3dTstat with oblique dataset

Dear AFNI experts,

I would like to compute standard deviation maps for individual subjects with partial-brain data acquired in oblique orientation. I tried using 3dTstat on un-preprocessed data and got the following message:

WARNING: If you are performing spatial transformations on an oblique dset,
such as TRAIN1.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.

Can someone provide me with more detail about the implications of computing a standard deviation map using an oblique dataset? I’d appreciate any additional information!

Thanks so much,

Shabnam Hakimi, Ph.D.
Center for Cognitive Neuroscience
Duke University

Mostly you have little to worry about. This is a fairly common warning that you can turn off if you like. Turn off the warnings with AFNI_NO_OBLIQUE_WARNING set to YES in your .afnirc file, in your shell or on the command line “-DAFNI_NO_OBLIQUE_WARNING=YES”. There are no implications for 3dTstat for oblique datasets other than what holds for other EPI datasets. Any spatial transformation before doing slice timing corrections (including 3dWarp) generally renders the slice timing correction incorrect or useless, with the exception of very small transformations.

This is super helpful! Thanks, Daniel!