<p dir="ltr">Thank you Robert. I hadn't realized the flags can be used multiple times.</p>
<p dir="ltr">Best wishes.<br>
Dorian</p>
<div class="gmail_quote">On Jul 22, 2014 10:47 PM, "Robert Smith" <<a href="mailto:robert.smith@florey.edu.au">robert.smith@florey.edu.au</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div><div><div><div>Dorian<br><br></div>Both the <span style="font-family:courier new,monospace">-include</span> and <span style="font-family:courier new,monospace">-exclude</span> options in <span style="font-family:courier new,monospace">filter_tracks</span> can be used multiple times in the one command invocation, just as they can in <span style="font-family:courier new,monospace">streamtrack</span>. So if you have two ROIs, and want to select only those streamlines that go through <i>both</i> of the ROIs (essentially a boolean AND operation), your usage should look something like:<br>
</div><span style="font-family:courier new,monospace">filter_tracks in.tck out.tck -include ROI1.mif -include ROI2.mif</span><br><br></div>From your text I am guessing that you have combined your two ROIs into a single image using <span style="font-family:courier new,monospace">mradd</span>, then passed this image to <span style="font-family:courier new,monospace">filter_tracks</span> using <span style="font-family:courier new,monospace">-include</span>? In this scenario, any streamline that enters <i>any</i> part of the ROI passed to <span style="font-family:courier new,monospace">filter_tracks</span> will be included (essentially a boolean OR operation): the command does not consider whether or not an individual ROI image contains discrete 'blobs', it just tests to see if the streamline intersects the ROI at any point along its length. This is most likely why your result contains unwanted streamlines: some of them traverse one endpoint of the optic tract but not the other.<br>
<br></div>Hopefully that clarifies the issue<br>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: <a href="tel:%2B61%203%209035%207128" value="+61390357128" target="_blank">+61 3 9035 7128</a><br>
Fax: <a href="tel:%2B61%203%209035%207301" value="+61390357301" target="_blank">+61 3 9035 7301</a><br><a href="http://www.florey.edu.au/" target="_blank">www.florey.edu.au</a><br>
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<br><br><div class="gmail_quote">On Wed, Jul 23, 2014 at 4:11 AM, Dorian P. <span dir="ltr"><<a href="mailto:alb.net@gmail.com" target="_blank">alb.net@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"><span style="font-family:arial,sans-serif;font-size:12.666666984558105px">Hi all,</span>
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<div style="font-family:arial,sans-serif;font-size:12.666666984558105px">I am currently using MRtrix2 (yeah, I know is the old version) to do tractography of the optic tract. I have success when using a seed (+ an include roi + an exclude roi). However, when
trying to select this pathway from full brain tractography it does not work for me. The command filter_tracks accepts only an include roi and an exclude roi. I collapsed my previous seed and include roi to obtain a new include roi for the full brian filter.
Yet, the result is not at all similar to the seed-based tractography, with a lot of pathways not related to the optic tract.</div>
<div style="font-family:arial,sans-serif;font-size:12.666666984558105px"><br>
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<div style="font-family:arial,sans-serif;font-size:12.666666984558105px">Is there a way to use better the filter_tracks, i.e., to have more than one include roi, such tracts are selected that pass both in roi1 AND in roi2. The help of filter_tracks states "-include:
Tracks that enter ALL such inclusion ROI will be included.". So doesn't seem to consider separate portions of rois to get the tracks that connect them.</div>
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<div style="font-family:arial,sans-serif;font-size:12.666666984558105px">P.s. I am using Windows.</div>
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<div style="font-family:arial,sans-serif;font-size:12.666666984558105px">Thank you</div>
<div style="font-family:arial,sans-serif;font-size:12.666666984558105px">Dorian</div>
<div style="font-family:arial,sans-serif;font-size:12.666666984558105px">TJU</div>
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