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I see where you are coming from now. So, using a 3-column format timing model, the third column would have "0.44" (probability I mentioned in previous e-mail), instead of "1". I will see how it goes. Thanks very much for the input. Liam. On 19 October 2011 14:09, Eugene Duff <[log in to unmask]> wrote: > Hi Liam - > > Are the probabilities changing from trial to trial - I think that is > how TDRLs usually work? If so, what I think you want to do is have > regressors where the height of the modelled response is modulated > according to the TDRL. If you use 3-column format timing model, the > height corresponds to the values in the third column, so you can > modulate this. Depending on your hypothesis, you may want to have > this regressor in addition to a mean response regressor. A lot of > the decision making studies from FMRIB use this sort of modelling, > without (I believe) a great deal of hacking of FSL. > > Eugene > > > On 19 October 2011 13:23, Liam Nestor <[log in to unmask]> wrote: > > Hi Eugene > > > > I have a monetary incentive delay (MID) task. I want to try and employ a > > temporal difference reinforcement learning (TDRL) model. > > > > The MID has a prepare period, 3 cue conditions and 6 outcome conditions > > (EV=10). > > > > The contrasts generated for each subject, for each run (n=3) from the > first > > level analysis are: > > Cope 1 = Loss Cue (EV 1) > > Cope 2 = Win Cue (EV 2) > > Cope 3 = Neutral Cue (EV 3) > > Cope 4 = Lost Outcome (EV 4) > > Cope 5 = Saved Outcome (EV 5) > > Cope 6 = Lost+Saved (EV 1+EV 2) > > Cope 7 = Won Outcome (EV 6) > > Cope 8 = Missed Outcome (EV 7) > > Cope 9 = Won+Missed (EV 6+EV 7) > > Cope 10 = Neutral Lost Outcome (EV 8) > > Cope 11 = Neutral Won Outcome (EV 9) > > Cope 12 = Prepare (EV 10) > > > > The TDRL model concerned involves the Win Cue period X probability (0.44) > - > > the "expected value". The "expected value" is calculated as the sum of > all > > possible outcomes (4.5) X probability (0.44). > > > > Therefore, I want to run the formula - Win cue X 0.44 - sum of all > possible > > outcomes (4.5) X probability (0.44) to generate a new image file. I have > > tried the following: > > > > fslmaths cope2.nii.gz -mul 0.44 -sub 4.5 -mul 0.44 cope13.nii.gz > > > > It generates cope13.nii.gz, but it won't threshold on this file when I > run a > > Fixed Effects level analysis averaging across the 3 runs. > > > > I have no knowledge of being able to use this formula when setting up the > > contrasts in the FSL GLM GUI, which is why I'm attempting to do this in > the > > "stats" directory afterwards. > > > > Thanks, > > > > Liam. > > > > > > On 19 October 2011 12:31, Eugene Duff <[log in to unmask]> wrote: > >> > >> Hi Liam - > >> > >> On 19 October 2011 12:14, Liam Nestor <[log in to unmask]> wrote: > >>> > >>> Dear FSL users > >>> > >>> Using fslmaths, I want run a formula, using files that go into the > >>> "stats" directory, which are generated from a first level analysis. The > >>> files that end up in this directory are cope; neff; pe; tstat; varcope > and > >>> zstat. The formula is very simple - merely multiplying one of the > contrasts > >>> by a number and subtracting another number. > >>> > >> > >> The cope and varcope files are the primary images used in higher level > >> analyses. Both will be affected by multiplication of the contrasts. You > >> might want to describe want you are trying to do to - I can't really > think > >> of a reason why you would want to do what you are saying. > >> Cheers, > >> Eugene > >> > >> > >> > >>> > >>> What I'm not sure about is which contrast files will go into the > formula? > >>> The cope; neff; pe; tstat; varcope or zstat files? All of them? I have > tried > >>> using the cope, tstat and zstat files in the formula, but when I run a > Fixed > >>> Effects analysis (averaging across runs), it will not create > thresholded > >>> zstat files for the new files that I have created using fslmaths. > >>> > >>> I'm not able to set this formula up using the FSL GUI when doing the > >>> first level analyses, which is why I am having to resort to this > formula > >>> subsequently. > >>> > >>> Thanks, > >>> > >>> Liam. > >>> > >>> > >>> -- > >>> Liam J Nestor PhD > >>> > >> > > > > > > > > -- > > Liam J Nestor PhD > > > > > > -- Liam J Nestor PhD