It does not seem to be cutting brain tissue from outside the brain. I am trying to register a monkey anatomical scan to a monkey diffusion scan.<br><br>Roman<br><br><br><div class="gmail_quote">On Wed, Mar 5, 2008 at 1:34 PM, MCLAREN, Donald &lt;<a href="mailto:[log in to unmask]"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind0803%26L%3DFSL%26E%3D7bit%26P%3D324251%26B%3D------%253D_Part_3499_15325968.1204754493257%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt; wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">(1) Check the BET output to make sure that it is not cutting off any brain tissue or including anything outside of the brain.<br>
<br>(2) What are you trying to register?<div><div></div><div class="Wj3C7c"><br><br><div class="gmail_quote">On Wed, Mar 5, 2008 at 12:29 PM, Roman Loonis &lt;<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind0803%26L%3DFSL%26E%3D7bit%26P%3D324251%26B%3D------%253D_Part_3499_15325968.1204754493257%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt; wrote:<br>

<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">I am trying to do tractography on monkey brains using FSL studio. I<br>
obtained my images in minc, did some preprocessing, and registered them in<br>
minc. I checked visually to make sure the the structural was well<br>
registered with the diffusion images in a minc based software. I<br>
subsequently converted the files into proper nifti files. Following this<br>
converison, my files were no longer registered properly... I am not too<br>
sure what kind of fix there is available for this error.<br>
<br>
Moreover, I tried registering the images using FSL&#39;s Bet extraction and<br>
then the &quot;registeration&quot; program. The files after the registration were<br>
not well registered. What should I do?<br>
</blockquote></div><br><br clear="all"><br></div></div>-- <br>Best Regards, Donald McLaren<br>=====================<br>D.G. McLaren<br>University of Wisconsin - Madison<br>Neuroscience Training Program<br>Tel: (773) 406 2464<br>
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