Difference between revisions of "User:Gumprecht"

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= Wikipage of Jan Gumprecht =
 
= Wikipage of Jan Gumprecht =
  
== About myself ==
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== About Myself ==
  
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
  
== 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==
* Totally understand GradientDiffusionFilterModule
 
 
 
== Project - 3D-Ultrasound integration in Slicer ==
 
 
 
The main part of the project will be the integration of the source code of [http://www.midasjournal.org/browse/publication/289 SynchroGrab] in Slicer by using CUDA support.
 
 
 
[[Image:SystemAufbau.png | 400px]]
 
 
 
<br> <br>
 
 
 
After discussing with Junichi I got a deeper understanding of how the technical solution might look like.
 
 
 
This will be the technical approach.
 
 
 
[[Image:ProjectWorkflow.png]]
 
 
 
=== 3D CUDA ===
 
==== TO DO ====
 
* Understand the CUDA source code of Nicholas and Ben
 
 
 
==== Contacts ====
 
* Ben Grauer: [http://www.slicer.org/slicerWiki/index.php/Slicer3:Volume_Rendering_With_Cuda Volume Rendering with CUDA]
 
* Nicholas Harlambang: CUDA Guru
 
 
 
=== Ultrasound tracking device ===
 
 
 
Hopefully most of this part is already done by [http://www.midasjournal.org/browse/publication/289 SynchroGrab]
 
 
 
==== TO DO ====
 
* Find out what is already coverd by Synchrograb
 
* Compile Synchrograb and see if everthing is working
 
 
 
==== Capture Video ====
 
* Existing Videocard: Hauppauge ImpactVCB [http://www.haupauge.com/site/products/data_impactvcb.html]
 
* Linux Driver: Video4Linux2
 
**There is existing C source for V4L2 on the web
 
**Should run on new fedora kernel
 
 
 
===== Contacts =====
 
* Christoph Ruetz
 
 
 
==== Tracker ====
 
Track data via vtk not itk <br>
 
=====Contacts=====
 
* Haiying Liu
 
  
==== Calibration ====
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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.
Description: To get correct information from the ultrasound device is has to be calibrated<br>
 
===== Contacts =====
 
* Raul San Jose
 
Information:
 
* I have serval links and information from Raul on which I have to go through
 
  
=== Infos on loadable Modules ===
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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].
  
[http://www.slicer.org/slicerWiki/index.php/Slicer3:Loadable_Modules:HOWTO HowTo Loadable Module] <br>
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[[Image:SystemStructure.png | 800px ]]
[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>
 
  
== Other Stuff to do ==
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=== Documentation of the System ===
=== Find a new cart for the ultrasound unit ===
 
* Infos in the intraweb
 
* Talk to Vai about this
 
  
=== Subscribe to different meetings ===
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* Download a presentation of the system [[Media:Gumprecht_Jan-4DUltrasound.pdf | here]]
* Journal Club
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* Download my thesis [[Media:Gumprecht_Jan-2009-Diploma_Thesis.pdf‎ |here]]
* 1st Monday Seminar
 
* Office OPRC
 
* Radiology Great Rounds
 
* Zimit Forum
 
  
== Time Schedule ==
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=== Technical Information ===
  
{| border="1"
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All technical Information can be found here: [[Technical Information]]
|- bgcolor="#abcdef"
 
! Month !! Week !! Done !! Date
 
|-
 
! September !! 39 = 22.09 - 28.09 !! !!
 
|-
 
|  || Totally Understand GradientDiffusion Filter Module || x || Thu Sep, 25th
 
|-
 
! October !! 40 = 29.09 - 5.10 !! !!
 
|}
 
  
== How to "Enable CUDA 2.0 in Fedora 8 for use with Slicer 3.3 Alpha" ==
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=== Progress ===
Date: Sept. 26th 2008
 
  
Fedora 8 is the newest Fedora version for which CUDA is available. The available CUDA Version is 2.0. <br>
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You can see the progress of my project [[4D Ultrasound Progress | here]]
To enable CUDA 2.0 in Fedora 8 for Slicer 3.3 Alpha follow the steps below:
 
  
=== Installation of Drivers ===
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=== Screenshots ===
  
* Download the CUDA installation files (Driver, Toolkit, SDK) here [http://www.nvidia.com/object/cuda_get.html] and remember the directory in which you downloaded them. I used
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[[Image:4DUltrasound-Screenshot-1.png | 600px]]
for the driver installation binary
 
  ~/Download/CUDA/Driver/
 
for the tool kit installation binary
 
  ~/Download/CUDA/Toolkit/
 
and for the SDK installation binary
 
  ~/Download/CUDA/SDK/
 
* For the installation there must not run a X-Server. Therefore we have to restart the computer. When you see the GRUB Bootscreen after the reboot press any key to enter the GRUB menu. Highlight the Fedora Version you want to boot and press
 
  a
 
Then type
 
  Type 3
 
and hit the 'Enter' key. Fedora will boot up without X Server and drop you at Command Line Login prompt.
 
* Login and change into root mode via:
 
  su
 
* Then switch to the directory where you downloaded the driver. For me this means:
 
  cd ~/Download/CUDA/Driver/
 
* Now we have to change the permissions for the driver-binary and make it executable. This works with
 
  chmod +a BINARY-NAME
 
(Replace 'BINARY-NAME' with the name of the driver binary)
 
* Now start the installation with:
 
  ./BINARU-NAME
 
I changed none of the default values during the installation
 
  
* For the sdk compilation follow this reference guide: [http://developer.download.nvidia.com/compute/cuda/2.0-Beta2/docs/SDK_Rel_Notes_Linux_2.0beta2.txt]<br> If you get the error message: "ld: cannot find -lglut", like I did, have a look at the reference under 'IV. Known Issues'
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[[Image:4DUltrasound-Screenshot-2.png | 600px]]
  
* In the next step we do the same for the toolkit and for the sdk, e.g chance to the according directory, change the permissions and run the installation with the default values
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[[Image:4DUltrasound-Screenshot-3.png | 600px]]
  
=== Enable CUDA in Slicer 3.3 Alpha ===
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[[Image:4DUltrasound-Screenshot-4.png | 600px]]
  
* Start with the installation manual of Ben Grauer. You find it here [http://www.slicer.org/slicerWiki/images/a/ae/Cuda2slicer3.pdf]<br> Below you find corrections to certains points that did not work for me the way it was explained in the manual
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[[Image:4DUltrasound-Screenshot-5.png | 600px]]
  
* In 1.1.2 Check out the following slicer branch instead and build it:
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[[Image:4DUltrasound-Screenshot-6.png | 600px]]
  
  svn co http://svn.slicer.org/Slicer3/trunk Slicer3
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[[Image:4DUltrasound-Screenshot-7.png | 600px]]
  ./Slicer3/Scripts/getbuildtest.tcl
 
  
* Before you can go on with step 1.2.2 you have to Uncomment:  
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[[Image:4DUltrasound-Screenshot-8.png | 600px]]
**''CudaSupport'' in Slicer3/Libs/CMakeLists.txt
 
**''VolumeRenderingCuda'' in Slicer3/Modules/CMakeLists.txt
 
  
* In step 1.2.2
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=== Images ===
**you have to use your build directory (Slicer-build) as parameter for ccmake
 
**for CUDA_INSTALL_PREFIX use /usr/local/cuda
 
**for FOUND_CUT use $HOME/NVIDIA_CUDA_SDK/common/lib/linux/libcudpp.a
 
**for FOUND_CUT_INCLUDE use $HOME/NVIDIA_CUDA_SDK/common/inc
 
  
* Step 1.2.3 was not necessary for me
 
  
* Just do a rebuild (run Slicer3/Scripts/getbuildtest.tcl) and the VolumeRenderingCUDA module is available
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[[Image:4DUltrasound-Image-1.JPG | 600px]]
  
This installation worked for me on a DELL machine with XEON Dual Core and a Nvidia G8800
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[[Image:4DUltrasound-Image-2.JPG | 600px]]

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