Hi Saad, <br><br>Thank you for your prompt reply. I am actually using the GUI from FSL 4.1.6. where when I check the option of reorienting the bvecs it asks me to specify a nifti file. <br><br>Should I move this script into the bin directory? If yes, I will need to ask the IT people to do it since I do not have permissions to that directory. <br>
<br>Also, will this script work through the GUI for correcting the bvecs?<br><br>Thanks and kind regards,<br>Shail <br><br><br><br><br><br><div class="gmail_quote">On 18 April 2012 13:57, Saad Jbabdi <span dir="ltr">&lt;<a href="mailto:[log in to unmask]"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1204%26L%3DFSL%26E%3Dquoted-printable%26P%3D2062888%26B%3D--f46d044268229a481504bdf3485b%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word"><div>It shouldn&#39;t ask for a nifti file.</div>Which script are you using? Please use the one attached.<span class="HOEnZb"><font color="#888888"><div>
<br></div><div>Saad</div><div><br></div><div><br></div><div> <div></div></div></font></span></div><br><div style="word-wrap:break-word"><div><div></div><div><br></div><div><br><div><div>On 18 Apr 2012, at 12:30, Shail Segobin wrote:</div>
<br><blockquote type="cite"><div class="gmail_quote">Dear experts, <br><br>I am very new to DTI and trying the processing steps for the very first time. <br><br>In the Eddy current correction step, I would like to know why the reorient bvecs wants a nifti image instead of transformation parameters and if anyone could please tell me where to get this file from?<br>


<br>I have sifted through questions on the mailing list and did not really get a concrete answer to this question. <br><br>Many thanks for your time and help<span><font color="#888888"><br><br>Shail <br>
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--</div><div style="margin:0px">Saad Jbabdi</div><div style="margin:0px">University of Oxford, FMRIB Centre</div><div style="margin:0px;min-height:14px"><br></div><div style="margin:0px">JR Hospital, Headington,<span> </span>OX3 9DU, UK</div>
<div style="margin:0px"><a href="tel:%28%2B44%291865-222466" value="+441865222466" target="_blank">(+44)1865-222466</a> <span> </span>(fax 717)</div><div style="margin:0px"><a href="http://www.fmrib.ox.ac.uk/%7Esaad" target="_blank">www.fmrib.ox.ac.uk/~saad</a></div>
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