Slice timing correction in two different datasets

AFNI Message Board
1

Dear AFNI experts,

I have two datasets with a different acquisition slice order (tpattern). I would like to make sure that the slice timing correction with 3dTshift is well done.

  1. First dataset.
    TR=2 seconds
    number of slices=35
    slice order= Interleaved (1,3,5,7…35; 2,4,6,8…34).
    Command used:

3dTshift  -tpattern Alt+z   -Fourier  -prefix s_001_stc.nii  s_001.nii
  1. Second dataset.
    TR=2 seconds
    number of slices=37
    slice order= Interleaved with jumps of 5 slices (1, 7, 13, 19, 25, 31, 37; 2, 8, 14, 20, 26, 32; 3, 9, 15, 21, 27, 33; 4, 10, 16, 22, 28, 34; 5, 11, 17, 23, 29, 35; 6, 12, 18, 24, 30, 36).
    Command used:

3dTshift  -tpattern Alt+z   -Fourier  -prefix s_001_stc.nii  s_001.nii

I am using the exact same tpattern for both datasets. Is this correct considering that the second dataset has different jumps between slices?
Note: The to3d program considered both datasets as Alt+z.
Thanks in advance.

Kind regards,
Karel

2

I responded on the other thread: https://afni.nimh.nih.gov/afni/community/board/read.php?1,166247,166248#msg-166248

Not sure why to3d is calling them both the same. We generally recommend using dcm2nii (or dcm2nii_afni in the distribution) at this point. This looks like multi-band / multi-slice data. Which scanner is it from?

-Peter