[Mrtrix-discussion] tensor storage and tracts coordinates

[Donald Tournier]

Hi Alessandro,

The algorithm used for tensor estimation in MRtrix is a simple linear fit
to the log signal - nothing fancy. The components are stored along the 4th
axis in the order you guessed: xx,yy,zz,xy,xz,yz.

And yes, the track coordinates are in scanner space, so you should be able
to use the transform matrix of your NIfTI image to convert back to voxel
coordinates.

Hope that helps.
Cheers,

Donald

--
Dr J-Donald Tournier (PhD)

Senior Lecturer, Biomedical Engineering
Division of Imaging Sciences & Biomedical Engineering
King's College London

A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH
T: +44 (0)20 7188 7118 ext 53613
W:
http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering

On 16 Jan 2014 13:45, "Alessandro Calamuneri" <alecalamuneri at gmail.com>
wrote:

> Hi, I am new to mrtrix.
> I have two questions:
>
> 1) You can create tensor components by means of dwi2tensor function. First
> of all, which kind of algorithm is used for tensor reconstruction (linear,
> non linear, constrained to be positive)? Then, if I use mrconvert to get
> tensor components stored into nifti format (i.e.)
>
> mrconvert tensors.mif tensors.nii
>
> nifti file which is generate is a 4d volume. What is the order in which
> components are stored? xx,yy,zz,xy,xz,yz or what?
>
> 2)My second question is related to mm coordinates that are into tck file.
> I would like to visualize them in matlab, I have used mat codes you provide
> to load tracts from tck format.  Then, what is the coordinate system they
> are related to? Scanner space?
> In that case I could obtain voxel coordinates just by using transformation
> matrix of one of nifti header of my original dwis, am I wrong?
>
> Hope to have clarified my points.
> Thanks a lot in advance!
>
> Best
>
> Alessandro
>
> --
> Alessandro Calamuneri
> M.Sc., PhD-student
> Department of Neurosciences, University of Messina, Italy
>
>
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