fslreorient2std did the trick for me. Thanks!<br><br>Tren<br><br><div class="gmail_quote">On Sun, Nov 20, 2011 at 10:19 AM, Mark Jenkinson <span dir="ltr">&lt;<a href="mailto:[log in to unmask]"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1111%26L%3DFSL%26E%3Dquoted-printable%26P%3D1408951%26B%3D--90e6ba6e8b1603284004b230719a%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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="word-wrap:break-word">Actually, please use fslreorient2std instead of fslswapdim.<div>All the best,</div><div>
<span style="white-space:pre-wrap">	</span>Mark</div><div><div></div><div class="h5"><div><br><div><div>On 20 Nov 2011, at 16:34, Stephen Smith wrote:</div><br><blockquote type="cite"><div bgcolor="#FFFFFF"><div>Hi try fslswapdim first, to match the orientation of mni152</div>
<div><br></div><div>Cheers<br><br>--------------------<div>Stephen M. Smith,  Professor of Biomedical Engineering</div><div>Associate Director,   Oxford University FMRIB Centre</div><div><br></div><div>FMRIB, JR Hospital, Headington,</div>
<div>Oxford. OX3 9 DU, UK</div><div><a href="tel:%2B44%20%280%29%201865%20222726" value="+441865222726" target="_blank">+44 (0) 1865 222726</a>  (fax 222717)</div><div><a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1111%26L%3DFSL%26E%3Dquoted-printable%26P%3D1408951%26B%3D--90e6ba6e8b1603284004b230719a%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a></div>
<div><a href="http://www.fmrib.ox.ac.uk/%7Esteve" target="_blank">http://www.fmrib.ox.ac.uk/~steve</a></div><div>----------------------</div></div><div><br>On 20 Nov 2011, at 15:45, Tren Huang &lt;<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1111%26L%3DFSL%26E%3Dquoted-printable%26P%3D1408951%26B%3D--90e6ba6e8b1603284004b230719a%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt; wrote:<br>
<br></div><div></div><blockquote type="cite"><div>Dear FSL experts,<br><br>With the default parameters set by the FSL GUI, I couldn&#39;t extract a subject&#39;s brain cleanly. I always saw some parts of the subject&#39;s neck left after using BET2 (non-iteration and iteration). My FSL version is 4.1.5, and I&#39;ve tried various thresholds and couldn&#39;t find an ideal trade-off value. Finally, the &quot;Biased field &amp; neck cleanup&quot; option seemed to work very well on the original T1 image.<br>

<br>However, SIENAX indicated that my spatial pre-processing was unsuccessful since brain extraction:<br><br><a href="http://cns.bu.edu/%7Etren/sienax/" target="_blank">http://cns.bu.edu/~tren/sienax/</a>      (A modified SIENAX report)<br>

<br>although my structure_brain.nii.gz (i.e., the first image in the report) looked just fine.<br><br>I wonder what factors caused these misalignments in spatial normalization and how to fix them?<br><br>Thanks!<br>Tren<br>

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