<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Donald,<div><br></div><div>Thanks for the reply! We figured it out already. </div><div><br></div><div>Originally, the vector output from find_SH_peaks can be displayed by FSLView (RGB line mode) but not correctly (not matched with anatomy knowledge). We went through the pre-processing, and found out all we have to do is to "flip" the x-axial, so that the output from find_SH_peaks can then be correctly displayed by FSLView. </div><div><br></div><div>Cheers</div><div><br></div><div>Yonghui</div><div><br><div><div>On 02/10/2013, at 9:27 PM, J-Donald Tournier wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Hi Yonghui,<div><br></div><div>There may be different reasons for this. Can you be more specific as to exactly what the problem is? Does FSL display the wrong directions, or does it fail to display anything at all? Are the directions somehow rotated or flipped when viewed in FSL? Some screenshots would also help.</div>
<div><br></div><div>Thanks,</div><div>Donald.</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 27 September 2013 03:26, Yonghui Li <span dir="ltr"><<a href="mailto:lyh710@gmail.com" target="_blank">lyh710@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all,<br>
<br>
We used find_SH_peaks to generate peaks vectors (default 3), which was all good. Now we want to put these vectors into FSL for display (for example in RGB line style). We expect the largest vector detected by find_SH_peaks should be consistent with main Eigenvector (V1) from FSL based on tensor model calculation. However, the display indicated otherwise.<br>
<br>
We believe it is not the calculation that went wrong, but somehow Mrtrix and FSL handle the "directions" of vector differently.<br>
<br>
We browse through the archive but can not find any solid solution for this topic. It will be highly appreciated if someone can kindly help us out. We tried mrconvert the output from find_SH_peaks before send it into FSL, but that does not work out. Anything we can make the vector generated from find_SH_peaks correctly read by FSLView, particularly for the RGB line style?<br>
<br>
Look forward to your help and many thanks in advance!<br>
<span class="HOEnZb"><font color="#888888"><br>
Yonghui Li_______________________________________________<br>
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</font></span></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></div>
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