some questions about the gPPI sample script

AFNI Message Board
1

Hey,

I’ve got a few questions about Gang’s gPPI sample script.

Could the ' be added to the end of the 3dDetrend line to prevent it erroring out?

What is supposed to be in the one1.1D file and how should be it be created?

With respect to the line:

waver -GAM -peak 1 -${TR} ${sub_TR} -input Inter_neu${cond}${cc}${sd}.1D -numout ${n_tp} > Inter_hrf${cond}${cc}${sd}.1D

I cannot find anything in the waver help that indicates that two TRs can be provided in the manner suggested above. Should this be

waver -GAM -peak 1 -TR ${sub_TR} -input Inter_neu${cond}${cc}${sd}.1D -numout ${n_tp} > Inter_hrf${cond}${cc}${sd}.1D

Thanks in advance,

Colm.

2

Hi Colm,

That webpage should be updated. Please follow the demo script here (also check out README.txt): https://afni.nimh.nih.gov/pub/dist/edu/data/CD.expanded/AFNI_data6/FT_analysis/PPI