3dttest++ ** FATAL ERROR: Option -setA: can't open dataset

AFNI Message Board
1

Hi,
I'm new to AFNI and was trying to run second-level analysis on the task fMRI data using 3dttest++.
As I run the command-
3dttest++ -prefix NogoIncFvsN -setA NogoIncFvsN 01 "01[NogoInCFvsN_GLT#0_Coef]" 02 "02[NogoInCFvsN_GLT#0_Coef]" 03 "03[NogoInCFvsN_GLT#0_Coef]" 04 "04[NogoInCFvsN_GLT#0_Coef]" 05 "05[NogoInCFvsN_GLT#0_Coef]" -options -covariates covariates.txt
This error is being displayed-
++ 3dttest++: AFNI version=AFNI_23.3.03 (Oct 30 2023) [64-bit]
++ Authored by: Zhark++
++ option -setA :: processing as LONG form (label label dset label dset ...)
** FATAL ERROR: Option -setA: can't open dataset '01[NogoInCFvsN_GLT#0_Coef]'

Please help me understand this. I'm not sure where this is going wrong.
Thank you in advance!

Best,
Nt

2

Hi, Nt-

Thanks for posting the full command being tried.

Here is an example of the syntax of running the program from the help file, similar to what you posted:

3dttest++ -setA Green sub001 a+tlrc'[3]' \
                      sub002 b+tlrc'[3]' \
                      sub003 c+tlrc'[3]' \
                        ...              \
             -covariates Cfile

Just taking a look at the start of the syntax from that:

3dttest++ \
     -prefix NogoIncFvsN \
     -setA NogoIncFvsN 01 "01[NogoInCFvsN_GLT#0_Coef]" \
                  ...

... I think the issue is that what you have put in the spot where the first filename+subbrick selector label would go (like, the a+tlrc'[3]' in the help example), you have "01[NogoInCFvsN_GLT#0_Coef]", and the 01 doesn't look like a filename. Indeed, 3dttest++ is complaining about not finding that as a valid filename.

Note that you certainly can use double quotes like you do, and that they can go around the whole filename+label, but you should replace 01 with your actual filename. The filename could be BRIK/HEAD or NIFTI (or GIFTI, or several other formats, even). Like, if it were sub-01 and a NIFTI file, then:

3dttest++ \
     -prefix NogoIncFvsN \
     -setA NogoIncFvsN 01 "sub-01.nii[NogoInCFvsN_GLT#0_Coef]" \
                  ...

would be fine. And the same replacement would need to be made across all the setA items.

--pt

3

Thank you for the quick response, PT
I tried running the command after making suggested corrections. I guess 3dttest is still not able to read the file, and displaying the error-
++ option -setA :: processing as LONG form (label label dset label dset ...)
** FATAL ERROR: Option -setA: can't open dataset 'sub-01.BRIK[NogoInCFvsN_GLT#0_Coef]'
Can you provide me with any other solution?

Thank you!

Nt

4

Hi, Nt-

I suspect your file name is not really "sub-01.BRIK" but instead either "sub-01+orig.BRIK" or "sub-01+tlrc.BRIK", for example.

What you should be able to do is:

ls FILENAME

... and see the filename in the terminal. If you can see that, you have the correct filename, and then use that filename exactly in the 3dttest++ command.

--pt

5

Thank you!