<div dir="ltr">Hi <span style="font-size:12.8px;white-space:nowrap">Ilaria,</span><div><span style="font-size:12.8px;white-space:nowrap"><br></span></div><div><span style="font-size:12.8px;white-space:nowrap">If you combine the two ROIs into a single image, then filter_tracks will treat that singular image as a single ROI, and<br>hence operate on any track that touches any highlighted voxel in that image.<br>This is why any track touching <i>either</i> of the two ROIs is being removed.</span></div><div><span style="font-size:12.8px;white-space:nowrap"><br></span></div><div><span style="font-size:12.8px;white-space:nowrap">In order to perform your desired operation (remove all tracks that touch both ROIs), you want to use the following:</span></div><div><span style="font-size:12.8px;white-space:nowrap"><br></span></div><div><span style="font-size:12.8px;white-space:nowrap"><font face="monospace, monospace">filter_tracks in.tck -include ROI1.mif -include ROI2.mif -invert out.tck</font></span></div><div><span style="font-size:12.8px;white-space:nowrap"><br></span></div><div><span style="font-size:12.8px;white-space:nowrap">By providing the two ROIs separately to filter_tracks using separate -include options, you are specifying that you are</span></div><div><span style="font-size:12.8px;white-space:nowrap">interested only in tracks that touch both ROIs. The -invert option then specifies that those streamlines elected by the</span></div><div><span style="font-size:12.8px;white-space:nowrap">ROIs are to be <i>excluded</i> from the output, rather than being the only streamlines included in the output.</span></div><div><span style="font-size:12.8px;white-space:nowrap"><br></span></div><div><span style="font-size:12.8px;white-space:nowrap">Cheers</span></div><div><span style="font-size:12.8px;white-space:nowrap">Rob</span></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><br>--<br><br><span style="color:rgb(255,102,0)"><b>Robert Smith, Ph.D</b><br>Senior 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: +61 3 9035 7128<br>Fax: +61 3 9035 7301<br><a href="http://www.florey.edu.au/" target="_blank">www.florey.edu.au</a><br></div></div><div dir="ltr"><br></div><div><i>MRtrix3</i>: Advanced tools for the analysis of diffusion MRI data</div><div><a href="http://www.mrtrix.org/" target="_blank">Website</a> - <a href="http://www.mrtrix.org/blog/" target="_blank">Blog</a> - <a href="https://github.com/MRtrix3/mrtrix3" target="_blank">Repository</a> - <a href="http://community.mrtrix.org/" target="_blank">Community forum</a></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Mon, Jun 12, 2017 at 4:18 AM, Ilaria Sani <span dir="ltr"><<a href="mailto:isani01@mail.rockefeller.edu" target="_blank">isani01@mail.rockefeller.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear All,<br>
<br>
I'm using Mrtrix 0.2<br>
<br>
I would like to remove some specific tracks from my connectome. Specifically all the tracks between two ROIs.<br>
<br>
The closest thing I found is filter_tracks.<br>
The ROI I’m using is the combination of the two ROIs.<br>
However filter_tracks removes all the streamlines touching one OR the other ROI.<br>
<br>
Is there a way to select only the streamlines touching both?<br>
Alternatively, is there any other tool that removes tracks between two ROIs from the connectome?<br>
<br>
Thanks!!<br>
<br>
Ilaria<br>
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