<p dir="ltr">Hi Alessandro,</p>
<p dir="ltr">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.</p>
<p dir="ltr">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.</p>
<p dir="ltr">Hope that helps.<br>
Cheers,</p>
<p dir="ltr">Donald<br></p>
<p dir="ltr">--<br>
Dr J-Donald Tournier (PhD)</p>
<p dir="ltr">Senior Lecturer, Biomedical Engineering<br>
Division of Imaging Sciences & Biomedical Engineering<br>
King's College London</p>
<p dir="ltr">A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St Thomas' Hospital, London. SE1 7EH<br>
T: +44 (0)20 7188 7118 ext 53613<br>
W: <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a><br>
</p>
<div class="gmail_quote">On 16 Jan 2014 13:45, "Alessandro Calamuneri" <<a href="mailto:alecalamuneri@gmail.com">alecalamuneri@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi, I am new to mrtrix. <div>I have two questions:</div><div><br></div><div>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.)</div>
<div><br></div><div>mrconvert tensors.mif tensors.nii</div><div><br></div><div>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?</div><div><br></div>
<div>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?</div>
<div>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?</div><div><br></div><div>Hope to have clarified my points.</div><div>Thanks a lot in advance!</div>
<div><br></div><div>Best</div><div><br></div><div>Alessandro</div><div><div><br></div>-- <br><div dir="ltr">Alessandro Calamuneri<br>
<div>M.Sc., PhD-student</div>
<div>Department of Neurosciences, University of Messina, Italy</div>
<div><br></div></div>
</div></div>
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