Hi Marc,<div><br></div><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><font face="Helvetica, Verdana, Arial"><span style="font-size:11pt">We have a couple of questions regarding the tractography mechanics involved in MRtrix<br>
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1. How does Mrtrix start sampling tracts from ROI’s? That is, if you provide an ROI how does MRtric decide where to start the tract from? From the boundary of the ROI or from the centre? Do you take into account if the ROI overlaps grey and white matter? <br>
</span></font></div></blockquote><div><br></div><div>The seeding is random, with uniform probability over the whole ROI. For a spherical ROI, any point within the specified radius of the specified centre is a candidate. For a mask ROI, any point with intensity greater than 0.5 after tri-linear interpolation is a candidate.</div>
<div><br></div><div>In terms of dealing with the overlap with grey/white matter: basically it'll try to seed regardless, but only succeed if the seed point and direction are appropriate. First a seed point is drawn from the ROI. Then a starting orientation is drawn at random with uniform probability over the sphere (unless initdir has been specified). Finally, if the starting conditions are satisfied, tracking will start from that seed along that direction. For tensor tracking, the starting condition is simply that the FA is above initcutoff. For SD-based tracking, the starting condition is that the FOD amplitude along the starting direction is above initcutoff.</div>
<div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><font face="Helvetica, Verdana, Arial"><span style="font-size:11pt">
2. We are also interested in your thoughts on putting a “weighting” on tract length. <br>
A number of studies suggest that if were using a simple deterministic tracking algorithm to measure connections between multiple ROI’s we should weigh long tracts since there is bias towards longer tracts. Does the same apply for your algorithms? We were even suspecting that using the probabilistic tracking option there would be bias against longer tracts? <br>
</span></font></div></blockquote><div><br></div><div>That's the first I've heard about penalising long tracts for deterministic tracking - maybe that's just a reflection of the fact that I'm somewhat biased towards probabilistic approaches... In any case, for probabilistic tracking (including streamtrack's SD_PROB method), the consensus is that there is a bias towards shorter tracks. How best to deal with it is something that still hasn't been addressed satisfactorily. Probably the most relevant work in this area is Morris et al., Neuroimage 42: 1329-1339. I'm not convinced this will necessarily solve the bigger problem though, which is how to properly interpret these 'connectivity' measures, a problem that Derek Jones describes very eloquently in his 2010 paper "Challenges and limitations of quantifying brain connectivity in vivo with diffusion MRI", Imaging in Medicine 2: 341-355.</div>
<div><br></div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br></div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><font face="Helvetica, Verdana, Arial"><span style="font-size:11pt">
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cheers<br>
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Marc<br>
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</span></font><blockquote><span style="font-size:11pt"><font color="#0080FF"><font face="Calibri, Verdana, Helvetica, Arial"><b>Marc Seal<br>
</b></font></font><font face="Calibri, Verdana, Helvetica, Arial"><b><font color="#000080">Group Leader, Developmental Imaging, Murdoch Childrens Research Institute<br>
Senior Research Fellow, Department of Paediatrics, The University of Melbourne<br>
<br>
</font></b>The Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia<br>
M 0423 606 185 | T +61 3 9345 4310 | F +61 3 9345 4325 <br>
E <a href="http://marc.seal@mcri.edu.au" target="_blank">marc.seal@mcri.edu.au</a><br>
<a href="http://www.mcri.edu.au" target="_blank">www.mcri.edu.au</a><br>
<br>
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