<div dir="ltr">Hi, <div><br></div><div>I'm afraid I have to idea about nipype... My only guess is that the MRtrix commands need to be available in your PATH, but that's just a guess. Your best bet is to contact the nipype people...</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 December 2014 at 17:37, anvi vora <span dir="ltr"><<a href="mailto:anvikvora@gmail.com" target="_blank">anvikvora@gmail.com</a>></span> wrote:<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div dir="ltr" style="font-size:13px">Hello,<div><br></div><div>I am attempting to run a pipeline from nipype which wraps mrtrix. </div><div><br></div><div>It is the script called dmri_mrtrix_dti</div><div><br></div><div>I have installed the mrtrix and compiled it successfully for my macbook.</div><div><br></div><div>I get the following error, which seems to indicate that I do not have all the required binaries: I looked and I couldn't find these commands in bin folder. Any help is appreciated!!! Thank you</div><div><br></div><div><pre style="white-space:pre-wrap;padding:0px;font-size:14px;color:rgb(0,0,0);border-top-left-radius:0px;border-top-right-radius:0px;border-bottom-right-radius:0px;border-bottom-left-radius:0px;margin-top:0px;margin-bottom:0px;line-height:17.000059127807617px;word-break:break-all;word-wrap:break-word;background-color:rgb(255,221,221);border:0px;vertical-align:baseline">ERROR:workflow:could not run node: dwiproc.tractography.tensor2fa.a0
INFO:workflow:crashfile: /Users/macbook/Desktop/crash-20141215-235215-macbook-tensor2fa.a0.npz
ERROR:workflow:could not run node: dwiproc.tractography.tensor2adc.a0
INFO:workflow:crashfile: /Users/macbook/Desktop/crash-20141215-235215-macbook-tensor2adc.a0.npz
ERROR:workflow:could not run node: dwiproc.tractography.tensor2vector.a0
INFO:workflow:crashfile: /Users/macbook/Desktop/crash-20141215-235215-macbook-tensor2vector.a0.npz
ERROR:workflow:could not run node: dwiproc.tractography.gen_WM_mask.a0
INFO:workflow:crashfile: /Users/macbook/Desktop/crash-20141215-235215-macbook-gen_WM_mask.a0.npz
ERROR:workflow:could not run node: dwiproc.tractography.threshold_b0.a0
INFO:workflow:crashfile: /Users/macbook/Desktop/crash-20141215-235215-macbook-threshold_b0.a0.npz
INFO:workflow:***********************************</pre></div></div><div style="font-size:13px"></div></div>
<br>_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
<br></blockquote></div><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>
</div>