Ok, so looking at the FIR analysis, when I advance it to time point 5, I see my activation (yay!) but does this mean my timewindow, etc is set up wrong, or is this just something you have to do when you do a FIR analysis?<br>

<br>Katie<br><br><div class="gmail_quote">On Wed, Nov 3, 2010 at 7:05 PM, Douglas N Greve <span dir="ltr">&lt;<a href="mailto:greve@nmr.mgh.harvard.edu">greve@nmr.mgh.harvard.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">

The FIR does not assume a shape to the HRF but fits each point within the given time window. You might not be seeing activation for several reasons. FIRs are much less efficient than gamma functions. Also, by default, the FIR analysis gives you a sig map at each time point in the FIR, so you might be looking at the activation 1.5 sec *before* stimulus onset (so it would be a good thing not to see any activation!). Try advancing the time point from the overlay config window.<br>


<br>
You can see the map from the gamma and the timecourse from the FIR with something like<br>
tksurfer-sess -analysis fir-analysis -map-analysis gamma-analysis ...<br>
<br>
I&#39;m not sure about the diffs with version 3. Why are you using such an old version?<br>
<br>
doug<br>
<br>
<br>
<br>
Katie Bettencourt wrote:<br>
<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">
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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