Hi all,
I'm still trying to figure out what's going on with the differences I'm getting between selxavg-sess and selxavg3-sess. I"m using freesurfer4.5. I was using selxavg3-sess (as suggested on the wiki) but I was getting weird activation maps when I compared any condition vs. baseline, where most of the brain was more activity for baseline (which was fixation) - see the attached picture for act-fix-gamma-selxavg3-rh.png. So I ran selxavg-sess which was what I used to run with an older version of freesurfer, and when I did this I got a more appropriate picture - see act-fix-gamma-rh.png
The experiment starts with fixation (baseline) so I tried running the analysis with and without skipping the first 2 TRs to account for the BOLD spike, but it makes no difference in the activation map.
These are essentially the commands I ran: mkanalysis-sess.new -analysis loc_loc -TR 2 -paradigm loc.dat -designtype blocked -funcstem fmc -runlistfile loc_runs.txt -inorm -nconditions 2 -timewindow 20 -gammafit 2.25 1.25
mkcontrast-sess -analysis loc_loc -contrast shape_vs_fix -a 2 -c 0
selxavg3-sess -s 101006SP_loc_loc -df loc_loc.dir -analysis loc_loc
Thoughts? Or should I just not use selxavg3-sess?
Katie
---------- Forwarded message ---------- From: Katie Bettencourt kcrum@bu.edu Date: Tue, Nov 2, 2010 at 2:31 PM Subject: Questions about event related processing and selxavg-sess and selxavg3-sess To: freesurfer maillist freesurfer@nmr.mgh.harvard.edu
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
