<div dir="ltr">Hi Ayca,<div><br></div><div>It's difficult to figure out what the problem from so little information - it would be better if you could provide the commands used, and any output from them. However, from what you say I think the most likely issue is that you've tried to use an image of atlas labels as an ROI in MRtrix? I don't think converting from nii to mif is going to make any difference here, the main issue is that streamtrack (or tckgen if you're using MRtrix3) expects each -seed, -include, -exclude or -mask image to be a binary ROI - it should only correspond to a single structure. The atlas-supplied ROIs are most likely integer images with different values for each structure. So it would be useless as a seed or include region, you need to extract the particular index you're interested in. I don't think there's a neat way to do this in MRtrix 0.2, but in MRtrix3, this would be a simple matter of "mrmath atlas.nii 4 -eq roi4.nii" to extract index 4 for example. </div><div><br></div><div>Apologies if that's not the problem - in that case, please post as much information as you can to help us figure out the issue.</div><div><br></div><div>Cheers,</div><div>Donald.</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 16 October 2015 at 22:57, Ayça Altınkaya <span dir="ltr"><<a href="mailto:ayca.altinkaya@gmail.com" target="_blank">ayca.altinkaya@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">
<p>Hi,</p>
<p><br></p>
<p>I want to use some anatomical structures from known atlases as ROI. I converted individual structure files from nii to mif. And tried to use the file’s path as seed or include ROI. </p>
<p>Program seems to be run and calculate a tract. But when I display the tract and ROI together, I never see the ROI. And tract seems doesn’t use my structure file.</p>
<p><br></p>
<p>Could you please help me?</p>
<p><br></p>
<p>Thank you,</p>
<p><br></p>
<p>Ayca</p></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><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></font></i></div><div><i><font color="#990000"><b>T:</b> +44 (0)20 7188 7118 ext 53613</font></i></div></div><div><i><font color="#990000"><b>W:</b> <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a></font></i><br></div></div></div>
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