Dear AFNI experts (especially Gang),
In trying to run 1dSVAR.R, I can get pretty far using the interactive interface, but I've been trying to make the process workable by creating a script I can give to 1dSVAR that contains all the answers to the interactive questions. Unfortunately, when I run my little custom script:
~/data/ambig_sam/fmr_scripts/make1dSVAR.csh
It errors out early on with this message:
[1] "#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
[1] " ================== Welcome to 1dSVAR.R ================== "
[1] "AFNI Structural Vector Auto-Regressive (SVAR) Modeling Package!"
[1] "#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
[1] "Version 0.0.3, June 21, 2011"
[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] "#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
Loading required package: network
network: Classes for Relational Data
Version 1.12.0 created on 2015-03-04.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
Mark S. Handcock, University of California -- Los Angeles
David R. Hunter, Penn State University
Martina Morris, University of Washington
Skye Bender-deMoll, University of Washington
For citation information, type citation("network").
Type help("network-package") to get started.
Package network loaded successfully!
[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, Daniel R. Glen, Ziad S. Saad, J. Paul Hamilton, Moriah E. Thomason, Ian H. Gotlib, and Robert W. Cox, Vector Autoregression, Structural Equation Modeling, and Their Synthesis in Neuroimaging Data Analysis. Under review. n
[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)?
Error in if (anaType == 1) { : missing value where TRUE/FALSE needed
Calls: source -> withVisible -> eval -> eval
Execution halted
I feel like this must be a scripting error on my part, since when I enter the required values by hand from the file my script generates, things go just fine.
So what I'm asking is, could you please provide an example of a text file containing hypothetical answers to the interface questions that actually works? Being able to work from an example would be hugely helpful.
For reference, here's what I'm trying to give it:
source ("/usr/lib/afni/bin/1dSVAR.R")
1
6
0
/home/wgraves/data/ambig_sam/data/001/mri/subj001_AG.1D
/home/wgraves/data/ambig_sam/data/001/mri/subj001_ATL.1D
/home/wgraves/data/ambig_sam/data/001/mri/subj001_IFJ.1D
/home/wgraves/data/ambig_sam/data/001/mri/subj001_IPS.1D
/home/wgraves/data/ambig_sam/data/001/mri/subj001_vOT.1D
/home/wgraves/data/ambig_sam/data/001/mri/subj001_PC.1D
AG
ATL
IFJ
IPS
vOT
PC
4
126
126
126
126
126
3
1
7
0
/home/wgraves/data/ambig_sam/data/001/mri/x.1D
/home/wgraves/data/ambig_sam/data/001/mri/y.1D
/home/wgraves/data/ambig_sam/data/001/mri/z.1D
/home/wgraves/data/ambig_sam/data/001/mri/dx.1D
/home/wgraves/data/ambig_sam/data/001/mri/dy.1D
/home/wgraves/data/ambig_sam/data/001/mri/dz.1D
/home/wgraves/data/ambig_sam/data/001/mri/noise.1D
x
y
z
dx
dy
dz
noise
0
0
1
1
1
0
0
0
0
/home/wgraves/data/ambig_sam/data/instant_effs.txt
1
1
/home/wgraves/data/ambig_sam/data/001/mri/instant_effs_mat.txt
1
/home/wgraves/data/ambig_sam/data/001/mri/instant_effs_mat_tvals.txt
1
/home/wgraves/data/ambig_sam/data/001/mri/PathLag1Subj001
0
Thanks in advance for any help!
-Will