about the analysis of PPI

AFNI Message Board
1

hi everyone
I am trying to do the analysis of PPI recently,however,after reading the ppt file named “connectivity” ,i still got some question about how to do it exactly. For instance,in the program-help page,there is an example about PPI in the command of 3dTfitter tells me that i need to input GAM.1D file, but i dont know how to get it.And i really dont know how to do this simply by reading ur ppt file and the program help information.I indeed need ur help,and hope u could tell me the command that make it happen.Thanks a lot.
a lost guy who starts to learn afni

2

Have you run a normal task analysis yet? Running a PPI
analysis is a somewhat difficult way to start using AFNI.
The PPI analysis depends on a task one.

In any case, an example of how to run a single subject
PPI analysis can be found at AFNI_data6/FT_analysis/PPI,
starting with the top-level script README.txt.

Download AFNI_data6.tgz to run your own analysis.

  • rick
3

Hello Mr. Reynolds,
Now i have done the task analysis,and read the command line on the homepage about ppi of Mr. Chen. But the example it gives is for block design, and now i do have two questions as below:
1, Did i should change “waver” to “3dDconvolve” to create a Gamma impulse response function for event-related design?.
2, What exactly about “sub_tr”, from the script of ur page, the stimulus duration is 3s, and tr is 2, and ‘sub_tr’ is 1. Why?

-Jack

4

Hi Jack,

  1. For the steps, please follow what is done under the example
    in AFNI_data6/FT_analysis/PPI.

  2. The stimulus durations should be passed to timing_tool.py
    via the stim_dur variable in cmd.ppi.2.make.regs, which is also
    where you can specify whether to use GAM or BLOCK as the shape
    of the basis function.

Regarding the oversampled TR, if you stick with TRup=0.1, as is
in the script, set TRnup according to your real TR.

  • rick