I am trying to run a basic ANOVA using 3dMVM. When I attempt to run the script, I get an accurate summary of data structure, however, the script ‘errors out’ after reading the input files. My error is as follows:
Reading input files now…
Possible reasons:
0) Make sure that R packages afex and phia have been installed. See the 3dMVM
help documentation for more details.
1) Inappropriate model specification with options -model, -wsVars, or -qVars.
Note that within-subject or repeated-measures variables have to be declared
with -wsVars.
2) Misspecifications in general linear test coding with -gltCode.
3) Mistakes in data table. Check the data structure shown above, and verify
whether there are any inconsistencies.
4) Not enough number of subjects. This may happen when there are two or more
withi-subject factors. For example, a model with two within-subject factors with
m and n levels respectively requires more than (m-1)*(n-1) subjects to be able to
model the two-way interaction with the multivariate approach.
** Error:
Quitting due to model test failure...
[b][i]I am using R version 3.2.5 and I have all the listed packages installed and updated.[/i][/b]
My script:
3dMVM -prefix test -jobs 1 \
-model bob \
-dataTable \
Subj bob InputFile \
000000022453 2.000 s888mwc1mprage000000022453.nii \
000000075717 2.000 s888mwc1mprage000000075717.nii \
000000106601 1.000 s888mwc1mprage000000106601.nii \
000000106871 1.000 s888mwc1mprage000000106871.nii \
000000112288 1.000 s888mwc1mprage000000112288.nii \
000000240546 2.000 s888mwc1mprage000000240546.nii \
000000297685 2.000 s888mwc1mprage000000297685.nii \
000000308867 2.000 s888mwc1mprage000000308867.nii \
000000397377 1.000 s888mwc1mprage000000397377.nii \
000000458976 1.000 s888mwc1mprage000000458976.nii \
000000459848 2.000 s888mwc1mprage000000459848.nii \
000000469693 2.000 s888mwc1mprage000000469693.nii \
000000540905 2.000 s888mwc1mprage000000540905.nii \
000000602062 1.000 s888mwc1mprage000000602062.nii \
000000613223 2.000 s888mwc1mprage000000613223.nii \
000000642263 1.000 s888mwc1mprage000000642263.nii \
000000663084 2.000 s888mwc1mprage000000663084.nii \
000000724314 1.000 s888mwc1mprage000000724314.nii
Any suggestions?
~BFair
Bob is a categorical variable (1 through 4) and it should be a between subjects factor as that is the variable of interest for my univariate ANOVA. Bob = latent class, but ‘class’ is a command in R, so I just changed the name to something silly to not run into any parsing errors.
** Error:
Expecting 1 parameters for option “-jobs”.
Have 3 parameter(s) in string “1 -bsVars ‘bob’” instead.
NOTE that -bsVars in bad option above is not a recognized option.
** Error:
Error parsing arguments. See 3dMVM -help for details.
I am not totally sure what this error message means.
Thank you so much for your response. I altered my quotations like you suggested without luck. I still receive this error:
** Error:
Expecting 1 parameters for option “-jobs”.
Have 3 parameter(s) in string “1 -bsVars bob” instead.
NOTE that -bsVars in bad option above is not a recognized option.
** Error:
Error parsing arguments. See 3dMVM -help for details.
I also ran the file_tool -test -infile your3dMVMscript command, but it didn’t seem to tell me much:
medlocals-iMac:Test_Folder Catherine$ file_tool -test -infile 3dMVM_noco.txt
3dMVM_noco.txt file type: UNIX
3dMVM_noco.txt has 0 bad characters
** Error:
Expecting 1 parameters for option “-prefix”.
Have 3 parameter(s) in string “test.nii -bsVars bob” instead.
NOTE that -bsVars in bad option above is not a recognized option.
** Error:
Error parsing arguments. See 3dMVM -help for details.
Updating the operating system and AFNI version did fix this issue.
Thank you for all of your help.
~BFair
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
Health (NIH), a component of the U.S. Department of Health and Human
Services.