DTI Task Card

Version 1.62 build 2003.05.28 for VA15/VA21

Updated: June 04, 2003 03:16:42 PM (EDT)    Download upgrade

This document describes how to use the task card for Diffusion Tensor Imaging (DTI Task Card) on a SIEMENS NUMARIS 4 satellite console. This task card allows visualization of diffusion tensor imaging data and white matter fiber tracking. A general knowledge of MRease usage is assumed.

Contents

Installation
Detailed Instructions

Loading Image Data
General Tensor Viewing
Tractography
Miscellanies

Known Issues

References

Acknowledgment

Further Information

Installation

Before installation please check if the following software/hardware requirements are met:

• Make sure the PC that is about to be installed on is a Satellite Console (DO NOT INSTALL THIS SOFTWARE ON MAIN CONSOLE), and the MRease and Syngo versions match one of the following versions:

  N4_VA21B_LATEST_XXXXXX
  syngo VB10I
  
  N4_VA15A_LATEST_XXXXXX
  syngo VA47V
  syngo VA49A

  To find out the version select Help -> Info and General tab.

• Due to extensive computation and memory usage of this software, a fast PC (e.g., Dual Intel P3 or P4 with 1~2Gb RAM) is preferred. Also, a mid/high end 3D graphics card by ATI or nVidia is STRONGLY recommended for better performance. Matrox G400/G450/G550 which was the default graphics card for old Syngo system is NOT recommended!

  Be sure to set the color depth of the Windows display to 32-bit or True color for best performance.

  If you insist to use Matrox G400/G450/G550 graphics cards (be ready to expect poor performance), be sure to download the latest drivers from Matrox website and set the Windows display to 24-bit or 16777216 colors because they do not work properly at 32-bit (true color) mode.

Also, please read the license and be aware of the following issues before installing the DTI Task Card software:

• Do not install this software on a scanner console.
• Do not install this software on a satellite console without approval by SIEMENS.
• Installation of this software may void any warranty.
• There is no SIEMENS support or warranty or liability for this software.
• There is no other support or warranty or liability for this software.

To install/upgrade/uninstall the DTI Task Card, run the setup file "DTI_TaskCard_VAXX.exe" that matches your system version and follow appropriate steps. DO NOT install unmatched version on your system.

NOTE: If, for any reason, the Syngo system could not start after the installation but you need it up urgently, you may run the installer again and choose remove. That should remove the DTI Task Card and restore your Syngo system.

Detailed Instructions

Loading Image Data

General Tensor Viewing

Viewing Mode Buttons

Select between Tensor or Tractography viewing mode.

	Tensor viewing mode.
	Tractography viewing mode.

Tool Buttons for Tensor Viewing

View

1:1. Set the current viewpage the same size of the viewport. 4:1. Split viewport to 2x2 viewpages. 9:1. Similar to above. 16:1. Similar to above. Zoom In. Zoom in the current selected image by a factor of 2. Zoom Out. Zoom out the current selected image by a factor of 2. Zoom... Zoom the current selected image by an arbitrary factor chosen by user. Restore. Restore the current image's size and position. Restore All. Restore all the images' size and position.

Image

Boxoid, Ellipsoids, Plain Color or Plain Grayscale. Set the rendering object to Boxoid or Ellipsoid for the visualization of diffusion tensor, or just plain color or grayscale map. The small dark arrow on the right bottom of the button indicates that a drop-down menu will be shown if clicked, allowing to select the object. Color Sphere. Show the color sphere indicating the direction-color coding for visualization. Unnormalized Scaling . Set unnormalized scaling for rendering of the diffusion tensor object. That is, use the three eigenvalues as the scaling factors for Boxoid or Ellipsoid object. This button is only enabled when Boxoid or Ellipsoid is chosen. Parallel Viewing. Set the projection mode to Parallel or Prospective. Interpolate. Turn on/off the interpolation for Plain Color or Plain Grayscale map. Noise Threshold. Manually set the noise threshold for rendering. Noise threshold is used to determine background in Low b image. Autoset Noise Threshold. Automatically set the noise threshold as the mean value plus 6 times standard deviation of low b background.

Map

FA. Set Fractional Anisotropy as the weighting factor for current visualization/maps. E2-E3. Set E2 minus E3 as the weighting factor for current visualization/maps. E1, E2 and E3 represent the three eigen-values of the diffusion tensor at each voxel. E1. Show E1 maps. Only generic grayscale map is valid at this mode. E2. Show E2 maps. Only generic grayscale map is valid at this mode. E3. Show E3 maps. Only generic grayscale map is valid at this mode. b0. Show b0 maps. Only generic grayscale map is valid at this mode. ADC. Show ADC maps. Only generic grayscale map is valid at this mode.

Plane

Sagittal. View Sagittal slices. Coronal. View Coronal slices. Axial. View Axial slices.

Patient

Load Pixel Data From File. Load pixel data from an existing .bshort file. Note: This function is very preliminary and not yet recommended to use. Close Patient. Close the current patient. Write New Series. Write new series into database. There will be a pop-up dialog allowing to selection what maps (FA, E2-E3, etc.) to write. The new images can be loaded into the Viewing Task Card. This button is only valid when data is loaded from database (not from files).

Mouse

At this cursor, hold left button and drag to move the image. At this cursor, hold left button and drag to zoom the image. Hold right button and drag to rotate the image. Hold middle button and drag to change windowing level of the image. (Note: Color and grayscale windowing are independent).

Right-click to bring up popup menu for more commands.

Tractography

Fiber Tracking Steps

1. Switch to Tractography viewing mode. Zoom/Pan/Rotate the image to appropriate position for better viewing. (Similar to Tensor viewing mode). Use the IS/RL/AP sliders on the upper right corner of the panel to select different slices. 2. Hold Ctrl Key + Left Mouse Button to select Seed Region (or Region Of Interest). 3. Release left mouse button and the program will do fiber tracking starting from the selected seed region. (NOTE: If Ctrl key is released before left mouse button, the selected region will be canceled and fiber tracking will not be performed.)

Tips: Shift Key + Left Mouse Button to "test-track" in the real time. Left Control Key + 1/2/3 to save the current viewing position. Click camera buttons at top-right corner of the image at any time to set the viewing position to the pre-saved ones. Right Control Key + 1/2/3 to remove the pre-saved viewing positions. Click right mouse button to bring up popup menu for the COMPLETE set of commands, such as: Enable/disable fast interactive viewing. Hide/Show/Delete/Save/Combine/Split fibers. When you have multiple groups of fibers and want to save them together, combining them together first will make saving a lot easier. Changing fiber name and tracking and rendering parameters. Save image to file or database. There are 5 different image formats supported: Jpeg, TIFF, Bitmap, PNG and PostScript. Hide/Show annotations and axes. Some of the commands are not available from the menu bar or the tool buttons.   Parameter setting: Tracking parameters Angle Threshold. If the turning angle is larger than this value, fiber tracking will stop. FA Threshold. If the FA is smaller than this value, fiber tracking will stop. Step Length. The step length for the streamline marching algorithm. Recommended setting: about 1/4 of the voxel size. Too small will cause much longer tracking time with little improvement on quality and accuracy. Number Of Samples Per Voxel Length. The sample rate for the seed region. Recommended value: 2 or 3. WARNING: Setting this value larger will tremendously increase the work load of the fiber tracking and rendering and may cause unexpected error (due to VTK's limitation) if a large seed region is selected. Smoothing and Interplation setting. Apply gaussian smoothing and interplation on raw data or tensor data. Rendering parameters Tube Radius. The radius of the fiber tracks visualized as the many tubes. Segment Length. The segment length to sample the fiber track spline for rendering. Recommended value: about 1/3 to 1/2 of the voxel size. Smaller value will cause dramatically larger load of rendering with no quality improvement visually, and may cause error if a large seed region is selected. Color Coding. Color codings for the fiber, include direction-coded color, solid color and FA-coded color. NOTE: From version 1.62, the direction-coded colors for fiber rendering use a new scheme for color mapping. It may not look as vivid as the old one but it represents the directions more accurately.

Tool Buttons for Tractography

View

FA Color. View FA color map. FA. View FA grayscale map. Low b. View Low b map. Sagittal. Show Sagittal slice. Coronal. Show Coronal slice. Axial. Show Axial slice. Restore. Restore viewing position.

ROI

Select Seed. Set current selection mode as selecting seed region. Fiber tracking will be performed right after selection. Select Target. Set current selection mode as selecting target region. Load Seed. Load seed region from a pre-saved ROI file. Fiber tracking will be performed. Load Target. Load target region from a pre-saved ROI file. Save Target. Save the current target region to an ROI file.

Sample Images

Fiber tracking visualization in the DTI Task Card. Fiber tracking images saved to the database by DTI Task Card and loaded in the Viewing task card afterwards.

Miscellanies

Known Issues

This software is not an official release and it is not as tightly integrated into MRease as an official SIEMENS task card. Due to this reason, the following known issues may or may not be solved in the near future.

• Current version of DTI Task Card can only deal with standard axial images with 6 diffusion directions and only works with single b-value series.
• The software can work with GE data collected in Massachusetts General Hospital but is not guaranteed to work with all kinds of GE data.
• Computation and pre-rendering are extremely CPU intensive and memory-consuming and might be a bit slow, especially in Ellipsoid rendering mode.
• Due to the limitation of the VTK engine, the tractography tool can not handle too huge amount of fibers together at the same rendering. Reducing the "Number of Samples Per Voxel Length" parameter and increasing the "Interpolation Length" parameter in Tracking Options... may help reduce the load of rendering and increase the limitation of the number of fibers that can be rendered together.

References

The algorithms used for fiber tracking are based on the following literature:

1. Mori S, Crain BJ, Chacko VP, van Zijl PC.
   Three-dimensional tracking of axonal projections in the brain by magnetic resonance imaging.
   Ann Neurol 1999; 45: 265-269.(PubMed abstract)
2. Basser PJ, Pajevic S, Pierpaoli C, Duda J, Aldroubi A.
   In vivo fiber tractography using DT-MRI data.
   Magn Reson Med 2000;44:625-632.(PubMed abstract)
3. B. Stieltjes, W.E. Kaufmann, P.C. van Zijl, K. Fredericksen, G.D. Pearlson, M. Solaiyappan and S.Mori.
   Diffusion tensor imaging and axonal tracking in the human brainstem.
   Neuroimage 14 (2001), pp.723-735.(PubMed abstract)
4. Mori S, Van Zijl PC.
   Fiber tracking: principles and strategies - a technical review.
   NMR Biomed. 2002 Nov-Dec;15(7-8):468-80.(PubMed abstract)

Acknowledgement

The DTI Task Card would not exist without prior idea and suggestion from David Tuch.

Further Information

If you have questions or problems about the DTI Task Card, please contact Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>.