Hi Gang,

I am looking at the output of the SEMscript.csh for an N=16, and it doesn't seem to make sense.
I'm wondering if there's an issue because the time series is scaled wrong, I it's scaled to 100 max value 200 (as is default in afni_proc.py). That being said, by subject time series files seem to have values between -2 and 2.
I also get a warning the "Input dataset is not 3D+time; assuming TR=1s" after 3dTstat runs. Our TR is actually 3s.

I have inluded the output matrices for Tree growth with covariance Matrix. I have tried Tree growth with correlation matrix and get a similar problem. I have also extended the limits to -3 3.

Thanks,
Steve

++ 1dSEM: AFNI version=AFNI_2008_07_18_1710 (Jul 28 2009) [64-bit]
++ Authored by: Daniel Glen, Gang Chen
Initial Theta Setup Matrix matrix: 2 x 2
# amy mpfc
amy 0.0 1.0000
mpfc 1.0000 0.0
++
++ Connection directionality is from column to row
++ Finding optimal theta values
++ Total number of iterations 33896
++ Cost is 18.5801
++ Chi Square = 15094.9
Connection coefficients matrix: 2 x 2
# amy mpfc
amy 0.0 -9.9995
mpfc 9.9999 0.0
1dSEM -theta thetas.1D -C SEM_cov.1D -DF 813.423 -psi SEM_resvar.1D -tree_growth -limits -3 3
++ 1dSEM: AFNI version=AFNI_2008_07_18_1710 (Jul 28 2009) [64-bit]
++ Authored by: Daniel Glen, Gang Chen
Initial Theta Setup Matrix matrix: 2 x 2
# amy mpfc
amy 0.0 1.0000
mpfc 1.0000 0.0
++
++ Connection directionality is from column to row
++ Number of non-required coefficients 0
++ Number of required coefficients is 2
++ cost = 23.205
Connection coefficients - minimum model matrix: 2 x 2
# amy mpfc
amy 0.0 3.0000
mpfc -3.0000 0.0
++ Chi Square 0 = 18852.285383 for minimum fit