<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.hoenzb
{mso-style-name:hoenzb;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="NL-BE" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hello everyone,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The analytic expression to convert forth and back between SH coefficients and tensor parameters has been described in this paper from Descoteaux
et al. (2006):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><a href="http://onlinelibrary.wiley.com/doi/10.1002/mrm.20948/full">http://onlinelibrary.wiley.com/doi/10.1002/mrm.20948/full</a>
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">…more specifically, matrix M in equation 17, of which the solution for the rank-2 tensor and SH basis up to order 2 is shown in figure 3. Be careful
however, as this assumes the orthornomal SH basis that Maxime Descoteaux defined in that paper in equation 11 (and typically used in most of his following works). The SH basis used in MRtrix is slightly different; a description of it can be found at e.g.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><a href="http://www.brain.org.au/software/mrtrix/commands/dwi2SH.html">http://www.brain.org.au/software/mrtrix/commands/dwi2SH.html</a>
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The differences are the omission of the conventional (-1)^m factor, as well as an additional factor sqrt(2) for the Y(l,m) coefficients where m
is not 0.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thijs<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#00A1D6">Thijs Dhollander</span></b><span style="font-family:"Arial","sans-serif";color:#1F497D"><br>
</span><span style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#595959">PhD Student</span><span style="font-family:"Arial","sans-serif";color:#595959"><br>
</span><span style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#595959"><br>
<a href="mailto:thijs.dhollander@uz.kuleuven.ac.be"><span style="color:#595959">thijs.dhollander@uz.kuleuven.ac.be</span></a><br>
tel. +32 16 34 90 37<br>
gsm. +32 475 36 44 27</span><b><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959"><br>
<br>
</span></b><b><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#00A1D6">Medical Image Computing (K.U.Leuven, ESAT/PSI, MIC)<br>
</span></b><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959">Medical Imaging Research Center | UZ Gasthuisberg | Herestraat 49 - bus 7003 | B-3000 Leuven |
<a href="http://www.medicalimagingcenter.be"><span style="color:#595959">http://www.medicalimagingcenter.be</span></a></span><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#595959"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> mrtrix-discussion-bounces@public.nitrc.org [mailto:mrtrix-discussion-bounces@public.nitrc.org]
<b>On Behalf Of </b>René Besseling<br>
<b>Sent:</b> Saturday, October 27, 2012 11:31<br>
<b>To:</b> Ariel Rokem<br>
<b>Cc:</b> Arnaud Boré; mrtrix-discussion@public.nitrc.org<br>
<b>Subject:</b> Re: [Mrtrix-discussion] Tensors in mrview<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">There is this analytical expression to express g'Dg in spherical harmonics, but it'quite a while back that I looked into that. I'll check in on monday on my pc at work.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">René<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">On Sat, Oct 27, 2012 at 1:47 AM, Ariel Rokem <<a href="mailto:arokem@gmail.com" target="_blank">arokem@gmail.com</a>> wrote:<o:p></o:p></p>
<p class="MsoNormal">Hi Rene, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I would actually like to see that. Is there an analytic expression for that, or do you perform some kind of approximation? Could you put the code somewhere (e.g.
<a href="http://gist.github.com" target="_blank">gist.github.com</a>)? <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thanks, <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="color:#888888"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span class="hoenzb"><span style="color:#888888">Ariel </span></span><o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Fri, Oct 26, 2012 at 3:41 PM, René Besseling <<a href="mailto:r.m.h.besseling@gmail.com" target="_blank">r.m.h.besseling@gmail.com</a>> wrote:<o:p></o:p></p>
<div>
<p class="MsoNormal">Jep, you can express their peanut-shaped representation (so not the ellipsoid) in spherical harmonics. If you're interested, I've got a Matlab script that takes the dt.nii from dwi2tensor as an input at outputs the SH representation.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">René<o:p></o:p></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal">On Fri, Oct 26, 2012 at 8:10 PM, Arnaud Boré <<a href="mailto:arnaud.bore@gmail.com" target="_blank">arnaud.bore@gmail.com</a>> wrote:<o:p></o:p></p>
</div>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm">
<div>
<div>
<div>
<p class="MsoNormal">Hello MRtrix users,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Just want to know if there is a way to see tensors in mrview.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thanks<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="color:#888888">Arnaud<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt">_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><o:p></o:p></p>
</blockquote>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
<br>
_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</body>
</html>