DTIstudio User Manual

3DMRI Readme

New features in DtiStudioV3.0.2:

1: Now DtiStudio can read and write Analyze format.

2: Image rotation (oblique slice) function is improved. In previous version, color map can be rotated but it works only for small rotation angle. This is because the format of color maps in DtiStudio (RGB format: byte array with 3xd1xd2xd3, where d1, 2, and 3 are matrix dimension) doesn’t contain full vector information. For example, if we have two pixels with principle eigenvectors of [1/sqrt(2), 1/sqrt(2), 0] and [1/sqrt(2), -1/sqrt(2), 0], both pixels have color representation of [128, 128, 0] (= x^2*256, y^2*256, z^2*256). Apparently, we don’t have enough information for accurate rotation. In this new version, the color map rotation can be done using the following procedure:

a: Load FA and Vector files. Click “oblique” radio button and specify specific rotation angles. You can also press “cancel” and use “shift-left mouse button” for rotation interactively.

b: apply the same rotations to FA and Vector images.

c: right-mouse click on the FA image and choose “save this image file as”. Choose “Analyze” and “Whole 3D-Volume” to save the rotated FA map as Analyze format

d: right-mouse click on the Vector image and choose “save this image file as”. Choose “Raw” and “whole 3D-volume” to save the rotated Vector map (Analyze format doesn’t support vector file).

e: open the rotated FA map in Analyze format in a new display window (use the “open” icon in the upper left corner of the software).

f: open the raw rotated Vector map using the “open” icon in the right column of the viewing window that is already open for the FA map. This will load both FA and Vector maps within one window.

g: use “Color Map” button to combine the FA and Vector maps to create a rotated color map.

h: current rotation algorithm still has a problem for vector phase wrapping. We are working on this issue. So, please use this function for visualization only.

3: Easy copy function is added by right-clicking on an image.

4: 3D images can be copied by “Copy 3D-View to Clipboard”. For the 3D window, right-click doesn’t work because it is assigned to zooming function.

5: Multiple b-value tensor calculation is now supported. The syntax for the gradient table is;

0: 0,0,0, 100

1: 1,0,0, 600

2: 0,1,0, 1000


the old gradient table format still works for single b-value cases.

6: Now b=[0,0,0] is not required.

Upgrade Notice for DtiStudio Version 2.3 and 3DMRI Veiwer:

In V2.3, following functions were added or improved.

1) Oblique angle: it allows rotating the 3D volume data to obtain oblique slices. When you choose “oblique” button, a new window appears in which you can type in arbitrary angles for the rotation. You can also simply press “ok” without setting any rotation angles. Then you can do shift+left-mouse-press-hold on one of the three 2D images to interactively change the rotation angle. You can rotate any images including color maps. However, in the current version, the color coordinates are not recalculated.

2) ROI drawing: In the older version, registration of mouse cursor and defined ROI was often not perfect. This was improved in the current version.

3) NOT operation: In the older version, NOT operation sometimes couldn’t remove all fibers that penetrate the ROI. This bug was fixed.

4) CUT operation: If you choose this operation and draw two ROIs, only fiber coordinates in between the two ROIs are reconstructed. In conventional two-ROI approach, there are three regions; left side of the left ROI, in between the two ROIs, and right side of the right ROI. These three areas have very different properties. In the second region (between ROIs), tracking is posed a strong anatomical constraint, in which no branching is allowed and the reconstruction more robust against noise. This approach is especially useful for the following quantitative approach.

5) Tract statistics: This new function gives you MR parameters of pixels occupied by reconstructed fibers. If you load a FA map, it’ll give average and STD of FA of the reconstructed fibers in addition to the number of the occupied pixels. You can load any quantitative maps such as ADC (traceTensor in this software) or T2 for tract-specific quantification as long as the maps are co-registered. Current version can give only the average / STD of the entire reconstructed fibers. We are working on “numbers-along-the-tract” approach.

6) Data format: Currently, Philips REC, Siemens DICOM, GE DICOM, Toshiba DICOM, and raw (integer) data are supported.

7) Manual can be downloaded from cmrm.med.jhmi.edu. Please go to “Diffusion Tensor Imaging Technology” and you can find the file.For the 3DMRI, you need to save the reconstructed fibers using “AMIRA format” in DtiStudio. Then 3DMRI can do 3D surface rendering.

We created dtistudio@mri.jhu.edu for opinions, suggestions, bug reports, complaints, or anything you think of. We are a bit undermanned but will do our best to respond.


Susumu Mori

Hangyi Jiang (DtiStudio)

Kegang Hua (3DMRI)

Xin Xu (Web master of http://cmrm.med.jhmi.edu & Administrator)

( To download DTI software, please go to http://www.mristudio.org )

Supported by NIH/NCRR grant P41RR015241