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Hi René,<br>
<br>
thank you for your reply! Unfortunately that did not fix my problem.
I attached an image of the ODF I get with my method (negative Lobes
are dark blue). The red lines indicate the peaks extracted from the
SH coefficient file using "find_SH_peaks". These peaks are correct
but the ODF is somehow rotated. The ODF should actually represent a
simple 90° crossing of two fibers corresponding to the two peaks.<br>
<br>
Here a code snippet of my SH basis calculation. Maybe someone can
directly identify the issue:<br>
<br>
<small>j=0;<br>
for (int l=0; l<=ShOrder; l=l+2)<br>
for (m=-l; m<=l; m++)<br>
{<br>
// evaluation of legendre polynome<br>
float mag =
sqrt((double)(2*l+1)/(4.0*M_PI)*factorial<double>(l-abs(m))/factorial<double>(l+abs(m)))
* legendre_p<double>(l,abs(m),cos(sphCoords(0)));<br>
<br>
if (m<0)<br>
m_ShBasis(j) = sqrt(2.0)*mag*cos(-m*sphCoords(1));<br>
else if (m==0)<br>
m_ShBasis(j) = mag;<br>
else<br>
m_ShBasis(j) = pow(-1.0,
m)*sqrt(2.0)*mag*sin(m*sphCoords(1));<br>
<br>
j++;<br>
}</small><br>
<br>
I also tried it without the sqrt(2.0) and pow(-1.0, m) terms, but
that does not change anything. <br>
<br>
Best,<br>
Peter<br>
<br>
<div class="moz-cite-prefix">On 01/03/2013 01:01 PM, René Besseling
wrote:<br>
</div>
<blockquote
cite="mid:CAHEtoki2DuVdNE+tKJk2SR+KcfptZ_KTeWBUzT_TLuRVnbuWcQ@mail.gmail.com"
type="cite">
<div>Hi Peter,</div>
<div> </div>
<div>I ran into this before; it has to do with the MRtrix SH basis
being orthogonal but not orthonormal, see the following quote
from an e-mail from Donald.</div>
<div> </div>
<div>Best regards and happy new year to you too,</div>
<div><br>
René</div>
<div><br>
Quote Donald:</div>
<div>
<div>"To answer your question: the matlab code does use an
orthonormal basis, but MRtrix unfortunately does not. Main
reason is that I didn't bother checking that the basis was
orthonormal in the MRtrix code until relatively recently, and
it's now too late to change it without making all current data
sets ambiguous (i.e. how do you know whether a data set uses
the orthonormal basis or not?). I have since changed the
matlab code though, which is why there is a difference.</div>
<div><br>
</div>
<div>It's pretty easy to convert between them: the m=0 terms are
not affected, while the m!=0 terms are all scaled by a factor
of <span class="il">sqrt</span>(<span class="il">2</span>) in
MRtrix compared with Matlab. Easy to fix, but very annoying I
have to admit."</div>
<div><br>
<br>
</div>
</div>
<div class="gmail_quote">On Thu, Jan 3, 2013 at 12:54 PM, Peter
Neher <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</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">Hi everyone and happy new year!<br>
<br>
I am trying to import the SH coefficient file (output of
csdeconv) into my own program but the ODFs are not displayed
correctly. The same method worked fine for the FSL coefficient
files so I guess you are calculating the SH basis in a
different way (the file format seems to be the same as the FSL
file format). MRview renders the ODFs correctly, so I wanted
to compare may code to the MRview code. Can you tell me the
location in the source code where I can find your calculation
and evaluation of the SH basis?<br>
<br>
Best,<br>
Peter<br>
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href="mailto:Mrtrix-discussion@www.nitrc.org"
target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
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href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion"
target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
</blockquote>
</div>
<br>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Dipl.-Inform. Peter Neher
German Cancer Research Center
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg
Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:p.neher@dkfz-heidelberg.de">p.neher@dkfz-heidelberg.de</a>, Web: <a class="moz-txt-link-abbreviated" href="http://www.dkfz.de">www.dkfz.de</a>
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