<div dir="ltr"><div dir="ltr"><div><div>Ralf<br><br></div>The apparent colour mismatch
of the corresponding antipodal FOD lobes is a bit of an illusion. The
lobes are not explicitly coloured based on the peak direction; rather,
every vertex on the mesh is coloured according to its direction from the
origin in order to render the surface. Then, because you are not
looking precisely at the peaks of each lobe but rather the side of each
lobe closest to the camera position, and each lobe has a finite angular
width, you are in fact not looking at antipodal vertices; hence the
apparent colour difference. Rest assured that if you looked precisely at
the peak of each antipodal lobe, and disabled any lighting effects, the
colours would be identical.<br>
<br></div>As far as interpreting the 'shape' of the FOD, I can think of three possible interpretations of the question:<br><ol><li>Size: See <a href="http://www.ncbi.nlm.nih.gov/pubmed/22036682" target="_blank">this paper</a>, and stay tuned for further updates :-P</li>
<li>Number of discrete fibre populations: <a href="http://www.ncbi.nlm.nih.gov/pubmed/22611035" target="_blank">This one</a> is worth a look.</li><li>Parameterisation
of the angular distribution of fibre orientations within discrete fibre
populations: This is a bit trickier; mostly people try to incorporate
e.g. measures of fibre orientation dispersion into their diffusion
models, so it's no longer spherical deconvolution-based. Think <a href="http://www.ncbi.nlm.nih.gov/pubmed/17596967" target="_blank">this one</a>
was the first, but don't quote me on that. Expect to see quite a bit on
this over the next couple of years, as it has implications for
tractography.<br>
</li></ol>Cheers<br>Rob</div><br clear="all"></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><br>--<br><br><span style="color:rgb(255,102,0)"><b>Robert Smith, Ph.D</b><br>Research Officer, Imaging Division</span><br>
<br>The Florey Institute of Neuroscience and Mental Health<br>Melbourne Brain Centre - Austin Campus<br>245 Burgundy Street<br>Heidelberg Vic 3084<br>Ph: +61 3 9035 7128<br>Fax: +61 3 9035 7301<br><a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br>
<span style="font-size:9pt;font-family:"Times New Roman","serif";color:red"></span></div></div>
<br><br><div class="gmail_quote">On Tue, Apr 29, 2014 at 5:47 PM, Thijs Dhollander <span dir="ltr"><<a href="mailto:thijs.dhollander@gmail.com" target="_blank">thijs.dhollander@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><div><div><div>Hi Ralf,<br><br></div>The shape of the FOD is easy to interpret: you basically start with a (unit) sphere, and then scale its radius along each orientation by the FOD amplitude for that orientation. It's basically the 3D version of polar coordinates ( <a href="http://en.wikipedia.org/wiki/Polar_coordinate_system" target="_blank">http://en.wikipedia.org/wiki/Polar_coordinate_system</a> ), but used to represent a 2D spherical function in a 3D space.<br>
</div>The RGB values for the colors are simply derived from a normalized vector that points along each direction. The colors are nothing more than a visual aid though; they help you navigate a field of FODs much easier.<br>
<br></div>The caption in figure 7 refers you to the webversion, because the printed version probably did not feature colors at the time. The word "interpretation" there, only means that whatever is written in the caption about colors, can only really be visually appreciated in the (colored) digital version. The normal PDF at Elsevier basically is that web version. :-)<br>
<br></div>Hope this clarifies some things!<br><br>Cheers,<br>Thijs<span class="HOEnZb"><font color="#888888"><br><div><br></div></font></span></div><div class="gmail_extra"><span class="HOEnZb"><font color="#888888"><br clear="all">
<div><div dir="ltr"><span style="color:rgb(68,68,68)"><b><font size="4">Thijs Dhollander</font><br>
<font><a href="mailto:thijs.dhollander@gmail.com" target="_blank">thijs.dhollander@gmail.com</a><br>Tel. <a href="tel:%2B32%20475%2036%2044%2027" value="+32475364427" target="_blank">+32 475 36 44 27</a></font></b><br><font size="1">Medical Image Computing (MIC), ESAT-PSI, Department of Electrical Engineering, KU Leuven</font></span></div>
</div></font></span><div><div class="h5">
<br><br><div class="gmail_quote">On Mon, Apr 28, 2014 at 3:46 PM, Luetzkendorf, Ralf <span dir="ltr"><<a href="mailto:Ralf.Luetzkendorf@med.ovgu.de" target="_blank">Ralf.Luetzkendorf@med.ovgu.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello MRTrix Community,<br>
<br>
I have a question about the color and shape of the FODs / ODFs<br>
I read through the papers and I have to be absolutely sure how to interpret them.<br>
<br>
At first in the Paper "Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution, 2004" Figure 7 referred you to a web version for color interpretation. Is there still a Web Version? I only found the normal PDF at Elsevier.<br>
<br>
Do these drop-shaped geometrical bodies, that face each other have exactly the same color? And its only a rendering problem, that they very often don't have it in figures, like in Figure 7 of the 2004 Article?<br>
<br>
Is there a description how to interpret the shape of the ODF /FOD. Something like a first and still established paper about it?<br>
<br>
Thanks for the help,<br>
<br>
Ralf<br>
<br>
<br>
<br>
<br>
<br>
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