<div class="csl-bib-body" style="line-height:1.35;padding-left:2em">
<div class="csl-entry">Hi Peter,</div><div class="csl-entry"><br></div><div class="csl-entry">This is probably what you're looking for:</div><div class="csl-entry"><br></div><div class="csl-entry">Tournier J, Calamante F, Connelly A (2012). MRtrix: Diffusion tractography in crossing fiber regions. International Journal of Imaging Systems and Technology 22: 53–66.</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_id=info%3Adoi%2F10.1002%2Fima.22005&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=MRtrix%3A%20Diffusion%20tractography%20in%20crossing%20fiber%20regions&rft.jtitle=International%20Journal%20of%20Imaging%20Systems%20and%20Technology&rft.volume=22&rft.issue=1&rft.aufirst=J%E2%80%90Donald&rft.aulast=Tournier&rft.au=J%E2%80%90Donald%20Tournier&rft.au=Fernando%20Calamante&rft.au=Alan%20Connelly&rft.date=2012-03-01&rft.pages=53-66&rft.spage=53&rft.epage=66&rft.issn=1098-1098"></span></div>
<div><br></div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><br><div class="gmail_quote">On 1 August 2012 23:25, Peter Neher <span dir="ltr"><<a href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Donald,<br>
<br>
thanks for your answers! Is there any publication or something else
that describes your probabilistic tracking implementation in more
detail? <br>
<br>
Best<span class="HOEnZb"><font color="#888888"><br>
Peter</font></span><div><div class="h5"><br>
<br>
<div>On 08/01/2012 02:03 AM, Donald Tournier
wrote:<br>
</div>
<blockquote type="cite">Hello again,
<div><br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">I have some questions
regarding the parameters of streamtrack:<br>
<ol>
<li>Should it basically be the same to use a 0.2
thresholded FA image as -mask input as to apply a
-cutoff 0.2? Because it is not. There seem to be
fibers present in low FA regions if I use the -cutoff
parameter. It does change something, but I am not sure
what exactly :)</li>
</ol>
</div>
</blockquote>
<div>Not quite the same, as you found out. The -cutoff applies
to the FA as computed after tri-linear interpolation of the
raw DWIs to the current point. For the mask, the cutoff
point is the 0.5 level after tri-linear interpolation (you
can use nearest-neighbour interpolation if you need to using
the -nomaskinterp option). That will lead to the FA=0.2
level being in a different position than the mask=0.5 level,
and in many cases, tracks will traverse regions where the
mask is zero, simply because they avoid those parts of the
voxel where the FA is below 0.2 after interpolation.</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<ol>
<li>How is the -num parameter applied internally? Don't
you just seed in every voxel of the mask image? <br>
</li>
</ol>
</div>
</blockquote>
<div>Nope. Seed points are generated randomly and uniformly
from within all seed regions, in continuous 3D space. Even
within a single voxel, the seed points will be distributed
uniformly within its volume, rather than all starting from
the centre of it. Streamlines will be generated until the
number specified has been reached, or the -maxnum number has
been reached (by default, this is 100x num). If you need to
make sure you use exactly N seed points, set both -num and
-maxnum to N.</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<ol>
<li>If I use the probabilistic version, how many times
is the trajectory originating from one seed point
sampled and how is the result combined into one final
fiber?</li>
</ol>
</div>
</blockquote>
<div>Once. Every streamline starts from a fresh seed.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
Donald.</div>
<div><br>
</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<ol>
</ol>
<p>Thanks in advance!<span><font color="#888888"><br>
</font></span></p>
<span><font color="#888888">
<p>Peter<br>
</p>
<pre cols="72">--
Dipl.-Inform. Peter Neher
German Cancer Research Centre
(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 href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>, Web: <a href="http://www.dkfz.de" target="_blank">www.dkfz.de</a>
The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.</pre>
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<br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
Jacques-Donald Tournier (PhD)<br>
Brain Research Institute, Melbourne, Australia<br>
Tel: +61 (0)3 9035 7033<br>
</div>
</blockquote>
<br>
<pre cols="72">--
Dipl.-Inform. Peter Neher
German Cancer Research Centre
(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 href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>, Web: <a href="http://www.dkfz.de" target="_blank">www.dkfz.de</a>
The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.</pre>
</div></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Jacques-Donald Tournier (PhD)<br>Brain Research Institute, Melbourne, Australia<br>Tel: +61 (0)3 9035 7033<br>