Hi Jesse,<div><br></div><div>A similar question came up on the mailing list just a couple of weeks ago, for which I gave quite a detailed answer. I'd recommend you have a look through it and see if it answers your question. It's archived here:</div>
<div><a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2013-April/000688.html">http://www.nitrc.org/pipermail/mrtrix-discussion/2013-April/000688.html</a></div><div><br></div><div>Hopefully that'll clarify everything for you, but don't hesitate to follow up if you still have questions.</div>
<div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br><div class="gmail_quote">On 12 April 2013 19:06, Jesse Ross-Jones <span dir="ltr"><<a href="mailto:jesse.rj@gmail.com" target="_blank">jesse.rj@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_quote"><div dir="ltr"><div><div><div><div><div>Dear MRtrix Users,<br><br></div>I am converting DICOM data from a Siemens Espree 1.5T machine for Fiber Tracking. Looking at the converted files I see that there is a difference between the raw gradients and the gradients once converted. I am interested to know where these differences come from. What pre processing steps are performed on the data during conversion? <br>
<br></div>I have included the gradient values I have obtained from various software here as reference. I have also summarized my findings below. <br><br></div>Your help in helping me to identify the source of these differences is much appreciated!!<br>
<br></div>Best Regards<br></div>Jesse<br><br>
<ol><li><p align="LEFT"><font size="3"><b>Raw Info of gradient</b></font></p>
<p style="font-weight:normal" align="LEFT"><font size="3">File:
RawDicomGradient.txt (The gradients are not sort as the output of
other tools)</font></p>
<p style="font-weight:normal" align="LEFT"><font size="3">0.000000
0.000000 0.000000 <br>0.999977 0.006051 0.003027 </font>
</p>
<p style="font-weight:normal" align="LEFT"><font size="3">-0.000006
-0.999982 0.006006 </font>
</p>
<p style="font-weight:normal" align="LEFT"><font size="3">-0.024989
-0.653018 -0.756930 </font>
</p>
<p style="font-weight:normal" align="LEFT"><font size="3">0.588672
0.769595 -0.247364 </font>
</p>
</li></ol>
<p align="LEFT"><br>
</p>
<ol start="2"><li><p align="LEFT"><font size="3"><b>MRTrix (dcm2mif)</b></font></p>
<p align="LEFT"><font size="3"><b>left->right\posterior->anterior\inferior->superior</b></font></p>
<p align="LEFT"><a><font size="3"><span style="font-weight:normal">File:MRtrix.mif</span></font></a></p>
<p style="font-weight:normal" align="LEFT"><font size="3">dw_scheme:
0,0,0,0<br>dw_scheme:
-0.999977,-0.00605102,0.00302703,1000<br>dw_scheme:
6.01e-006,0.999982,0.00600569,1000<br>dw_scheme:
0.0249894,0.653018,-0.75693,1000<br>dw_scheme:
-0.588672,-0.769595,-0.247363,1000</font></p>
</li><li><p align="LEFT"><font size="3"><b>3DSlicer (dcm2nrrd)</b></font></p>
<p align="LEFT"><font size="3"><b>left-posterior-superior</b></font></p>
<p style="font-weight:normal" align="LEFT"><a><font size="3">File:3DSlicer.dwi</font></a></p>
<p style="font-weight:normal" align="LEFT"><font size="3">DWMRI_gradient_0000:=0
0 0<br>DWMRI_gradient_0001:=-0.999977 -0.00605102
-0.00302703<br>DWMRI_gradient_0002:=-6.01148e-006 -0.999982
0.00600569<br>DWMRI_gradient_0003:=-0.0249893 -0.653018
-0.75693<br>DWMRI_gradient_0004:=-0.588672 -0.769595 0.247363</font></p>
</li><li><p align="LEFT"><font size="3"><b>MRCron (dcm2nii)</b></font></p>
<p align="LEFT">File:MRCron.txt</p>
<p align="LEFT">dw_scheme:0.000000 0.000000 0.000000
<br>dw_scheme:0.999659 -0.004982 -0.025617 <br>dw_scheme:-0.008158
0.962864 -0.269862 <br>dw_scheme:-0.052384 0.418964 -0.906491
<br>dw_scheme:0.587632 -0.807968 -0.043309
</p></li></ol><ol><li><font size="3"><b>MRIConverter (dcm2nii)</b></font><br>
<p align="LEFT">File:MRIConverter.txt</p>
<p align="LEFT">dw_scheme:0.000000 0.000000 0.000000
<br>dw_scheme:0.999660 -0.004982 -0.025588 <br>dw_scheme:-0.008132
0.962882 -0.269799 <br>dw_scheme:-0.052352 0.419028 -0.906463
<br>dw_scheme:0.587622 -0.807974 -0.043334
</p>
</li></ol>
<p align="LEFT"><br>
</p>
</div>
</div><br></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><font color="#ff6600" size="1"><b>Dr Jacques-Donald Tournier<br></b></font><div><font color="#ff6600" size="1">Research Fellow</font></div><div><font size="1"><br>
</font></div><div><font size="1">The Florey Institute of Neuroscience and Mental Health</font></div><div><font size="1">Melbourne Brain Centre - Austin Campus</font></div><div><font size="1">245 Burgundy Street</font></div>
<div><font size="1">Heidelberg Vic 3084</font></div><div><font size="1">Ph: +61 3 9035 7033</font></div><div><font size="1">Fax: +61 3 9035 7307</font></div><div><font size="1"><a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a></font></div>
<br>
</div>