Hi, Gang,
I'm just testing for Granger causality between the seed and one other node, just to get the hang of the program. My progress through the program from the beginning and to the error constitutes the first paragraph below. The second and third paragraphs are the seed and node ROI file data, respectively.
Thanks for your time.
"> source("/home/andrew/afni/1dGC.R")
[1] "#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
[1] " ================== Welcome to 1dGC.R ================== "
[1] "AFNI Vector (or Multivariate) Auto-Regressive (VAR or MAR) Modeling Package!"
[1] "#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
[1] "Version 1.0.8, April 8, 2009"
[1] "Author: Gang Chen (gangchen@mail.nih.gov)"
[1] "Website: [
afni.nimh.nih.gov];
[1] "SSCC/NIMH, National Institutes of Health, Bethesda MD 20892"
[1] "#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
[1] "Package network successfully loaded!"
[1] "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
[1] "Visit [
afni.nimh.nih.gov] and makse sure"
[1] "you've acquired the data for the analysis in desirable data format."
[1] "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
[1] "################################################################"
[1] "Please consider citing the following if this program is useful for you:"
Gang Chen, J. Paul Hamilton, Moriah E. Thomason, Ian H. Gotlib, Ziad S. Saad
Robert W. Cox, Granger causality via vector auto-regression (VAR) attuned for
FMRI data analysis. ISMRM 17th Scientific Meeting, Hawaii, 2009.
[1] "################################################################"
[1] "Use CNTL-C on Unix or ESC on GUI version of R to stop at any moment."
Analysis type (0: quit; 1: individual; 2: group)? 1
[1] "Package gsl successfully loaded!"
[1] "Package vars successfully loaded!"
Number of regions/nodes (e.g., 6)? 2
[1] "Header with one line of labels is optional in multi-column files, but NOT allowed in one-column files."
ROI time series data type (0: MULTIPLE one-column files; 1: ONE multi-column file)? 0
No. 1 ROI time series file name: /home/andrew/experiments/GCM_test/S1/ROI_1_sub_1.1D
[1] "No. 1 file just read in: ROI_1_sub_1.1D"
No. 2 ROI time series file name: /home/andrew/experiments/GCM_test/S1/ROI_2_sub_1.1D
[1] "No. 2 file just read in: ROI_2_sub_1.1D"
Name for region/node number 1? A
Name for region/node number 2? B
[1] "#++++++++++++++++++++++++++++++++++++++++++++"
[1] "If there are n consecutive chunks of data, enter n-1 here."
[1] "If all the time series are consecutive, enter 0 breaks."
Number of breaks in the time series? 5
Length of number 1 run/segment? 112
Length of number 2 run/segment? 112
Length of number 3 run/segment? 112
Length of number 4 run/segment? 112
Length of number 5 run/segment? 112
Length of number 6 run/segment? 112
[1] "#++++++++++++++++++++++++++++++++++++++++++++"
[1] "Prior detrending is NOT recommended due to potential complications. "
[1] "Trend can be modeled through specifying the order of a polynomial here, "
[1] "or can be included as part of covariates later on. If you plan to model the"
[1] "trend with your own regressors or don't need to model it, choose -1 here."
[1] "If trend has already been removed (not recommended), choose 0 here."
Order of polynomials for drifting effects (note: -1 means no trend removal!)? 2
[1] "#++++++++++++++++++++++++++++++++++++++++++++"
Any other covariates or confounding effects than drifting (0: no; 1: yes)? 1
Number of covariates (e.g., 6)? 6
[1] "Header with one line of labels is optional in multi-column files, but NOT allowed in one-column files."
Covariates data type (0: MULTIPLE one-column files; 1: ONE multi-column file)? 0
Error in read.table(inFile[[ii]], header = FALSE) :
'file' must be a character string or connection"
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-0.08
-0.14
-0.21
0.1
-0.19
-0.17
-0.17
0.03
0.16
-0.13
-0.11
-0.08
0.05
0.03
0.27
0.69
0.48
0.41
0.67
0.66
0.09
-0.09
-0.39
-0.15
0.32
0.53
0.37
0.03
-0.47
-0.55
-0.41
0.02
0.01
-0.37"
