Wait, I&#39;m confused, in v 4.5 (which I&#39;m using) the paradigm files have 4 values per line (starting time, condition, length, and weight), so don&#39;t they have the lengths in there?  I know you could use an older paradigm file with only 2 columns (starting time, condition), and in this case I would list each TR and the condition there, but the wiki says that v. 4.5 can use the 4 column paradigm files.  Is that not true?  I mean it obviously uses the weights....<div>

<br></div><div>I ran an event related analysis with -noautostimdur in the analysis, with a 4 column paradigm file.  I did not list every TR, but used the 3rd column to list the length of time.  I got what appears to be valid data out.  When I redid it with -autostimdur, I got very little activation.  But if the -noautostimdur assumes that each event is equal to the TR (which is shorter than the actual durations I have), then wouldn&#39;t the analysis have had problems because I didn&#39;t cover all the TRs in the paradigm file? But it worked fine.</div>

<div><br></div><div>I&#39;m very confused here.<br><div><br>Also, is there a difference between the way this is used in FIR and Gamma analyses?<br><br></div><div>Katie</div><div><br></div><div><br><div class="gmail_quote">

On Fri, Apr 15, 2011 at 2:33 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">

FYI: autostimdur is not valid in version 5.X because the stimulus duration is supplied in the paradigm file. For earlier versions, there was no info in the par file about the duration. The -autostimdur will compute the duration of the stimulus from the paradigm file based upon the time to the next stimulus entry this works as long as all time is accounted for in the parfile and no stimuli overlap. If you use -no-autostimdur, then it will assume that the duration of the event is equal to the TR.<br>


<br>
doug<div><div></div><div class="h5"><br>
<br>
Katie Bettencourt wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I&#39;m a bit confused about what the -autostimdur and -noautostimdur flags in mkanalysis-sess do.  I&#39;ve checked the help files, but the wording is a bit confusing, and when I run them on my event related design, I get different results depending on which flag I use, with the -noautostimdur being more of what I expect as far as results go.<br>


<br>
Also, they are only used in event related and AB designs, not blocked, correct?<br>
<br>
Katie<br>
</blockquote>
<br></div></div>
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