<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; ">Thanks Donald,<div><br></div><div>our problem is that the tracks I described above go through regions where white matter is missing, </div><div><br></div><div>what do you think about using a white matter mask instead of an FA derived one?</div><div><br></div><div>in this case I would use a WM mask obtained by a well registered (to DTI) and well segmented T1w volume, </div><div>for example by using ANTS with multivariate registration T1w->FA and T1w->b0 </div><div><br></div><div>fabrizio</div><div><br></div></span><div><div>On Sep 20, 2011, at 10:42 AM, Donald Tournier wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Fabrizio,<div><br></div><div>You might find your question has already been partly answered here:</div><div><a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2011-May/000207.html">http://www.nitrc.org/pipermail/mrtrix-discussion/2011-May/000207.html</a><br>
<br></div><div>This is the relevant section:</div><div><br></div><div><div><i>For both SD_ methods, the cutoff actually refers to the FOD amplitude in the direction of tracking - FA is NEVER considered for these tracking methods. </i></div>
</div><div><br></div><div>If you truly want the tracking to stop based on FA, you could threshold the FA map at your desired level and use the resulting mask with streamtrack and the -mask option. I wouldn't recommend this though, the whole point of MRtrix and CSD is to avoid using tensor-derived measures since they are hopelessly inadequate in crossing fibre regions...</div>
<div><br></div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br><div class="gmail_quote">On 20 September 2011 18:30, Fabrizio Fasano <span dir="ltr"><<a href="mailto:hank7v@gmail.com">hank7v@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Dear all,<div><br></div><div>I used the following command </div><div><br></div><div>>streamtrack SD_PROB CSD10.mif -seed ROIseed.nii -include ROItarget.nii -mask mask.mif -num 100 -maxnum 100000 seed2target.tck</div>
<div>
<br></div><div>and the resulting tracks in mrview go through regions with very low FA (0.03, 0.07, etc) when it was expected a cutoff of FA>0.1, the same happened when I directly used the option -cutoff 0.1</div><div>
NB. in mrview I didn't use a slice thickness (crop to slab) 2.0 and my slice thickness is 1.5mm</div>
<div><br></div><div>any suggestion to be sure to force the procressing to stop if FA>0.1?</div><div><br></div><div>thank you a lot,</div><div><br></div><font color="#888888"><div>fabrizio</div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Jacques-Donald Tournier (PhD)<br>Brain Research Institute, Melbourne, Australia<br>Tel: +61 (0)3 9035 7033<br>
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