Hello. I know my slice timing should be siemens style – so with an even number of 32 slices like this: [2:2:32 1:2:31]. However, the way this was done in the scanner, the NIFTI files do not have this specific information, so when I use dcm2niix the json files do not have correct record of the slice timing (rather, it refers to some variable that I assume outputs the correct numbers).
I am attempting to run my data both through AFNI alone, and through fmriPrep. So I would really like/need to update my JSON files to have the correct slice timing information. I know fmriprep calls upon afni for the slice timing with 3dtshift. So, I thought I would ask here how I need to update my JSON files.
I assume the line would be something like
“SliceTiming”: “[2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 1 3 5 … 31]”
?
Or, what is the correct way to update these JSON files for fmriprep to be calling afni 3dtshift correctly?
Thanks!