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<p class="MsoNormal"><span style="color:#1F497D">Dear Thijs<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thank you for the quick response!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I understand what you have said, and it makes sense. Do you recommend either option as being more ‘anatomically’ correct?
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">What is interesting is that with option b, I got a better tract, even though as you say more streamlines may have stayed in there…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thanks again!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">z<o:p></o:p></span></p>
<p class="MsoNormal"><span style="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";mso-fareast-language:EN-GB">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-fareast-language:EN-GB"> mrtrix-discussion-bounces@www.nitrc.org
[mailto:mrtrix-discussion-bounces@www.nitrc.org] <b>On Behalf Of </b>Thijs Dhollander<br>
<b>Sent:</b> 22 May 2013 20:57<br>
<b>To:</b> mrtrix-discussion@www.nitrc.org<br>
<b>Subject:</b> [Mrtrix-discussion] RE: mask ROI<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Hi Zita,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">There is in fact a difference between both scenarios: tracks which enter an exclusion ROI are entirely discarded, while tracks which leave a mask are just stopped (but not discarded if they meet
the other requirements, e.g. the minimum track length, at that point).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Qualitatively, in the final distribution of accepted tracks, you are thus likely to see (a lot) less tracks ending “on” (i.e. very near) the boundary of the exclusion ROIs in scenario (a), as opposed
to scenario (b). Also, scenario (a) will take longer to obtain an equal amount of accepted tracks, as opposed to scenario (b).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Thijs<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="NL-BE" style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#00A1D6;mso-fareast-language:NL-BE">Thijs Dhollander</span></b><span lang="NL-BE" style="font-size:12.0pt;font-family:"Arial","sans-serif";color:#1F497D;mso-fareast-language:NL-BE"><br>
</span><span lang="NL-BE" style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#595959;mso-fareast-language:NL-BE">PhD Student</span><span lang="NL-BE" style="font-size:12.0pt;font-family:"Arial","sans-serif";color:#595959;mso-fareast-language:NL-BE"><br>
</span><span lang="NL-BE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#595959;mso-fareast-language:NL-BE"><br>
<a href="mailto:thijs.dhollander@uzleuven.be"><span style="color:#595959;text-decoration:none">thijs.dhollander@uzleuven.be</span></a><br>
tel. +32 16 34 90 37<br>
gsm. +32 475 36 44 27</span><b><span lang="NL-BE" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959;mso-fareast-language:NL-BE"><br>
<br>
</span></b><b><span lang="NL-BE" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#00A1D6;mso-fareast-language:NL-BE">Medical Image Computing (KU Leuven, ESAT/PSI, MIC)<br>
</span></b><span lang="NL-BE" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959;mso-fareast-language:NL-BE">Medical Imaging Research Center | UZ Gasthuisberg | Herestraat 49 - bus 7003 | B-3000 Leuven |
<a href="http://www.medicalimagingcenter.be/"><span style="color:#595959;text-decoration:none">http://www.medicalimagingcenter.be</span></a></span><span lang="NL-BE" style="font-family:"Arial","sans-serif";color:#595959;mso-fareast-language:NL-BE"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="NL-BE" style="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";mso-fareast-language:NL-BE">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-fareast-language:NL-BE">
<a href="mailto:mrtrix-discussion-bounces@public.nitrc.org">mrtrix-discussion-bounces@public.nitrc.org</a> [<a href="mailto:mrtrix-discussion-bounces@public.nitrc.org">mailto:mrtrix-discussion-bounces@public.nitrc.org</a>]
<b>On Behalf Of </b>Patai, Zita<br>
<b>Sent:</b> Wednesday, May 22, 2013 21:39<br>
<b>To:</b> <a href="mailto:mrtrix-discussion@www.nitrc.org">mrtrix-discussion@www.nitrc.org</a><br>
<b>Subject:</b> [Mrtrix-discussion] mask ROI<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal">Dear MrTrixers<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Just checking that there is no difference in the ‘quality’ or ‘number of streamlines’ generated if I do<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="mso-list:Ignore">a)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>a mask of whole brain but include many exclusion ROIs<o:p></o:p></p>
<p class="MsoListParagraph">or<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo2"><![if !supportLists]><span style="mso-list:Ignore">b)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>a mask ROI which is smaller than the whole brain and is already excluding those regions which I did as –exclude above<o:p></o:p></p>
<p class="MsoNormal">?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Many thanks!<o:p></o:p></p>
<p class="MsoNormal">zita<o:p></o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">_________________________<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Eva Zita Patai<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Postdoctoral Research Associate<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">UCL, Institute of Child Health<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB"><a href="mailto:e.patai@ucl.ac.uk">e.patai@ucl.ac.uk</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">020 7905 2730<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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