<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Perfect, thanks!<br>
<br>
<div class="moz-cite-prefix">On 08/01/2012 03:28 PM, Donald Tournier
wrote:<br>
</div>
<blockquote
cite="mid:CAPP9hqRtj10B3NxOzU2vtz-CNrcnoqZ8Zpb6+Apc5r6rEhESeg@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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 moz-do-not-send="true" href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>, Web: <a moz-do-not-send="true" 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>
</font></span></div>
<br>
_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a moz-do-not-send="true"
href="mailto:Mrtrix-discussion@www.nitrc.org"
target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
<a moz-do-not-send="true"
href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion"
target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
<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 moz-do-not-send="true" href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>, Web: <a moz-do-not-send="true" 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>
</blockquote>
<br>
<pre class="moz-signature" 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 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>
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>
</body>
</html>