<div dir="ltr"><div>$ streamtrack SD_PROB csd.mif -seed seed_mask.nii -include target_mask.nii your_tracks.tck</div><div><br></div>This should all be documented here:<div><a href="http://www.brain.org.au/software/mrtrix/tractography/tracking.html#mask">http://www.brain.org.au/software/mrtrix/tractography/tracking.html#mask</a><br>
</div><div class="gmail_extra">Hopefully this is sufficiently detailed to answer any other questions you might have.</div><div class="gmail_extra"><br></div><div class="gmail_extra">Cheers,</div><div class="gmail_extra">Donald.</div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On 18 November 2013 11:27, Markus Gschwind <span dir="ltr"><<a href="mailto:markus.gschwind@gmail.com" target="_blank">markus.gschwind@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Yachao Xie</b> <span dir="ltr"><<a href="mailto:yachaoxiexie@gmail.com" target="_blank">yachaoxiexie@gmail.com</a>></span><br>
Date: 2013/11/18<br>Subject: Re: Mrtrix discussion<br>To: Markus Gschwind <<a href="mailto:markus.gschwind@gmail.com" target="_blank">markus.gschwind@gmail.com</a>><br><br><br><div dir="ltr">Hi friends,<div> I have <span style="font-family:arial,sans-serif;font-size:14px">created two separate files.What about the next step?</span></div>
<div><span style="font-family:arial,sans-serif;font-size:14px"> Best wishes.</span></div>
</div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/11/18 Yachao Xie <span dir="ltr"><<a href="mailto:yachaoxiexie@gmail.com" target="_blank">yachaoxiexie@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi，<div>I will try it soon.Thank you very much.</div><div>Best wishes.</div></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/11/18 Markus Gschwind <span dir="ltr"><<a href="mailto:markus.gschwind@gmail.com" target="_blank">markus.gschwind@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>Hi,</div>
<div> </div>
<div>this is manual editing as a explained in my former mail. either you cut the mask in 2 halves or you copy it twice and erase the other ROI in each of them. I do not know with what tools you are familair, but it should be possible in every package.</div>
<div> </div>
<div>Best.</div><div><div>
<div>Markus<br></div>
<div class="gmail_quote">2013/11/18 Yachao Xie <span dir="ltr"><<a href="mailto:yachaoxiexie@gmail.com" target="_blank">yachaoxiexie@gmail.com</a>></span><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div dir="ltr">Hi dear friends,
<div> Thanks for your reply.Can you give me some codes or processes about this question？</div>
<div> Best wishes.</div></div>
<div>
<div>
<div class="gmail_extra"><br><br>
<div class="gmail_quote">2013/11/18 Markus Gschwind <span dir="ltr"><<a href="mailto:markus.gschwind@gmail.com" target="_blank">markus.gschwind@gmail.com</a>></span><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div>Hi,</div>
<div> </div>
<div>You would need to separate the two ROIs and create two separate files (copy the file and erase manuall on ROI in both files)</div>
<div> </div>
<div>Best,</div>
<div>Markus<br><br></div>
<div>
<div>
<div class="gmail_quote">2013/11/18 Yachao Xie <span dir="ltr"><<a href="mailto:yachaoxiexie@gmail.com" target="_blank">yachaoxiexie@gmail.com</a>></span><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div dir="ltr">Hi friends,
<div> Excuse me for disturbing you.I knew you from the NITRC.I have a question about the mrtrix.I have a nii file with only two ROIs.I want to track fibers form one ROI to another.Could you give some suggestion to me?</div>
<div> Hope for your reply.</div>
<div> thank you.best wishes.</div></div></blockquote></div><br></div></div></blockquote></div><br></div></div></div></blockquote></div><br>
</div></div></blockquote></div><br></div>
</div></div></blockquote></div><br></div>
</div></div></div><br></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><b><font color="#990000">Dr J-Donald Tournier (PhD)</font></b><br><div><font color="#990000"><br></font></div><i><font color="#990000">Senior Lecturer, </font></i><i><font color="#990000">Biomedical Engineering</font></i><div>
<i><font color="#990000">Division of Imaging Sciences & Biomedical Engineering<br>King's College London</font></i><div><i><font color="#990000"><br></font></i></div><div><i><font color="#990000"><b style="font-family:Calibri,sans-serif;font-size:15px"><span style="font-size:10pt">A:</span></b><span style="font-family:Calibri,sans-serif;font-size:10pt"> Department of Perinatal Imaging & Health, 1<sup>st</sup> Floor South Wing, St Thomas' Hospital, London. SE1 7EH</span><br>
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