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FYI, this was addressed over my personal email. Cheers, Jeanette On Thu, Feb 23, 2017 at 2:12 PM, Rosenblau, Gabriela < [log in to unmask]> wrote: > Hi, > > > > I came across a tutorial to compute percent signal change by Jeanette > Mumford and still had some questions. > > > > I have an event related design and I m interested in parametric EVs. At > the 1st level I have 3 parametric EVs. Because I have 3 runs per subject, I > also ran a second level within subject analysis. At the 3rd level I m > comparing groups (e.g. 1 -1 contrast for cope3.feat). I see group > differences and would like to plot percent signal change to inform the > activation maps. > > > > So I would like to use every subject's second level. The tutorial > distinguishes between 1st and 2nd level, and I don't quite understand the > distinction. It says this: > > > > This is the paragraph I m referring to: > > Figure out your scale factor. – scale factor = 100∗(baseline-to-max > range) (contrast fix) – e.g. Contrast from a first level design. I’m using > an isolated 1 second long event where the double-gamma HRF was used, and a > contrast [1 1 -1 -1] was used. ∗ baseline/max range= 0.2086. ∗ number I’d > divide my contrast by=contrast fix =2. ∗ scale factor = > (100)(0.2086)/2=1.043. > > – For second level, scale factor = 100∗(baseline-to-max range > lev1)(baseline-to-max range lev2) (contrast fix lev1)(contrast fix lev2) > > > > I got the baseline to max range from the attached table but I don't know > what the difference is between the first and second level specification. I > wanted to run the following command on the second level cope of interest. > Is this ok? > > > > fslmaths filtered_func_data.nii.gz -mul 64.71 (this would be 100*0.6471 > (for 5 s events based on your table)/1) -div mean_func.nii.gz -mul > paracing_rating_sphere_10-2_46_16.nii output_percent.nii > > Thank you! > > >