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.


[down]Detailed Instructions

[down]Loading Image Data
[down]Tensor Viewing

[down]Known Issues
[down]Further Information


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

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

Also, please read the license and be aware of the following issues before installing the DTI Task Card 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[top]

Loading Image Data

Open the Patient Browser. Select the series of the original diffusion data to be used for diffusion tensor map calculation and visualization. Then click on the DTI button on the toolbar of the Patient Browser and select the appropriate type of sequence to load the data into the DTI Task Card.

NOTE: To add your own DTI gradient directions, modify the configuration file C:\MedCom\Config\DTI\gradient_directions.ini. DO NOT MESS WITH THAT FILE UNLESS YOU KNOW WHAT YOU ARE DOING.

New! Starting from version 1.63, the DTI Task Card can take mosaic data. No need to split the mosaic images anymore.

After data is loaded and calculated, the diffusion tensors can now be visualized in different patterns and white matter fiber tracking (tractography) can also be performed.

Note: According to D. Jones' paper (see references), more diffusion gradient directions and less averages appears preferable for tractography to less diffusion directions and more averages. We would recommend using more number of diffusion directions (e.g., 12 or 24 or even more) for tractography study.


Tensor Viewing[top]

Viewing Mode Buttons

Select between Tensor or Tractography viewing mode.

Tensor Tensor viewing mode. Tensor View
Tractography Tractography viewing mode. Tractography View

Tool Buttons for Tensor Viewing[top]

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

Image image
Plain ColorPlain Grayscale
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 Color Sphere. Show the color sphere indicating the direction-color coding for visualization.
Unnormalized Scaling 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 Parallel Viewing. Set the projection mode to Parallel or Prospective.
Interpolate Interpolate. Turn on/off the interpolation for Plain Color or Plain Grayscale map.
Slider Noise Threshold. Manually set the noise threshold for rendering. Noise threshold is used to determine background in Low b image.
Auto Threshold Autoset Noise Threshold. Automatically set the noise threshold as the mean value plus 6 times standard deviation of low b background.

Map Map
FA 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 LOWB. Show LOWB maps. Only generic grayscale map is valid at this mode.
ADC ADC. Show ADC maps. Only generic grayscale map is valid at this mode.
DWI DWI. Show DWI maps. Only generic grayscale map is valid at this mode.
EXP EXP. Show Exponential maps. Only generic grayscale map is valid at this mode.

Plane Map
Sagittal Sagittal. View Sagittal slices.
Coronal Coronal. View Coronal slices.
Axial Axial. View Axial slices.

Patient Patient
New Series 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.
Open Save Map As Analyze File. Save maps (FA, ADC, LOWB, etc. and even tensor and vectors) to local files in analyze format. (NEW!)
Close Close Patient. Close the current patient.


  • All of the above commands except the ones in "Patient" category can be found in the main menu on top of the task card.

  • Move the mouse cursor over each button to show its tooltip. Tooltip can only be shown when the button is not grayed.

  • Loading a new series (new patient data) will close the current loaded patient and clear all the previously rendered images.


Move At this cursor, hold left button and drag to move the image.
Zoom At this cursor, hold left button and drag to zoom the image.
Rotate 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. Popup Menu


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.
Tractography View
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.
Select ROI
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 >>.


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. 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.
Popup Menu

ROI Menu

ROI property
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.
Tracking Parameters
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.
Rendering Parameters

Tool Buttons for Tractography[top]

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

Define 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 Undo Last ROI Editing. Undo the last ROI editing.
Load ROI 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[top]

Fiber tracking visualization in the DTI Task Card. Sample1 Fiber tracking images saved to the database by DTI Task Card and loaded in the Viewing task card afterwards. Sample2


Click the copyright texts on the lower right corner of the screen to bring up About window with version info and link to this online documentation. Also click the "Live Update" button to check the latest update of the DTI Task Card.


Known Issues[top]

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.


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)


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

Further Information[top]

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