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 class="HOEnZb"><font color="#888888"><br>
</font></span></p><span class="HOEnZb"><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>
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