Hi Lara,<div>for a blob, one solution is to say sth like:</div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="border-collapse: separate;"><br>

</span></span></font></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 12px; border-collapse: collapse; ">fslmaths $FSLDIR/data/standard/MNI152_T1_2mm -mul 0 -add 1 -roi 50 1 50 1 50 1 0 1 point -odt float<br>

fslmaths point -s 5 sphere -odt float</span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 12px; border-collapse: collapse; "><br></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 12px; border-collapse: collapse; ">and then threshold the &#39;</span><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 12px; border-collapse: collapse; ">sphere&#39; at whatever value that makes the blob suitable for you case ...</span></div>

<div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 12px; border-collapse: collapse; ">(e.g., divide it by its max, and thresh at .2)</span></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>

</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Cheers<br></span></font><br><div class="gmail_quote">On Wed, Apr 20, 2011 at 10:44 PM, Lara Foland <span dir="ltr">&lt;<a href="mailto:[log in to unmask]"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1104%26L%3DFSL%26E%3Dquoted-printable%26P%3D1970883%26B%3D--0016e64653c668251804a16096ef%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;">Hi FSLers,<br>
<br>
I&#39;m using fslmaths to create a spherical roi with a radius of 15mm:<br>
<br>
fslmaths $FSLDIR/data/standard/MNI152_T1_2mm -mul 0 -add 1 -roi 50 1 50 1 50 1 0 1 point -odt float<br>
fslmaths point -kernel sphere 15 -fmean sphere -odt float<br>
<br>
The output roi however looks distorted. Any clues as to what&#39;s going on?<br>
<br>
Many thanks in advance for the help,<br>
<font color="#888888">Lara<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Reza Salimi-Khorshidi DPhil MSc BSc  <br>
Analysis Group, FMRIB Centre of the University of Oxford<br>
Oxford-Man Institute for Quantitative Finance, University of Oxford<br>
<br>
Email: <a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1104%26L%3DFSL%26E%3Dquoted-printable%26P%3D1970883%26B%3D--0016e64653c668251804a16096ef%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>; Tel: +44 (0) 1865 222704;  Fax: +44 (0)1865 222717<br>
Address: FMRIB Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK<br>
</div>