DoDTI utilizes several excellent online sources contributd by anonymous developers.
We have tried to give credit where appropriate.
DoDTI is running on MATLAB v6.0 (Mathworks) and later.
DoDTI can run independently of SPM (Wellcome Department, UK).
However, we recommend you to use either SPM99 or SPM2 if you want to utilize SPM's excellent modules such as segmentation and registration.
Also, if you are interested in combining diffusion tensor imaging with functional imaging such as PET or fMRI study, it would be necessary to use SPM.
Currently the basic tensor file format of DoDTI in most processing is
VTK (Kitware co.) DATASET
STRUCTURED_POINTS format.
We call it DVTK format in this documentation.
1. DVTK file format
----------------------------------------------------
# vtk DataFile Version 3.0
AX:[DTI:t2w xx xy xz
yy yz zz]
BINARY
DATASET STRUCTURED_POINTS
DIMENSIONS 256 256 43
SPACING
0.859375 0.859375 3.000000
ORIGIN -109.570312 -109.570312 -63.000000
POINT_DATA
2818048
SCALARS scalars float 7
LOOKUP_TABLE default
=>from hereBINARY
DATA Image Blocks
[Block T2W][Block Dxx][Block Dxy][Block Dxz]
[Block Dyy][Block Dyz][Block Dzz]
-----------------------------------------------------
The second line of the file describes the image orientation stored in the
file and channels of the gradient directions.
The first channel is the
T2W image for anatomical reference, the second to seventh channels are Dxx,
Dxy, Dxz, Dyy, Dyz, Dzz in sequence, which are components of a tensor image.
They are stored from the image volume block of the first channle to the image
volume block of the last channel.
2. The coordinate system of Tensor Image
DVTK is stored as RAS coordinate system, i.e. left to right (x), posterior to anterior(y) and inferior to superior(z).
DoDTI assumes the stored tensor image in neurological convention, i.e., Left figure is left hemisphere and right is right hemisphere.
3. How to convert conventional MRI Diffusin weighted data to DVTK format
Currently, DoDTI supports conversion tool for LSDI files of GE MRI and REC file of EPI sequence at Philips MRI.
We are planning to add more conversion tools for other machines. We would greatly appreicate for any contributions for this.
If you have other MRI machines than above two MRIs, you can also generate DVTK file from analyze files.
It is rather simple to create DVTK if you can manage matlab. DoDTI also provides some codes for writing Tensor array to DVTK.
We would greatly appreciate if users can contribute the conversion code to DoDTI communities.
4. The file format of Gradient directions
In order to compose tensors from diffusion weighted images, DoDTI requires several types of information, such as direction vectors of Gradients and index of non-diffusion weighted image. It could be easily modified with a text editor.
grad/xxx.grad