Technical Information

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Technical information about the Connection of Synchrograb to Slicer

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SynchroGrab 2.0

SynchroGrab 2.0 generates 3D ultrasound volumes and sends them to an OpenIGTLink server. In order to generate the 3D volume it records ultrasound images and position and orientation information. The images can either be provided by an ultrasound device or by the ultrasound simulator of SynchroGrab 2.0. The tracking matrices are either generated by an NDI tracking device (e.g. Aurora) or by the included tracker simulator. The devices and simulators can be used in any kind of combination.

History

The original SynchroGrab was developed at Queen's University Kingston, Canada. It generates 3D ultrasound volumes. In order to create the 3D image it collects image data from an ultra sound device and combines them with the position data of a tracking device. With the combination of images and positions Synchrograb generates a 3D volume. At the end this 3D image is send to Slicer via OpenIGTLink.

In summary the original 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
  • Transfer of the raw ultrasound images, the 3D volumes and the probe tracking information to an OpenIGTLink-compliant system

Build Instructions

It is highly recommended to have a compiled version of Slicer and to have good knowledge about cmake.

  1. Check out SynchroGrab from http://svn.na-mic.org/NAMICSandBox/trunk/SynchroGrabJGumprecht

  2. Configure via ccmake (version > 2.6) in your build directory

    You need a compiled version of VTK

    There are options to use either the device or the simulator of either the ultrasound or the tracker

  3. Compile Synchrograb: Type $ make in your build directory

Running Synchrograb

You need a working version of Slicer with OpenIGTLink

  1. Copy "CalibrationFile.txt" from YOUR_SOURCE_DIR to YOUR_BUILD_DIR/bin
  2. Run Slicer
  3. Add an "activer Server Connector" in the OpenIGTLink module which is waiting for data at port 18944
  4. Run Synchrograb on the same machine you run Slicer
 $YOUR_BUILD_DIR/bin/SynchroGrab -c CalibrationFile.txt --reconstruct-volume

TO DO

Priority MUST
Update vtkTrackerSimulator
DONE Complete vtkVideoSourceSimulator
DONE Use CaptureCard to acquire images
Priority SHOULD
Use splitted up vtkSynchroGrabPipeline
Clean up start parameters (Add new ones etc.)
Priority COULD


  • Replace image acquistion part. We have to use a frame grabber card instead of reading the images directly from memory
  • Crate and use a tracking device simulator
  • Create and use a ultrasound simulator
  • Find out what is already coverd by Synchrograb
  • Compile Synchrograb and see if everthing is working

Check the following

  • greyscale YUV
  • RGB grab
  • xawtv
  • change memory copy
  • implement my own deinterlacing

Contacts

  • Jonathan Boisver
    • Post Doc from Canada who implemented most of Synchrograb
    • E-Mail: boisvert ( a t ) cs.queensu.ca

Ultrasound device

The ultrasound images are received via a video capture card. Linux uses V4L2 to support the card.

Capture Card - Hauppauge WIN-TV PCI Board ImpactVCB Model 558

Linux (Ubuntu 8.10 , Fedora 5)
  • The card is automatically correct detected. No further configuration needed.
  • Linux Driver: Video4Linux2 bt878
    • "bt" stands for Brooktree the original Manufacturer. Now bought by Conexant
  • The Linux driver (bttv) for the WinTV card is now part of the Linux kernel (version 2.6.xxx and newer).
  • Hauppage Linux Information
  • Linux installation hints [1]
  • Modprobe option # for specific drivers: http://tldp.org/HOWTO/BTTV/cards.html
    • The Impact VCB has # 10
    • enable kernel module via: "$ modprobe bttv card=10" or add to /etc/modprobe.conf the following line "options bttv card=10 "
    • to switch to another card first remove the module via: "$ modprobe -r bttv"
  • The card uses NTSC video interlacing per default
Hardware Information
  • Channel 3 delivers the s-video signal
    • To set the channel add the following at the end of void vtkV4L2VideoSource::InitDevice(void):

 int channel = 3;
 if (-1 == xioctl (fd,VIDIOC_S_INPUT , &channel))
   errno_exit ("VIDIOC_S_INPUT");

  • Specific Hardware information: [2] !!be carefull huge page, takes a long time to load!!

Video4Linux2

Video4Linux is part of the Linux kernel since version 2.6.xx

  • V4L2 wiki [3]
  • API Specificattion: [4]
  • xawtv software for video preview from the guy who wrote the bt8xx driver
Old links may soon be dead

Contacts

Tracking device

Synchrograb includes an NDI tracker class which works out of the box with the Aurora NDI tracker

Contacts
  • Haiying Liu

Calibration

Description: To get the 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

Slicer

I am using the trunk version of Slicer (3.3) since this has the OpenIGTLink module and the CUDA module.

Python Synchrograb Module

I implemented a Pyhton module for Slicer to start Synchrograb. The module can be found in this svn repository. Basically it starts a new shell and calls the Synchrograb binary within this shell. All Synchrograb commandline options are available in the module. So fare it is not part of the Slicer repository.

3D CUDA

I might not use Cuda acceleration since there is no real performance advantage at this point

TO DO

  • Nothing

Contacts

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

Links

  • Sandbox page [7]

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 [8] 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: [9]
    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 [10]
    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).

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