Using nilearn with 3dttest++?

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Hello,

I’d like to try out AFNIs 3dttest++ function for my 2nd level analysis using the 1st level zmaps I generated using nilearn.

I was wondering whether inputting sub-xyz_zmap.nii files into 3dttest++ works and if not what is the easiest way to convert them into the shape its expects without having to do the 1st level analysis in AFNI.

Thanks

2

Hi-

You can use NIFTI datasets with 3dttest++ (or any other volumetric AFNI program), yes.

If you have exported valid NIFTIs from nilearn, then you should be good to go.

In case it is useful, you can also use AFNI’s gen_group_command.py to generate a 3dttest++ (or several other stats programs) command, which can simplify some syntax. An example of doing so from an actual paper is provided here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/codex/fmri/2021_YangEtal.html#s3-2021-yangetal-gen-ttest-tcsh

–pt

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