Hmmm, not sure what's going on with that. Can you verify that the registration is correct in the v5 results? The only other thing that I can think of is that the whitening may be a bit different between 4.5 and 5.0. Try turning off the whitening in v5 (-no-whiten when running mkanalysis-sess).
doug Katie Bettencourt wrote: > 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've done something wrong with the way I set up my version 5 > analysis, but I don't knwo what it is. Any help would be appreciated. > > version 5: > 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 > mkcontrast-sess -analysis supIPS-gamma-5rh -contrast act_vs_fix -a 1 > -a 2 -a 3 -a 4 -a 5 -c 0 > selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis supIPS-gamma-5rh > tksurfer-sess -s 101103TM_supIPS -a supIPS-gamma-5rh-c act_vs_fix -df > supIPS.dir > > version 4.5 > 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 > mkcontrast-sess -analysis supIPS-gamma -contrast act_vs_fix -a 1 -a 2 > -a 3 -a 4 -a 5 -c 0 > tksurfer-sess -s 101103TM_supIPS -df supIPS.dir -a supIPS-gamma -c > act_vs_fix -hemi rh > > > Katie > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
