<div>Yep, that's the references I meant. And I found my script, but it's not suitable for stand-alone redistribution. However, it's quite simple and I didn't even use the analytical expression; I simply calculated b g' D g for every voxel and fitted this to SHs up to order 2. I used Donald's m-file gen_scheme to construct the SH basis. When writing the SHs to nii to load into MRtrix, indeed keep in mind to mutiple the m=~0 components by sqrt(2)</div>
<div> </div><div>René<br></div><div class="gmail_quote">On Sun, Oct 28, 2012 at 11:23 AM, Thijs Dhollander <span dir="ltr"><<a href="mailto:thijs.dhollander@uzleuven.be" target="_blank">thijs.dhollander@uzleuven.be</a>></span> wrote:<br>
<blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote">
<div lang="NL-BE" vlink="purple" link="blue">
<div>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt">Hello everyone,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt" lang="EN-US">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):<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt" lang="EN-US"><a href="http://onlinelibrary.wiley.com/doi/10.1002/mrm.20948/full" target="_blank">http://onlinelibrary.wiley.com/doi/10.1002/mrm.20948/full</a>
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt" lang="EN-US">…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.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt" lang="EN-US"><a href="http://www.brain.org.au/software/mrtrix/commands/dwi2SH.html" target="_blank">http://www.brain.org.au/software/mrtrix/commands/dwi2SH.html</a>
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt" lang="EN-US">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.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt" lang="EN-US">Cheers,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt" lang="EN-US">Thijs<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="color:rgb(0,161,214);font-family:"Arial","sans-serif";font-size:10.5pt">Thijs Dhollander</span></b><span style="color:rgb(31,73,125);font-family:"Arial","sans-serif""><br>
</span><span style="color:rgb(89,89,89);font-family:"Arial","sans-serif";font-size:10.5pt">PhD Student</span><span style="color:rgb(89,89,89);font-family:"Arial","sans-serif""><br>
</span><span style="color:rgb(89,89,89);font-family:"Arial","sans-serif";font-size:9pt"><br>
<a href="mailto:thijs.dhollander@uz.kuleuven.ac.be" target="_blank"><span style="color:rgb(89,89,89)">thijs.dhollander@uz.kuleuven.ac.be</span></a><br>
tel. <a href="tel:%2B32%2016%2034%2090%2037" target="_blank" value="+3216349037">+32 16 34 90 37</a><br>
gsm. <a href="tel:%2B32%20475%2036%2044%2027" target="_blank" value="+32475364427">+32 475 36 44 27</a></span><b><span style="color:rgb(89,89,89);font-family:"Arial","sans-serif";font-size:8pt"><br>
<br>
</span></b><b><span style="color:rgb(0,161,214);font-family:"Arial","sans-serif";font-size:8pt">Medical Image Computing (K.U.Leuven, ESAT/PSI, MIC)<br>
</span></b><span style="color:rgb(89,89,89);font-family:"Arial","sans-serif";font-size:8pt">Medical Imaging Research Center | UZ Gasthuisberg | Herestraat 49 - bus 7003 | B-3000 Leuven |
<a href="http://www.medicalimagingcenter.be" target="_blank"><span style="color:rgb(89,89,89)">http://www.medicalimagingcenter.be</span></a></span><span style="color:rgb(89,89,89);font-family:"Arial","sans-serif";font-size:11pt"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:"Calibri","sans-serif";font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="font-family:"Tahoma","sans-serif";font-size:10pt" lang="EN-US">From:</span></b><span style="font-family:"Tahoma","sans-serif";font-size:10pt" lang="EN-US"> <a href="mailto:mrtrix-discussion-bounces@public.nitrc.org" target="_blank">mrtrix-discussion-bounces@public.nitrc.org</a> [mailto:<a href="mailto:mrtrix-discussion-bounces@public.nitrc.org" target="_blank">mrtrix-discussion-bounces@public.nitrc.org</a>]
<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; <a href="mailto:mrtrix-discussion@public.nitrc.org" target="_blank">mrtrix-discussion@public.nitrc.org</a><br>
<b>Subject:</b> Re: [Mrtrix-discussion] Tensors in mrview<u></u><u></u></span></p><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></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.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p style="margin-bottom:12pt" class="MsoNormal">René<u></u><u></u></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:<u></u><u></u></p>
<p class="MsoNormal">Hi Rene, <u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></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>)? <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Thanks, <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="color:rgb(136,136,136)"><u></u> <u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span><span style="color:rgb(136,136,136)">Ariel </span></span><u></u><u></u></p>
<div>
<div>
<p style="margin-bottom:12pt" class="MsoNormal"><u></u> <u></u></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:<u></u><u></u></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.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">René<u></u><u></u></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:<u></u><u></u></p>
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<p class="MsoNormal">Hello MRtrix users,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Just want to know if there is a way to see tensors in mrview.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Thanks<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="color:rgb(136,136,136)">Arnaud<u></u><u></u></span></p>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
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