I was attempting to run an analysis that was previously done in freesurfer 4.5 in version 5 to see if I cuold switch over to the new version.  However, I am getting very different results for the two versions.  Below are the commands I ran in both and attached are pictures of the differences.  I get much much less activation (and much less than expected)  when using version 5.  I assume this is because I&#39;ve done something wrong with the way I set up my version 5 analysis, but I don&#39;t knwo what it is.  Any help would be appreciated.<br>

<br>version 5:<br>mkanalysis-sess -analysis supIPS-gamma-5rh -TR 1.5 -paradigm supIPS.dat -event-related -runlistfile supIPSruns.txt -nskip 2 -nconditions 6 -gammafit 2.25 1.25  -surface self rh -fwhm 0 -refeventdur 6 <br>

mkcontrast-sess -analysis supIPS-gamma-5rh -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0<br>selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis supIPS-gamma-5rh<br>tksurfer-sess -s 101103TM_supIPS -a supIPS-gamma-5rh-c act_vs_fix -df supIPS.dir<br>

<br>version 4.5<br>mkanalysis-sess -analysis supIPS-gamma -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -tpexclude tpexclude.dat -nconditions 6 -gammafit 2.25 1.25 -noautostimdur<br>

mkcontrast-sess -analysis supIPS-gamma -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 <br>tksurfer-sess -s 101103TM_supIPS -df supIPS.dir -a supIPS-gamma -c act_vs_fix -hemi rh<br><br><br>Katie<br>