Very helpful Gang. I hope you can bear with a few clarification questions ~Dane

> help file for 3dfim+ appears to say its old and not being maintained. Is 3dDeconvolve now the preferred approach these days?

>>Even though 3dfim+ will not be updated, it can still be used as long as you adopt the same or similar model formulations. In fact, you can directly obtain the output for correlation values from 3dfim+ without conversion like 3dDeconvolve.

>>> What exactly do you mean by "similar model formulations"? Do you mean using same polort# and Pearson's vs Spearman's correlation, or something else? e.g. perhaps "modeling" like stim_time_IM vs AM, and block vs. tent? If so, how would you specify it in 3dfim+?

> What is proper polort # and other basic parameters to use?

>>The order of polynomial fit is purely empirical. If I remember it correctly, a rule of thumb is one order per 150 seconds of data. For Beta Series analysis, probably easier to use the option -stim_times_IM.

>>> From a theoretical standpoint, is use of polort deconvolution even necessary if it was already applied at previous step to create the Betaseries estimations used in this subsequent correlation step? If not, would one use polort 0 or 1 to not apply it?

>>>In regards to stim_times_IM, do you mean using this in the second 3ddeconvolve when labeling the seed signal for correlation to wholebrain?

> What is the proper Coef and R^2 subbriks outputs to use in the following square root step
> 'ispositive(b)*sqrt(a)-isnegative(b)*sqrt(a)' equation, the FULL_model, or the Stim_file_1_SEED?

>>The 'a' part is the regression coefficient and 'b' is R^2.

>>> Apologies I think this question was confusing. In the bucket file output there are two groups of subbrik outputs: the "Full model" (#0 & #1) and "the seed" as specified in the stim_time1 (#2 thru #4). See image attached from the GUI. Both can have coef and R^2. Just not sure which represents the desired correlation.



Edited 2 time(s). Last edit at 08/23/2022 05:32AM by daanderson.