<div dir="ltr">Hi Ralf,<div><br></div><div>I'm assuming you're supplying your own DiffusionVectors file, and comparing them to the MRtrix directions read from the DICOM headers? If so, this is normal, and is due to a difference in the conventions used: DICOM uses a LPS reference frame, whereas MRtrix (and NIfTI) assume a RAS frame. That should mean that the X & Y components are reversed between the two. </div>
<div><br></div><div>As to the b=0 no longer being zero, this is most likely due to the online calculation of the effective DW scheme taking account of the imaging gradients. The system applies the right DW gradients, but computes the b-value and gradient direction based on <i>all</i> gradients between excitation and echo. You'll get a small non-zero b-value even if you specify b=0 due at least to the crushers around the 180° refocusing pulse(s). You'll probably also find that your DW scheme changes slightly with different slice orientations, due to the different orientations of the imaging pulses...</div>
<div><br></div><div>Cheers,</div><div>Donald.</div><div><br></div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On 2 April 2014 10:50, Luetzkendorf, Ralf <span dir="ltr"><<a href="mailto:Ralf.Luetzkendorf@med.ovgu.de" target="_blank">Ralf.Luetzkendorf@med.ovgu.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi to all,<br>
<br>
I have a little problem with the vector scheme.<br>
<br>
I noticed a sign difference between the scanner directions, that I fill in and MRTrix reading out from the data.<br>
Even if Im measuring straight axial, like the documentation said.<br>
I hope that is normal.<br>
<br>
Is it okay to use them both or should I ever use the directions that MRTrix is gathering from the data?<br>
<br>
<br>
Now I have a second problem. I used the same direction scheme like before, but now MRTrix doesnt only change the signs.<br>
It has different values for every B0 data set. The other values are still the same.<br>
<br>
The B0 direction looks like that:<br>
<br>
0.5 -0.5 0.707107 5<br>
<br>
instead of:<br>
<br>
0 0 0 0<br>
<br>
<br>
Did somebody encouter the same problem? Which should I use?<br>
<br>
I hope somebody can help,<br>
<br>
<br>
Cheers Ralf<br>
<br>
+++++++++++++++++++++++++++++++++++++++++++++++<br>
Ralf Lützkendorf<br>
Department for Biometry and Medical Informatics<br>
University of Magdeburg, Germany<br>
<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><b><font color="#990000">Dr J-Donald Tournier (PhD)</font></b><br><div><font color="#990000"><br></font></div><i><font color="#990000">Senior Lecturer, </font></i><i><font color="#990000">Biomedical Engineering</font></i><div>
<i><font color="#990000">Division of Imaging Sciences & Biomedical Engineering<br>King's College London</font></i><div><i><font color="#990000"><br></font></i></div><div><i><font color="#990000"><b style="font-family:Calibri,sans-serif;font-size:15px"><span style="font-size:10pt">A:</span></b><span style="font-family:Calibri,sans-serif;font-size:10pt"> Department of Perinatal Imaging & Health, 1<sup>st</sup> Floor South Wing, St Thomas' Hospital, London. SE1 7EH</span><br>
</font></i></div><div><i><font color="#990000"><b>T:</b> +44 (0)20 7188 7118 ext 53613</font></i></div></div><div><i><font color="#990000"><b>W:</b> <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a></font></i><br>
</div></div>
</div>