DTI Task Card

Version 1.71 build 2006.12.11 for VA25/VB11/VB12/VB13

Updated: February 06, 2007 01:15:49 PM (EST)    Download upgrade  
Please read the update log for information about all the changes.

Note: For users who were unable to install the DTI Task Card version 1.70 on VB13 workstations, please contact us for version 1.71 fresh installer.

Note: New Siemens gradient tables have been added as of December 19, 2006. For those who downloaded the v1.71 upgrade before that date (and therefore have problem with new Siemens 12 dir data), please download it again and re-update. Sorry for the inconvenience.

Note: For VB13, you will need 'DTI Evaluation package' (MR_3D_DIFFUSION_BASE) license from Siemens to run DTI Task Card.

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 (tractography). A general knowledge of MRease usage is assumed.

Contents

Installation
Detailed Instructions

Loading Image Data
Tensor Viewing
Tractography
Miscellanies

Known Issues

References

Acknowledgment

Further Information

Installation

Note: Starting from v1.71, VA21 & VB23 are no longer supported.

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_VB13A_LATEST_XXXXXXXX
  syngo VE31E
  
  N4_VB11A_LATEST_XXXXXXXX
  syngo VD20L
  
  N4_VA25A_LATEST_2004XXXX
  syngo VD20L
  

  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 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.

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_vXXXX.exe" 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.

Attention for VA25/VB11/VB13 version (Windows XP based): After installation the DTI task card will not show up until the data loading starts. It can also be brought up from "Applications" menu.

Detailed Instructions

Loading Image Data

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, Ellipsoid, 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. Note: Ellipsoid rendering can only be allowed when the view page layout is set to 1:1. 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. E1, E2, E3 or E1-E2. Show E1, E2, E3 or E1-E2 map respectively. Only generic grayscale map is valid at E1, E2 or E3 mode. LOWB. Show LOWB maps. Only generic grayscale map is valid at this mode. ADC. Show ADC maps. Only generic grayscale map is valid at this mode. DWI. Show DWI maps. Only generic grayscale map is valid at this mode. EXP. Show Exponential maps. Only generic grayscale map is valid at this mode.

Plane

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

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. The scale factor is 1000 for FA map and 1000,000 for E1, E2, E3, E2E3 and ADC maps. Save Map As Analyze File. Save maps (FA, ADC, LOWB, etc. and even tensor and vectors) to local files in analyze format. (NEW!) Close Patient. Close the current patient.

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 a group of voxels as an ROI (Region Of Interest). New from v1.67: Hold Ctrl + Shift + Left Mouse Button to delete voxels. New from v1.68: Hold Ctrl + Middle Mouse Button to fill closed ROI region. 3. Click right mouse button on the ROI to bring up the ROI menu and select the appropriate tracking method. Fiber tracking using that ROI as the seed region will be performed. NOTE: Starting from version 1.65, fiber tracking will NOT be performed automatically after ROI is selected. User needs to trigger fiber tracking from ROI menu. Both ROI file and Fiber volume file are in Analyze format. Starting from version 1.70, new binary format of track point file is introduced. Explanation of the new format >>.

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. Shift Key + Right Mouse Button to view the current voxel info. 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 fibers/ROIs. NOTE: Saved track points are for reference only and can not be loaded back into the task card. However, ROIs can be saved and loaded. Save fiber as Analyze format volume.(NEW!) Make finished ROI editable.(NEW!) View mean FA, ADC and DWI values of ROI. (NEW!) 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. Switch on/off stereo rendering. (Needs red/blue 3D glasses to view). 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 1/5 ~ 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: 1, 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 used. Smoothing and Interpolation setting. Apply Gaussian smoothing and interpolation on raw data or tensor data. Rendering parameters Tube Radius. The radius of the fiber tracks visualized as the many tubes. Decimation Factor. Decimation can reduce the number of polygons of the fiber objects without reducing the rendering quality visually. Thus the rendering needs less resources and will be faster. Decimation factor here determines how much decimation to be done. Recommended value: 50%~70%. That means the number of polygons to be rendered is reduced to 50%~30% of the original. Color Coding. Color codings for the fiber, includes direction-coded color, solid color and FA-coded color. NOTE: From version 1.62, the DTI Task Card uses a new scheme for direction-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 To Sagittal. Restore viewing position to Sagittal. Restore To Coronal. Restore viewing position to Coronal. Restore To Axial. Restore viewing position to Axial.

ROI

Define ROI. Define the previously selected voxels as an ROI. The next selected voxel will start a new ROI. If fiber tracking has been performed with previously selected voxels, they are already automatically defined as an ROI. Undo Last ROI Editing. Undo the last ROI editing. Load ROI. Load ROI from a saved ROI file. Starting from v1.68, ROI file uses analyze format. Old format is still readable but not writable any more.

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 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 slow, especially in Ellipsoid rendering mode and/or with high resolution images (e.g., 256x256).
• Due to the limitation of the VTK engine, the tractography tool can not handle too large amount of fibers together at the same rendering. Reducing the "Number of Samples Per Voxel Length" parameter and increasing the "Decimation Factor" 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)
5. Jones DK, Horsfield MA, Simmons A.
   Optimal strategies for measuring diffusion in anisotropic systems by magnetic resonance imaging.
   Magn Reson Med. 1999 Sep;42(3):515-25.(PubMed abstract)

Acknowledgement

Thanks to David Tuch for the initial idea of tensor visualization.

Further Information

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