | === Images === |
− | * [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> | + | [[Image:4DUltrasound-Image-1.JPG | 600px]] |
− | [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:How_to_implement_an_Interactive_Module_GUI HowToLoadable Module GUI]<br> | |
− | [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 ===
| + | [[Image:4DUltrasound-Image-2.JPG | 600px]] |
− | * 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
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