User:Gumprecht

Wikipage of Jan Gumprecht

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.

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

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

What I am working on at the moment

• Make 3D Volume Reconstruction of SynchroGrab work

Project - 3D-Ultrasound integration in Slicer

The main part of the project will be the integration of the source code of SynchroGrab in Slicer by using CUDA support.

After discussing with Junichi I got a deeper understanding of how the technical solution might look like.

This will be the technical approach.

Steps to do

Create 3D volume with Synchrograb
	Create volume with data from the ultrasound device and the tracker
	Create volume with mockup images and tracking information from the tracker
DONE	Create volume with mockup images and mockup tracking information
Synchrograb
DONE	Send 3D volume data via OpenIGTLink to Slicer and display data in Slicer
DONE	Compile Synchrograb core i.d. uncomment unnecessary parts (Ultrasound, Tracker)
Preparation
DONE	Display 3D volume data received via OpenIGTLink with the volume rendering module
DONE	Create stand alone software to send volume data to Slicer via OpenIGTLink
DONE	Compile and run Slicer with OpenIGTLink and volume rendering

3D CUDA

TO DO

• Understand the CUDA source code of Nicholas and Ben

Contacts

• Ben Grauer: Volume Rendering with CUDA
• Nicholas Harlambang: CUDA Guru

Documentation: VolumeRenderingCuda Module

• Adjust the threshold (scroll bar below 'Component Weights Scrollbars') to correct values. Especially the lower value. Normally > 0
• Scalar Opacity Mapping: Shows a histogram of the used values an their transparence. Low transparent, high solid
• Scalar Color Mapping: You can click into and than in the color circle above and select certain colors for a specific value
• Composite: Here you can select different rendering modes
• Volume: You can also select just to display a slice instead of the whole volume. You can transform the slice in the Transforms Module and than select the transformation matrix in Slice Matrix
• Plus/Minus: Select if you want to see everything or just the volume on one side of the slice and on the other

Ultrasound tracking device

Hopefully most of this part is already done by SynchroGrab

SynchroGrab

In summary SynchroGrab does:

• Continuous acquisition of ultrasound images using an open-interface ultrasound system;
• Continuous acquisition of tracking information using a pose measurement system;
• Explicit synchronization of the two acquisition threads;
• Reconstruction of 3D ultrasound volumes using the synchronized data; and
• Transfer of the raw ultrasound images, the 3D volumes and the probe tracking information to an OpenIGTLink-compliant system.

TO DO

• Find out what is already coverd by Synchrograb
  • Adjust the tracker part, so that our tracker is working
  • Replace image acquistion part. We have to use a frame grabber card instead of reading the images directly from memory
• Compile Synchrograb and see if everthing is working

Capture Video

• Existing Videocard: Hauppauge ImpactVCB [1]
• Linux Driver: Video4Linux2
  • There is existing C source for V4L2 on the web
  • Should run on new fedora kernel

Contacts

• Christoph Ruetz
  • Project Page

Tracker

Track data via vtk not itk

Contacts

• Haiying Liu

Calibration

Description: To get correct information from the ultrasound device it has to be calibrated

Contacts

• Raul San Jose

Information:

• I have serval links and information from Raul on which I have to go through

Infos on loadable Modules

HowTo Loadable Module
HowToLoadable Module GUI
Infos about Executable Modules inSlicer

Other Stuff to do

Find a new cart for the ultrasound unit

• Infos in the intraweb
• Figure out what hardware and how much space on the cart I need
  • CUDA Card
  • Capture Card
  • Ultrasound device
  • Tracker device
  • Uninterruptible power supply

Subscribe to different meetings

• Journal Club
• 1st Monday Seminar
• Office OPRC
• Radiology Grand Rounds
• Cimit Forum

Time Schedule

Month	Week # : Start Date - End Date	Done	Date Done
September	Week 39: 22.09 - 28.09
	Totally Understand GradientDiffusion Filter Module	x	Thu Sep, 25th
	Set up Fedora 8 on th303_d4_6	x	Fri Sep, 26th
October	Week 40: 29.09 - 5.10
	Set up CUDA driver on th303_d4_6	x	Tue Sep, 30th
	Get CUDA Rendering Volume working in Slicer	x	Wed Oct, 2nd
	Week 41: 06.10 - 12.10
	Understand and Use OpenIGTLink	x	Tue Oct, 7th
	Week 42: 13.10 - 19.10
	Compile SynchroGrab (using latest OpenIGTLink Library)	x	Tue Oct, 14th
	Send Volume Data via OpenIGTLink from SynchroGrab to Slicer	x	Tue Oct, 14th
	Week 43: 20.10 - 26.10
	Starting work on "Creating a 3D-Volume with Synchrograb"
November	Week 44: 27.10 - 02.11
	Week 45: 03.11 - 09.11
	Video 4 Linux Video Source works	x	Tue Nov, 4th
	Week 46: 10.11 - 15.11
	Tracker Simulator works	x	Thu Nov, 13th

How to "Enable CUDA 2.0 in Fedora 8 for use with Slicer 3.3 Alpha"

Date: Sept. 26th 2008

Fedora 8 is the newest Fedora version for which CUDA is available. The available CUDA Version is 2.0.
To enable CUDA 2.0 in Fedora 8 for Slicer 3.3 Alpha follow the steps below:

Installation of Drivers

• Download the CUDA installation files (Driver, Toolkit, SDK) here [2] and remember the directory in which you downloaded them. I used

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: [3]
  If you get the error message: "ld: cannot find -lglut", like I did, have a look at the reference under 'IV. Known Issues'

• 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

Enable CUDA in Slicer 3.3 Alpha

• Start with the installation manual of Ben Grauer. You find it here [4]
  Below you find corrections to certains points that did not work for me the way it was explained in the manual

• In 1.1.2 Check out the following slicer branch instead and build it:

 svn co http://svn.slicer.org/Slicer3/trunk Slicer3
 ./Slicer3/Scripts/getbuildtest.tcl

• Before you can go on with step 1.2.2 you have to Uncomment:
  • CudaSupport in Slicer3/Libs/CMakeLists.txt
  • VolumeRenderingCuda in Slicer3/Modules/CMakeLists.txt

• In step 1.2.2
  • 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

This installation worked for me on a DELL machine with XEON Dual Core and a Nvidia G8800. For fast rendering make sure not enable compiz(Desktop Effects).