Can you tell me how to check that because I&quot;m having the same problem with spmregister-sess with my linux as well and I&#39;ve never used SPM at all, and honestly can&#39;t even figure out how to open it.<div><br></div>

<div>Katie<br><br><div class="gmail_quote">On Thu, Feb 3, 2011 at 11:21 PM, Y.V. Jiang <span dir="ltr">&lt;<a href="mailto:yuhong.jiang@gmail.com">yuhong.jiang@gmail.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">

Hi Maryam,<br><br>You should check your spm defaults to see whether it uses radiology or neurology convention. Most likely your spm has flipped your image, and the spmregister-sess is trying to match the left hemisphere of your functionals to the right hemisphere of your anatomical. <br>


<br>-Yuhong<br><br><div class="gmail_quote"><div><div></div><div class="h5">On Thu, Feb 3, 2011 at 9:59 PM, Maryam Vaziri Pashkam <span dir="ltr">&lt;<a href="mailto:mvaziri.p@gmail.com" target="_blank">mvaziri.p@gmail.com</a>&gt;</span> wrote:<br>

</div></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex"><div><div></div><div class="h5">
<div dir="ltr">







<p>Hi,</p>
<p><br></p>
<p>I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 computer using freesurfer 4.5. I have  SPM 8 and FSL also installed.</p>
<p><br></p>
<p>I have two versions of matlab (matlab R2009b &amp; R2008a) on my computer. I think spm runs through the R2009b on my computer. I have added the SPM path to the startup.m of both matlabs by adding the following line (they both point to the same startup.m ):</p>



<p>path(path,&#39;/Applications/spm8&#39;);</p>
<p><br></p>
<p>I run preprocessing on the data using the following command:</p>
<p><span>preproc-sess -nosmooth </span>-sf retino-sess -df retino.dir</p>
<p><br></p>
<p>then I run automatic registration with the following command:</p>
<p>spmregister-sess -sf retino-sess -df retino.dir</p>
<p><br></p>
<p>It runs smoothly and there seems to be no errors. But when I try to check the registration with this command:</p>
<p><br></p>
<p>tkregister-sess -sf retino-sess -df retino.dir -inorm</p>
<p><br></p>
<p>what I see is not a good registration. Isn&#39;t spm register supposed to do a good job in automatic registration? The one that I get still needs a lot of manual adjustment. Am I doing something wrong? I have attached the log files for spmregister and tkregister and a screen shot of the image that I get after running tkregister. I would appreciate any help in this matter. </p>




<p><br></p>
<p><br></p>
<p>Thanks,</p>
<p>Maryam</p>
<p><br></p></div>
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<br></blockquote></div><font color="#888888"><br><br clear="all"><br>-- <br>----------------------------------------------------------<br>Yuhong Vanessa Jiang, PhD, <br>Associate Professor &amp; McKnight Presidential Fellow<br>

Department of Psychology, Univ of Minnesota<br>
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