In fact, I had to use selxavg-sess and not selxavg3-sess to do the FIR analysis because fast-selxavg3-sess failed during the FIR analysis (I dont&#39; have the error on me right now, but I can send it in tomorrow if it&#39;s important).<div>

<br></div><div>Katie<br><br><div class="gmail_quote">On Thu, Nov 4, 2010 at 12:29 PM, Katie Bettencourt <span dir="ltr">&lt;<a href="mailto:kcrum@bu.edu">kcrum@bu.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">

<div class="gmail_quote"><div class="im"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
I&#39;m not sure about the diffs with version 3. Why are you using such an old version?<br>
<br>
</blockquote><div><br></div></div><div>I&#39;m not sure I understand your question, why am I using the &quot;old version&quot;  selxavg-sess or selxavg3-sess?  I&#39;m using Freesurfer 4.5, but I tried using selxavg-sess because I was confused by the results I was getting from selxavg3-sess (which is what the wiki says to use), and I was used to using selxavg-sess in my old lab, which was probably because we were using a much older version of Freesurfer.  I assumed that selxavg3-sess was the newer version as it didnt&#39; seem to need to have stxgrinder done on it to get maps out.  am I wrong?  It really is only when you compare against the baseline condition that you see differences in the two, but the selxavg3-sess is what is giving me the really weird whole brain more active for baseline maps.</div>


<div><br></div><font color="#888888"><div>Katie</div></font><div><div></div><div class="h5"><div><br></div><div><br></div><div><br></div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

doug<br>
<br>
<br>
<br>
Katie Bettencourt wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div>
Hi all,<br>
<br>
I&#39;ve been trying to analyses both an event related and block design experiments and have noticed a couple things that are confusing me and I would appreciate any help anyone could give me.<br>
<br>
1.  In trying do the event-related analysis, I&#39;m am a bit confused by the FIR vs Gamma analysis and the use of the time window and tprestim in the FIR analysis.  I have an experiment with 6 set size conditions and 1 fixation condition.  each trial is 6s long with a TR of 1.5<br>



<br>
I have run both of these commands:<br>
<br>
 mkanalysis-sess.new -analysis supIPS_loc -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -nskip 2 -nconditions 6 -gammafit 2.25 1.25<br>
<br>
mkanalysis-sess.new -analysis supIPS_loc -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -nskip 2 -nconditions 6 -tprestim 2 -timewindow 20<br>
<br>
<br>
The FIR gives me a time course window, which makes me think that perhaps that is the one I want to use, but it shows very little activation.  This data has been previously analyzed in Brain Voyager, so I know it&#39;s not a case of the conditions not actually causing activation, but for some reason, the FIR analysis doesn&#39;t show any.  I&#39;m not sure if this is due to a bad time window/tprestim settings, or something else.  However the gamma fit analysis shows a bunch of activity where I expect to see it, but no time course window.  (attached are pngs of the differences for the act_vs_fixation comparison). <br>



<br>
2.  In addition, in both the event related (gamma) and a normal block design (different experiment) I get very different results (at least for certain comparisons) depending on whether I use selxavg-sess (with stxgrinder-sess for each contrast) or selxavg3-sess.  The differences are shown in the attached pngs (act_vs_fix-gamma.png (which is the selxavg-sess and stxgrinder-sess analysis and act_vs_fix-gamma-selxavg3).  In the block design, both selxavg3 and selxavg (+stxgrinder) give me very similar activation when comparing two non-null conditions (ie. shape_vs_noise) but very different (and similar to the differences in the attached pictures) activations when comparing against the null (ie shape_vs_fix or noise_vs_fix).  What am I doing wrong here?<br>



<br>
Thanks for your help!<br>
<br>
Katie<br>
<br></div></div>
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