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<p>Hi,</p>
<p>please open the file "dwi2cond", which is in the simnibs/bash_modules
subfolder of your simnibs installation and change (around line 56)<br>
</p>
<p>EDDYOPT=<span class="pl-s"><span class="pl-pds">'</span>--repol<span
class="pl-pds">'</span></span></p>
<p><span class="pl-s"><span class="pl-pds">to</span></span></p>
<p><span class="pl-s"><span class="pl-pds">EDDYOPT=<span
class="pl-s"><span class="pl-pds">'</span><span
class="pl-pds">'</span></span></span></span></p>
<p><span class="pl-s"><span class="pl-pds"><span class="pl-s"><span
class="pl-pds">Best regards,</span></span></span></span></p>
<p><span class="pl-s"><span class="pl-pds"><span class="pl-s"><span
class="pl-pds">Axel</span></span></span></span></p>
<p><span class="pl-s"><span class="pl-pds"><span class="pl-s"><span
class="pl-pds"><br>
</span></span></span></span></p>
<div class="moz-cite-prefix">On 11/26/2021 10:24 AM, Zhen Li wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAL6PzgpQbGEzKbdnV1prPhYg0C9+bQBxxD+n6=Pxi63U8KC8Cw@mail.gmail.com">
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<div dir="ltr">
<div>Dear researchers,</div>
<div><span style="font-family:arial,sans-serif"><br>
</span></div>
<div><span style="font-family:arial,sans-serif">When I run codes
to prepare DTI images in SimNIBS on Mac:</span></div>
<div><span
style="color:rgb(62,67,73);background-color:rgb(251,229,78)"><font
face="arial, sans-serif"><br>
</font></span></div>
<div><font face="arial, sans-serif"><span
style="color:rgb(62,67,73);background-color:rgb(238,238,238)">dwi</span><span
style="color:rgb(62,67,73);background-color:rgb(238,238,238)">2cond
--all --eddy --phasedir=-y --readout=0.05 ernie
org/ernie_dMRI.nii.gz org/ernie_dMRI.bval
org/ernie_dMRI.bvec org/ernie_dMRI_rev.nii.gz</span></font></div>
<div><span
style="color:rgb(62,67,73);background-color:rgb(238,238,238)"><font
face="arial, sans-serif"><br>
</font></span></div>
<div><font face="arial, sans-serif">The error shows mainly like
this:</font></div>
<div><font face="arial, sans-serif"><span
style="color:rgb(0,0,0)"><br>
</span></font></div>
<div><font face="arial, sans-serif"><span
style="color:rgb(0,0,0)"><b>eddy: msg=--rep_ol cannot be
used for this version of eddy</b></span><br>
</font></div>
<div><font face="arial, sans-serif"><span
style="color:rgb(0,0,0)"><br>
</span></font></div>
<div><font face="arial, sans-serif"><span
style="color:rgb(0,0,0)">but for the given patch here : </span><a
href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Patches"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Patches</a>,</font></div>
<div><font face="arial, sans-serif">there is no other version as
its recommendation:<b> <span style="color:rgb(0,0,0)">e.g.
5.0.0 to 5.0.2</span></b></font></div>
<div><span style="font-family:arial,sans-serif;color:rgb(0,0,0)">I
can only download </span><span
style="font-family:arial,sans-serif;color:rgb(0,0,0)"><b>5.0.9
to 5.0.X or </b></span><span
style="font-family:arial,sans-serif;color:rgb(0,0,0)"><b>5.0.9
to 5.0.8</b>.</span><br>
</div>
<div><span style="color:rgb(0,0,0)"><font face="arial,
sans-serif"><br>
</font></span></div>
<div><span style="color:rgb(0,0,0)"><font face="arial,
sans-serif">I am not sure if it is to do with the version
issue.</font></span></div>
<div><span style="color:rgb(0,0,0)"><font face="arial,
sans-serif">Could you please help me with that?</font></span></div>
<div><span style="color:rgb(0,0,0)"><font face="arial,
sans-serif">I appreciate it😊.</font></span></div>
<div><span style="color:rgb(0,0,0)"><font face="arial,
sans-serif"><br>
</font></span></div>
<div><span style="color:rgb(0,0,0)"><font face="arial,
sans-serif">Best regards,</font></span></div>
<div><span style="color:rgb(0,0,0)"><font face="arial,
sans-serif">Zhen</font></span></div>
</div>
<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
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</pre>
</blockquote>
<pre class="moz-signature" cols="72">--
Dr. Axel Thielscher
Professor of Neurophysics and Neuroimaging
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
<a class="moz-txt-link-abbreviated" href="http://www.drcmr.dk">www.drcmr.dk</a>
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
<a class="moz-txt-link-freetext" href="http://www.healthtech.dtu.dk/">http://www.healthtech.dtu.dk/</a></pre>
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