Hi  - you may find that running fslreorient2std on your images beforehand will help. <br><br>On Thursday, March 19, 2015, Alex Bonthrone &lt;<a href="mailto:[log in to unmask]"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1503%26L%3DFSL%26E%3Dquoted-printable%26P%3D3941715%26B%3D--001a113fb1584d44a50511aa71d3%26T%3Dtext%252Fhtml%3B%2520charset%3DUTF-8%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt; wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi All,<br>
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I am new to FSL so forgive me if this is a simple issue. I am trying to run FSL FIRST on a data set of MPRAGES and I am having some problems with the registration of some of the images, they are zoomed and rotated relative to the template brain. This occurs in 15/27 subjects. I am running FIRST according to the pipeline on your WIKI pages, the results are the same whether I use run_first_all or first_flirt.<br>
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Any help would be much appreciated!<br>
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Best Wishes,<br>
<br>
Alex<br>
</blockquote><br><br>-- <br>Niels Bergsland<br>Integration Director<br>Buffalo Neuroimaging Analysis Center<br>100 High St. Buffalo NY 14203<br><a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1503%26L%3DFSL%26E%3Dquoted-printable%26P%3D3941715%26B%3D--001a113fb1584d44a50511aa71d3%26T%3Dtext%252Fhtml%3B%2520charset%3DUTF-8%26pending%3D" target="_parent" >[log in to unmask]</a></a><br>