<div dir="ltr">Hi David,<div><br></div><div>I don't think there's any way of doing what you're trying to achieve in MRtrix 0.2.x - MRtrix3 on the other hand includes the whole <a href="http://www.ncbi.nlm.nih.gov/pubmed/22705374">ACT framework</a>, which is designed for this, amongst other things.</div><div><br></div><div>Cheers,</div><div>Donald.</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 5 December 2014 at 10:13, Romascano David <span dir="ltr"><<a href="mailto:david.romascano@epfl.ch" target="_blank">david.romascano@epfl.ch</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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<p class="MsoNormal">Hi everyone, <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span lang="EN-US">I’m trying to generate 100'000 fibers that start and end near the GM, and seeding randomly from the WM.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Following this post (<a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2011-October/000289.html" target="_blank">www.nitrc.org/pipermail/mrtrix-discussion/2011-October/000289.html</a>), I manage to create tracks that connect
the left thalamus with the left cortex for example, by running the following command:<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">streamtrack -seed WM_mask.nii -mask WM_mask.nii -include R_thalamus_mask.nii -include R_cortex_mask.nii -number 10000 -maxnum 100000 -minlength 10 -step 1 -nomaskinterp -stop SD_PROB FODsh.mif fibers.tck<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">I then tried to generate fibers that start and end near the GM. To filter tracks that end near the GM, I dilated my GM mask and set it twice as an inclusion ROI in the command:<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">streamtrack -seed WM_mask.nii -mask WM_mask.nii -include GM_dil_mask.nii -include GM_dil_mask.nii -number 10000 -maxnum 100000 -minlength 10 -step 1 -nomaskinterp -stop SD_PROB FODsh.mif fibers.tck<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">But then some of the selected fibers end inside the WM… Assigning them to the nearest GM region doesn’t seem realistic.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">I tried to run using ‘-include ROI1.nii –include ROI2.nii’ where ROI1 and ROI2 are both copies of the GM_dil_mask, but it didn’t change the output. Running the command without the “-mask” option didn’t help either.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">I thought about running streamtrack separately for each of the GM dilated regions, using ROI1 = the corresponding dilated GM region and ROI2 = all other dilated regions, and then concatenate all the track files, but this
would bias the tracking because of the different sizes of the GM regions right ?<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Does anyone have an idea on how I could proceed ?<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks in advance and best regards,<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">David Romascano<u></u><u></u></span></p>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><b><font color="#990000">Dr J-Donald Tournier (PhD)</font></b><br><div><font color="#990000"><br></font></div><i><font color="#990000">Senior Lecturer, </font></i><i><font color="#990000">Biomedical Engineering</font></i><div><i><font color="#990000">Division of Imaging Sciences & Biomedical Engineering<br>King's College London</font></i><div><i><font color="#990000"><br></font></i></div><div><i><font color="#990000"><b style="font-family:Calibri,sans-serif;font-size:15px"><span style="font-size:10pt">A:</span></b><span style="font-family:Calibri,sans-serif;font-size:10pt"> Department of Perinatal Imaging & Health, 1<sup>st</sup> Floor South Wing, St Thomas' Hospital, London. SE1 7EH</span><br></font></i></div><div><i><font color="#990000"><b>T:</b> +44 (0)20 7188 7118 ext 53613</font></i></div></div><div><i><font color="#990000"><b>W:</b> <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a></font></i><br></div></div></div>
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