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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Zhuang<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">Here’s some thoughts about your questions:<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="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo2"><![if !supportLists]><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><span style="mso-list:Ignore">1)<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">At the moment, there’s the “colour” option for the tracks2prob command. However, one colour from that map can in general still correspond
to a maximum of 4 different directions. As a simple example, consider a yellow colour: it could be a direction from front-left to back-right, but also from front-right to back-left (both mix up red and green, resulting in yellow; it’s the same “problem” also
present in a DEC FA map). So, if you really need the true direction, the colours are not specific enough. Apart from that, I’m not exactly sure what you mean by “where crossing fibers have been removed”: do you want everything mixed up (i.e. an average direction,
ignoring the fact that there are possible contributions from different crossing bundles), or rather separated (i.e. so you can consider the bundles separately without influence from each other). I’m presenting an abstract at the upcoming ISMRM in Salt Lake
City that includes a technique which can do both of these for you (however, in the abstract, I’m subsequently using this kind of information for an entirely different purpose than statistical analysis). A journal paper with more details is on its way as well.
I’ve extended the tracks2prob command’s functionality to be able to calculate it automatically (still version 2.10, so I might still merge it with the changes in 2.11); I might release that code soon (when the journal paper is more or less out in the open).<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo2"><![if !supportLists]><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><span style="mso-list:Ignore">2)<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The best option here is to consider the FOD’s magnitude, which is related to the apparent fiber density (AFD) metric. There’s a hefty
paper on that (with a lot of indept discussion): <a href="http://www.sciencedirect.com/science/article/pii/S1053811911012092">
http://www.sciencedirect.com/science/article/pii/S1053811911012092</a> . It might probably be available in the next major release of MRtrix. A possibility that is “accessible” in the mean time, is to consider the average AFD (over all directions) in each
voxel. To generate it… well you don’t even have to, cause it’s already present in your FOD file resulting from CSD: just open it directly in the MRtrix viewer (not in the orientation plot part, but just directly as an image). The first thing you’ll see,
is the order 0 SH coefficient map from the FOD’s, which is –up to a constant factor– directly showing you an average AFD map.<br>
Appart from that, there also exists something called the “GFA” (generalized FA), which basically is the standard deviation normalized by the root mean square of the FOD’s (or any other angular function) magnitude. It’s not very “mainstream”, and suffers more
or less (maybe a bit less) from the same problems as the FA. Not very worthwhile to put effort in, in my opinion.<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo2"><![if !supportLists]><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><span style="mso-list:Ignore">3)<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">That’s a tough one (feel the controversy coming up… ;-)). In general, it fully depends on your fiber tracking algorithm, strategy, parameters,
and just about everything else involved (e.g. seeding strategy/distribution, amongst others…). That basically renders it very tricky for a true physical/biological/…real-worldish…/… interpretation. I’ve been ranting a bit on that on different occasions last
year (best source is probably last year’s ISMRM abstract I attached to this mail). But being critical for my own work on that: it just considered 1 kind of way to do TDI (more or less the most basic one, based on how it’s done in the original TDI paper).
Everything changes with your specific tracking setup. Here’s another article that discusses some things on the (lack of) meaning of track counts (also applies to fractions, they deliver the same contrast):
<a href="http://www.sciencedirect.com/science/article/pii/S1053811912007306">http://www.sciencedirect.com/science/article/pii/S1053811912007306</a> . As you might notice, I’m (a bit) on the sceptical side here. It could be done better, if you do the tracking
in a “responsible” way though. Responsible in this context, would in my opinion be the combination of these strategies:
<a href="http://www.sciencedirect.com/science/article/pii/S1053811912005824">http://www.sciencedirect.com/science/article/pii/S1053811912005824</a> and
<a href="http://www.sciencedirect.com/science/article/pii/S1053811912011615">http://www.sciencedirect.com/science/article/pii/S1053811912011615</a> . They should also be included in the next major release of MRtrix! Whatever you do, you have to carefully
think about what it still means: don’t forget that tracks are just generated by an algorithm with a lot of heuristic assumptions. Fiber tracking may as such be a good (great) segmentation and visualisation tool, the densities on the other hand where never
(originally) ment to be something really meaningful.<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">Hope this helps; I’m sure that there are a lot of other people around here that also have interesting ideas and opinions on these (difficult) topics!<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">Regards,<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"><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"">
<a href="mailto:mrtrix-discussion-bounces@public.nitrc.org">mrtrix-discussion-bounces@public.nitrc.org</a> [<a href="mailto:mrtrix-discussion-bounces@public.nitrc.org">mailto:mrtrix-discussion-bounces@public.nitrc.org</a>]
<b>On Behalf Of </b>Zhuang Song<br>
<b>Sent:</b> Thursday, March 21, 2013 19:09<br>
<b>To:</b> <a href="mailto:mrtrix-discussion@public.nitrc.org">mrtrix-discussion@public.nitrc.org</a><br>
<b>Subject:</b> [Mrtrix-discussion] statistical analysis after fiber tracking<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Dear MRtrixers,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">There are several questions regrading statistical analysis after fiber tracking, which may not necessarily relate to each other. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">1) Given the tracking output file *.tck, is there any way to read out the mean direction of selected fibers in every voxel where crossing fibers have been removed? This voxelwise directional information is anatomically specific and therefore
can be very useful in statistical analysis. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">2) For the purpose of statistics (not fiber tracking), what kinds of metric would you recommend to derive from either the original ODF or fiber ODF? I haven't seen much this kind of work yet in literature. It would be nice to have some
brainstorming here. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">3) I was wondering how to interpret properly the physical meaning of the track number or density that streamtrack generates.<span class="apple-style-span"><span style="font-size:10.0pt;font-family:"Arial","sans-serif""> </span></span>The
program streamtrack can generate arbitrary large number of tracks by manipulating the option "-number". T<span class="apple-style-span"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">he track density (i.e. "-fraction" outputs of tracks2prob) seems
to remain quite stable even if I increase </span></span>the total tracking number <span class="apple-style-span"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">1000 times in streamtrack with option</span></span> "<span class="apple-style-span"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">-number".
Different than the TDI method based on whole brain tracking, I am only interested in the tracks within a ROI.</span></span> It seems to me it makes more sense to use the track density instead of track numbers in statistical analysis. Is it reasonable to do
so even if the tracking is restricted in a ROI?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thanks, <o:p></o:p></p>
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<p class="MsoNormal">Zhuang<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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