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Dear AFNI users-

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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

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ArielK
February 10, 2015 10:19AM
Hello,

I am quite new to AFNI, and am trying to run a one sample ttest with covariates. The script works without covariates, but when I try to add in -covariates COVAR_FILE, it breaks. Furthermore, the terminal window disappears so I can't read any error messages that may have come up, and the -debug command doesn't change anything about that. I would appreciate any help or advice!

Here is my ttest script (sensitive information has been redacted):

3dttest++ -prefix groupOutput -covariates COVAR_FILE -cmeth MEAN \
-setA 1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
1NNN_fcmp_poscing-z-mni-rv.nii \
2NNN_fcmp_poscing-z-mni-rv.nii \
2NNN_fcmp_poscing-z-mni-rv.nii



And here is my covariate file:

subject AgeFirst
1NNN_fcmp_poscing-z-mni-rv.nii 15
1NNN_fcmp_poscing-z-mni-rv.nii 20
1NNN_fcmp_poscing-z-mni-rv.nii 17
1NNN_fcmp_poscing-z-mni-rv.nii 18
1NNN_fcmp_poscing-z-mni-rv.nii 17
1NNN_fcmp_poscing-z-mni-rv.nii 25
1NNN_fcmp_poscing-z-mni-rv.nii 17
1NNN_fcmp_poscing-z-mni-rv.nii 20
1NNN_fcmp_poscing-z-mni-rv.nii 17
1NNN_fcmp_poscing-z-mni-rv.nii 20
1NNN_fcmp_poscing-z-mni-rv.nii 18
1NNN_fcmp_poscing-z-mni-rv.nii 21
1NNN_fcmp_poscing-z-mni-rv.nii 17
1NNN_fcmp_poscing-z-mni-rv.nii 14
1NNN_fcmp_poscing-z-mni-rv.nii 19
1NNN_fcmp_poscing-z-mni-rv.nii 20
1NNN_fcmp_poscing-z-mni-rv.nii 16
1NNN_fcmp_poscing-z-mni-rv.nii 18
2NNN_fcmp_poscing-z-mni-rv.nii 15
2NNN_fcmp_poscing-z-mni-rv.nii 16


I have also tried a version of the covariate file without all the file extensions; i.e. subject: 1NNN, 2NNN, etc.
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Subject Author Posted

3dttest++ breaks when I try to use -covariates

ArielK February 10, 2015 10:19AM

Re: 3dttest++ breaks when I try to use -covariates

rick reynolds February 10, 2015 10:56AM

Re: 3dttest++ breaks when I try to use -covariates

ArielK February 10, 2015 03:33PM

Re: 3dttest++ breaks when I try to use -covariates

rick reynolds February 10, 2015 04:37PM