It sounds like it is set up correctly. If you want a single map of the activation, you'll have to set up a proper contrast to do it. In mkcontrast-sess you can simply use -sumdelays; this will create a map based on the summation of the delays in the FIR. You can also choose a time point in the FIR with -sumdelays -setwdelays. It will prompt you for a list of N numbers (N being the number of points in the FIR window). You can give is something like 0 0 0 0 1 0 0 0 0 0 0 to extract time point 5. I usually recommend -sumdelays.
doug Katie Bettencourt wrote: > 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? > > Katie > > On Wed, Nov 3, 2010 at 7:05 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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. > > You can see the map from the gamma and the timecourse from the FIR > with something like > tksurfer-sess -analysis fir-analysis -map-analysis gamma-analysis ... > > I'm not sure about the diffs with version 3. Why are you using > such an old version? > > doug > > > > Katie Bettencourt wrote: > > Hi all, > > I'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. > > 1. In trying do the event-related analysis, I'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 > > I have run both of these commands: > > 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 > > 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 > > > 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's not a case of the conditions not > actually causing activation, but for some reason, the FIR > analysis doesn't show any. I'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). > > 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? > > Thanks for your help! > > Katie > > > ------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > -- 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
