AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

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The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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August 17, 2015 04:57PM
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
Subject Author Posted

1dSVAR example script?

wgraves August 17, 2015 04:57PM

Re: 1dSVAR example script?

jkeidel August 17, 2015 05:01PM

Re: 1dSVAR example script?

wgraves August 17, 2015 05:33PM

Re: 1dSVAR example script?

gang August 19, 2015 03:53PM

Re: 1dSVAR example script?

jkeidel August 19, 2015 06:18PM

Re: 1dSVAR example script?

gang August 18, 2015 04:52PM

Re: 1dSVAR example script?

wgraves August 18, 2015 04:55PM