Gabriel<br><br>When placing your exclusion regions, bear in mind that a streamline only has to enter that region <u>at any point along its length</u> to be excluded from the output. Therefore, you ideally want to draw these regions such that they do not interfere with your pathway of interest whatsoever, but all of the spurious tracks that you do wish to remove enter at least one of them, even if it is only for a short section of their length.<br>
<br>An alternative to excluding these spurious pathways during tracking would be to perform your tracking using inclusion regions only, and later sub-divide the track data using the <span style="font-family: courier new,monospace;">filter_tracks</span> program I distributed earlier this year. This program uses the same <span style="font-family: courier new,monospace;">-include </span>/<span style="font-family: courier new,monospace;"> -exclude</span> syntax as <span style="font-family: courier new,monospace;">streamtrack</span>, but applies this logic to an existing track file, rather than the streamlines as they are generated. This may be preferable to iteratively tracking and then refining your regions of interest, and has the added benefit of being able to see exactly which streamlines are being included / excluded by comparing the track files before and after filtering (if one of your exclusion regions interferes with your pathway of interest during tracking, you may not be made aware of it). You can find this program within the <a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2011-September/000269.html" target="_blank">discussion archives</a>.<br clear="all">
<br>Happy tracking!<br>Rob<br><br>--<br><br>Robert Smith<br>Melbourne Brain Centre<br>245 Burgundy Street<br>Heidelberg VIC 3084<br>Telephone: <a href="tel:%28%2B61%203%29%209035%207128" value="+61390357128" target="_blank">(+61 3) 9035 7128</a><br>
Fax: <a href="tel:%28%2B61%203%29%209035%207301" value="+61390357301" target="_blank">(+61 3) 9035 7301</a><br>Email: <a href="mailto:r.smith@brain.org.au" target="_blank">r.smith@brain.org.au</a><br>
<a href="http://www.fni.edu.au" target="_blank">www.florey.edu.au</a> <a href="http://www.brain.org.au" target="_blank">www.brain.org.au</a><br><span style="font-size: 9pt; font-family: "Times New Roman","serif"; color: red;"></span><br>
<br><br><div class="gmail_quote">On Sat, Nov 26, 2011 at 12:05 AM, Gabriel Gonzalez Escamilla <span dir="ltr"><<a href="mailto:ggonesc@upo.es" target="_blank">ggonesc@upo.es</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div style="font-family: 'Times New Roman'; font-size: 16px;">Thank you so much Rob, now everything works just fine.<br><br>I have i little doubt about the tracking, when I do it, some regions have spurious tracks, so as you said I will include some exclude ROIs but, my doubt is, the track I don't want are in regions belonging other tracts that i will track latter, should I use a mask of each tract as excluding region, or just some parts of them??'<br>
<br><br><span>El 25/11/11, <b>Robert Smith </b> <<a href="mailto:r.smith@brain.org.au" target="_blank">r.smith@brain.org.au</a>> escribió:</span><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite">
<div><div><div>Gabriel<br clear="all"></div><div><br></div><div>From that error message, it looks like you're running either MRtrix 0.2.8 or 0.2.9. The files I provided were from the subversion repository (which contains the most up-to-date code), but it would seem that there's an incompatibility between this code and the numbered releases.</div>
<div><br></div><div>The attached files (again to replace those in src/dwi/tractography/tracker/) should compile on either 0.2.8 or 0.2.9. They will fix the issue with the -stop command, without modifying the tracking in any other way.</div>
<div><br></div>Rob<br clear="all"><br>--<br><br>Robert Smith<br>Melbourne Brain Centre<br>245 Burgundy Street<br>Heidelberg VIC 3084<br>Telephone: <a href="tel:%28%2B61%203%29%209035%207128" value="+61390357128" target="_blank">(+61 3) 9035 7128</a><br>
Fax: <a href="tel:%28%2B61%203%29%209035%207301" value="+61390357301" target="_blank">(+61 3) 9035 7301</a><br></div>Email: <a href="mailto:r.smith@brain.org.au" target="_blank">r.smith@brain.org.au</a> <<a href="mailto:r.smith@brain.org.au" target="_blank">r.smith@brain.org.au</a>><br>
<a href="http://www.fni.edu.au" target="_blank">www.florey.edu.au</a> <a href="http://www.brain.org.au" target="_blank">www.brain.org.au</a><div><br><br>
<br><br><div class="gmail_quote">On Fri, Nov 25, 2011 at 8:23 PM, Gabriel Gonzalez Escamilla <span dir="ltr"><<a href="mailto:ggonesc@upo.es" target="_blank">ggonesc@upo.es</a> <<a href="mailto:ggonesc@upo.es" target="_blank">ggonesc@upo.es</a>>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div style="font-family: 'Times New Roman'; font-size: 16px;">Dear Robert, <br>I was trying to compile again the MRtrix, but it gave an error message:<br><br>ERROR: [CC] cmd/streamtrack.o<br><br>g++ -c wall -march=native -fPIC -fno-strict-aliasing -DGL_GLEXT_PROTOTYPES -DUSE_TR1 -03 -pthread -I/user/include/glibmm-2.4 -I/user/lib/glibmm-2.4/include -I/user/include/sigc++-2.0 -I/user/lib/sigc++-2.0/include -I/user/include/glib-2.0 -I/user/lib/glib-2.0/include -Ilib -Isrc cmd/streamtrack.cpp -o cmd/streamtrack.o<br>
<br>failed with ourtput:<br><br>cmd/streamtrack.cpp: In member function ´void Threader::execute(MR::DWITractography::Tracker::Base*)´:<br>cmd/streamtrack.cpp.270: error: no matching function for call to MR::DWI::Tractography::Tracker::Base::new_seed(const MR::Point&)´<br>
src/dwi/tractography/tracker/base.h:65: note: candidates are: void MR::DWI::Tractography::Tracker::Base::new_seed(const MR::Point&, float)<br><br><br><span>Do you have any idea of what's happening?<br><br>Best Regards,<br>
Gabriel<br></span></div>
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</div></div></blockquote></div><div><div><br>-- <br><font size="3">--------------------------<br>PhD. student Gabriel González-Escamilla<br>Laboratory of Functional Neuroscience<br>Department of Physiology, Anatomy, and Cell Biology<br>
University Pablo de Olavide<br>Ctra. de Utrera, Km.1<br>41013 - Seville<br>- Spain -<br><br>Email: <a href="mailto:ggonesc@upo.es" target="_blank">ggonesc@upo.es</a><br><a href="http://www.upo.es/neuroaging/es/" target="_blank">http://www.upo.es/neuroaging/es/</a></font>
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