Zita<div><br></div><div>Thijs is entirely correct in his description of the difference between the two cases.</div><div><br></div><div>The reason you get a 'better' tract with the second approach is because all streamlines that leave the mask are terminated, and most likely the vast majority of those streamlines will be retained. With the first option, whether or not a streamline is kept or discarded will depend on whether it terminates just before the exclusion mask, or just reaches the exclusion mask. This is placing a large emphasis on the appropriate termination of streamlines, which is notoriously difficult using only the diffusion information.</div>
<div><br></div><div>For instance, consider a situation where you have used the brain parenchyma as the tracking mask, and the area outside the brain as an exclusion mask. In one grey matter voxel with a supra-threshold FOD, the streamlines may cross the voxel, enter the exclusion region, and be rejected; while in the voxel adjacent to it with a sub-threshold FOD, the streamlines are terminated in that voxel, and therefore retained (as they do not reach the exclusion mask). This will result in a poorly reconstructed tract, as many of its components will be missing.</div>
<div><br></div><div>The ill-posed problem of streamline termination is precisely why I implemented the <a href="http://www.sciencedirect.com/science/article/pii/S1053811912005824">Anatomically-Constrained Tractography</a> framework. If you have image data for performing EPI susceptibility distortion correction, you'll be able to use this in the next major MRtrix release.</div>
<div><br></div><div>Remember: an exclusion mask results in the complete rejection of any streamlines that enter it. If you want to 'exclude' streamlines from traversing a particular area, i.e. terminate any streamlines that attempt to enter that area (but still keep those streamlines), omit that area from your propagation mask.</div>
<div><br></div><div>Rob</div><div><br>--<br><br><span style="color:rgb(255,102,0)"><b>Robert Smith</b><br>Post-Doctoral Researcher, 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><span style="font-size:9pt;font-family:"Times New Roman","serif";color:red"></span></div>
<br><br><div class="gmail_quote">On Thu, May 23, 2013 at 6:15 AM, Patai, Zita <span dir="ltr"><<a href="mailto:e.patai@ucl.ac.uk" target="_blank">e.patai@ucl.ac.uk</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"><span style="color:#1f497d">Dear Thijs<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d">Thank you for the quick response!<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d"><u></u> <u></u></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?
<u></u><u></u></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…<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d">Thanks again!<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d">z<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d"><u></u> <u></u></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""> <a href="mailto:mrtrix-discussion-bounces@www.nitrc.org" target="_blank">mrtrix-discussion-bounces@www.nitrc.org</a>
[mailto:<a href="mailto:mrtrix-discussion-bounces@www.nitrc.org" target="_blank">mrtrix-discussion-bounces@www.nitrc.org</a>] <b>On Behalf Of </b>Thijs Dhollander<br>
<b>Sent:</b> 22 May 2013 20:57<br>
<b>To:</b> <a href="mailto:mrtrix-discussion@www.nitrc.org" target="_blank">mrtrix-discussion@www.nitrc.org</a><br>
<b>Subject:</b> [Mrtrix-discussion] RE: mask ROI<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1f497d">Hi Zita,<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1f497d"><u></u> <u></u></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).<u></u><u></u></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).<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1f497d">Cheers,<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1f497d">Thijs<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1f497d"><u></u> <u></u></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">Thijs Dhollander</span></b><span lang="NL-BE" style="font-size:12.0pt;font-family:"Arial","sans-serif";color:#1f497d"><br>
</span><span lang="NL-BE" style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#595959">PhD Student</span><span lang="NL-BE" style="font-size:12.0pt;font-family:"Arial","sans-serif";color:#595959"><br>
</span><span lang="NL-BE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#595959"><br>
<a href="mailto:thijs.dhollander@uzleuven.be" target="_blank"><span style="color:#595959;text-decoration:none">thijs.dhollander@uzleuven.be</span></a><br>
tel. <a href="tel:%2B32%2016%2034%2090%2037" value="+3216349037" target="_blank">+32 16 34 90 37</a><br>
gsm. <a href="tel:%2B32%20475%2036%2044%2027" value="+32475364427" target="_blank">+32 475 36 44 27</a></span><b><span lang="NL-BE" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959"><br>
<br>
</span></b><b><span lang="NL-BE" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#00a1d6">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">Medical Imaging Research Center | UZ Gasthuisberg | Herestraat 49 - bus 7003 | B-3000 Leuven |
<a href="http://www.medicalimagingcenter.be/" target="_blank"><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"><u></u><u></u></span></p>
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<p class="MsoNormal"><span lang="NL-BE" style="color:#1f497d"><u></u> <u></u></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"">
<a href="mailto:mrtrix-discussion-bounces@public.nitrc.org" target="_blank">mrtrix-discussion-bounces@public.nitrc.org</a> [<a href="mailto:mrtrix-discussion-bounces@public.nitrc.org" target="_blank">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" target="_blank">mrtrix-discussion@www.nitrc.org</a><br>
<b>Subject:</b> [Mrtrix-discussion] mask ROI<u></u><u></u></span></p>
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<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal">Dear MrTrixers<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Just checking that there is no difference in the ‘quality’ or ‘number of streamlines’ generated if I do<u></u><u></u></p>
<p><u></u><span>a)<span style="font:7.0pt "Times New Roman"">
</span></span><u></u>a mask of whole brain but include many exclusion ROIs<u></u><u></u></p>
<p>or<u></u><u></u></p>
<p><u></u><span>b)<span style="font:7.0pt "Times New Roman"">
</span></span><u></u>a mask ROI which is smaller than the whole brain and is already excluding those regions which I did as –exclude above<u></u><u></u></p>
<p class="MsoNormal">?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Many thanks!<u></u><u></u></p>
<p class="MsoNormal">zita<u></u><u></u></p>
<p class="MsoNormal"><span>_________________________<u></u><u></u></span></p>
<p class="MsoNormal"><span>Eva Zita Patai<u></u><u></u></span></p>
<p class="MsoNormal"><span>Postdoctoral Research Associate<u></u><u></u></span></p>
<p class="MsoNormal"><span>UCL, Institute of Child Health<u></u><u></u></span></p>
<p class="MsoNormal"><span><a href="mailto:e.patai@ucl.ac.uk" target="_blank">e.patai@ucl.ac.uk</a><u></u><u></u></span></p>
<p class="MsoNormal"><span>020 7905 2730<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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