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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">Hi Gabriel,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">Your tracks are seeded (i.e. started) from a seed region, and they are constrained to stay in the mask (i.e. they stop -but are not discarded- if
they bump into the edge of your mask). So if I understand your goal right (you want to perform a "within-ROI-tractography"), you'd want to set your ROI as both your seed and mask region.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">Using the full brain as a seed and the ROI (which is a sub-region of the brain, I suppose) as mask, makes no sense (even though the results will
be the same): no tracks will start from the full brain, outside the ROI, anyway; as they are already outside your mask.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">In conclusion, it's of no use to seed in regions that are not at least contained within the mask.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">Hope this helps! :-)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">Greetings,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">Thijs<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#00A1D6">Thijs Dhollander</span></b><span style="font-family:"Arial","sans-serif";color:#1F497D"><br>
</span><span style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#666666">PhD Student</span><span style="font-family:"Arial","sans-serif";color:#1F497D"><br>
</span><span style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D"><br>
</span><span style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#666666">thijs.dhollander@uz.kuleuven.ac.be<br>
tel. +32 16 34 90 37<br>
gsm. +32 475 36 44 27</span><b><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#00A1D6"><br>
<br>
Medical Image Computing (K.U.Leuven, ESAT/PSI, MIC)<br>
</span></b><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#666666">Medical Imaging Research Center | UZ Gasthuisberg | Herestraat 49 - bus 7003 | B-3000 Leuven | http://www.medicalimagingcenter.be</span><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> mrtrix-discussion-bounces@public.nitrc.org [mailto:mrtrix-discussion-bounces@public.nitrc.org]
<b>On Behalf Of </b>Gabriel Gonzalez Escamilla<br>
<b>Sent:</b> vrijdag 21 oktober 2011 17:40<br>
<b>To:</b> mrtrix-discussion@public.nitrc.org; mrtrix-discussion@public.nitrc.org<br>
<b>Subject:</b> [Mrtrix-discussion] help with streamtrack<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">Hello dear mrtrix experts and users, I'm new in usin this excellent tool.<br>
<br>
And as I'm new with it, I have a doubt, which I guess is not so complicated to you,<br>
<br>
I'm wondering which would be the best way to perform the streamtrack for a within ROI tractography. I'd look at the options, an saw that I can use a seed region and a mask region for this proposal, as describeed in the documentation I know that must use the
-mask option but wondering if I should use the same ROI as seed region, or should enter the entire brain mask?.<br>
<br>
Any help will be appreciated<br>
<br>
Thanks in advanced,<br>
Gabriel<br>
<br>
<o:p></o:p></span></p>
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