<div dir="ltr"><div><div>Hmmm... Looking at those pancake-shaped FODs in the ventricles, my best guess is that you've tried to manually extract only the DWIs corresponding to a particular b-value, but erroneously included one volume with a lower b-value (and with a diffusion sensitisation direction normal to those pancakes). I'd check your extracted DWI volumes to see if one is much brighter than the others; also run dwi2SH on the extracted volumes and check the result in the viewer orientation plot, make sure the diffusion profile shapes are correct. This should hopefully fix the tractography problem.<br><br></div><div>(P.S. MRtrix3 has a command for automatically extracting DWI volumes corresponding to a particular b-value shell... just sayin' :-P )<br></div><div><br></div>In terms of the FOD asymmetry, it looks to me as though there's a strong bias field left-right (check out the sizes of the erroneous FODs in the ventricles). I'd have a peek at any HCP-provided pre-processing images that may be there, or calculate and visualise the mean DWI intensity across volumes for the shell you're analysing, maybe an explicit bias field correction has been performed on the DWIs and has gone wrong. But it's tough to speculate on those FOD geometry asymmetries until the weird ventricle FODs have been solved.<br><br></div>Rob<br></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></div></div>
<br><div class="gmail_quote">On Sat, Sep 27, 2014 at 7:00 AM, Anna Varentsova <span dir="ltr"><<a href="mailto:avarents@gmail.com" target="_blank">avarents@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div dir="ltr">Dear all,
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<div>I am trying to analyze Human Connectome data and faced some issues. Tractoraphy results show lines in X-Y plane (<a href="http://postimg.org/image/depga0wul/" target="_blank">http://postimg.org/image/depga0wul/</a>). I checked FOD field (<a href="http://postimg.org/image/za93ht1lb/" target="_blank">http://postimg.org/image/za93ht1lb/</a>).
FODs on the left-hand side and right-hand side do not look the same. I am not sure what can be causing this effect.</div>
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<div>I have seen previous discussion about Human Connectome (<a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2013-January/000626.html" target="_blank">http://www.nitrc.org/pipermail/mrtrix-discussion/2013-January/000626.html</a>), but didn't see this issue
to be reported before.</div>
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<div>Thank you,<br>
</div>
<div>Anna </div>
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