Hello,

I am working with a data set in which the raw epi data are in 4-dimensional nifti files and the t1 data in 3d nifti files. I have two sets of questions regarding what AFNI thinks about these nifti files:

1)
I decided to first change these to BRIK/HEAD files before running them through afni_proc. When doing so, the epi files were put given the “+tlrc” tag, whereas the t1 files were given the “+orig” tag. Because both are raw files, these should both be in original space (+orig). If I try to run the nifti files directly through the afni_proc script, AFNI also believes these epi files are in Talaraich space.

Is it possible that afni falsely put the epi files into Talaraich space? If so, I know that I can use “3drefit” to force AFNI to attribute these files as in original space. Or, was there some transformation on these files of which I am not aware?

2)
If I do go ahead and do 3drefit and run the afni_proc script, during 3dTshift I receive a warning which says that my dataset is already aligned in time (see error message below). If this is raw data, why may I receive this warning message?


—-
++ Output dataset ./pb01.337.r01.despike+orig.BRIK
end
foreach run ( 01 )
3dTshift -tzero 0 -quintic -prefix pb02.337.r01.tshift pb01.337.r01.despike+orig
++ 3dTshift: AFNI version=AFNI_18.2.06 (Jul 31 2018) [64-bit]
*+ WARNING: dataset is already aligned in time!
*+ WARNING: ==>> output dataset is just a copy of input dataset