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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!