Hi!
I convert our DICOMS to .nii via dcm2niix and when running 3dinfo -slice_timing ../../data/sub01/rest1.nii I got worried:
3dinfo -slice_timing ../../data/sub01/rest1.nii
** AFNI converts NIFTI_datatype=4 (INT16) in file ../../data/sub01_TF/rest1.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000
To me that indicates that there is no information in the .nii file to find for the AFNI-function, right? This means that my preprocessing is just copying my data and don't preform any slice timing corrections?
When running pre-processing on this particular dataset the output of tshift is:
3dTshift -tzero 0 -quintic -prefix pb02.rest2_sub32.r01.tshift pb01.rest2_sub32.r01.despike+orig
++ 3dTshift: AFNI version=AFNI_17.2.07 (Aug 9 2017) [64-bit]
If it is the case that AFNI does not know the order how do I tell afni_proc.py that it is ascending? Would this be correct?
-tshift_opts_ts -tpattern seq-z
