I'm not sure about the diffs with version 3. Why are you using such an old version?
I'm not sure I understand your question, why am I using the "old version" selxavg-sess or selxavg3-sess? I'm using Freesurfer 4.5, but I tried using selxavg-sess because I was confused by the results I was getting from selxavg3-sess (which is what the wiki says to use), and I was used to using selxavg-sess in my old lab, which was probably because we were using a much older version of Freesurfer. I assumed that selxavg3-sess was the newer version as it didnt' seem to need to have stxgrinder done on it to get maps out. am I wrong? It really is only when you compare against the baseline condition that you see differences in the two, but the selxavg3-sess is what is giving me the really weird whole brain more active for baseline maps.
Katie
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.
- 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).
- 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
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