Hi Gang,

Thank you very much for your reply.
Let me confirm your comments. So you mean that the reason might be that the regressors in my 3dDeconvolve model are not fully independent with each other. Especially, the regressor -stim_times_IM 7 and regressors of -stim_times_AM1 8~11 are at some extent correlated. That's indeed possible in my regression model.

According to your comments (if my interpretation is correct), I expect the two approaches (i.e., 3dDeconvolve with -stim_times_IM, and 3dDeconvolve PLUS 3dTfitter) would generate closer results if I remove the regressors of -stim_times_AM1 8~11 from the model of 3dDeconvolve, i.e, integrating the uninterested factors into the trial onsets and reserve the head motion effects as the baseline regressors.
I tried the above processing on one scan data in a 50-voxel mask, and finally got 4 data sets including previous ones:
A) estimated beta values for each trial using 3dDeconvolve and -stim_times_IM, with uninterested factors removed;
B) estimated neuronal responses at the onset time for each trial using 3dDeconvolve with uninterested factors removed, and later 3dTfitter;
C) estimated beta values for each trial using 3dDeconvolve and -stim_times_IM, with uninterested factors integrated;
D) estimated neuronal responses at the onset time for each trial using 3dDeconvolve with uninterested factors integrated, and later 3dTfitter.
A and B are the results generated previously, and C and D are new.

I calculated the correlation in the four data sets, including correlation between A&B, C&D, A&C, B&D. Corr(A, B) is generally low (-0.09~0.33, mean=0.17); corr(C, D) does not change too much (-0.02~0.35, mean=0.16); corr(A, C) indicates the impact from the uninterested factors on the beta values (0.19~0.87, mean=0.48); surprisingly, corr(B, D) is very high (0.91~1.00, mean=0.99), indicating removing the uninterested factors does not impact the estimated neuronal responses very much.
Since I am considering PPI analysis for later processing, 3dTfitter would be a necessary step. Thus, I am interested in how to use the command in a proper way. But with a low correlation between C and D (and also between A and B), I am kind of unsure about the correct usage of the command.

Thanks again for your help!
Bests,
Nan



Edited 3 time(s). Last edit at 03/30/2018 05:02AM by Nan.