Hello both,

Many thanks for your replies. It seems indeed that the slice timing information is limited in NIFTI headers and cannot be automatically read out in for example FSL. This is one of the reasons why I switched to AFNI. By converting the dicoms using to3d the slice timing information is preserved in the header and can be applied in slice timing corrections (see output 3dinfo -slice_timing below).

Allow me to give a better illustration of the slice timing artifacts I saw in my images. Although there are undoubtably better ways of quantifying slice timing errors I used InstaCorr to see if odd/even slices correlate more strongly with each other creating blue-red horizontal stripes. The image attached illustrates better shows how slice timing affects the images. Does this make sense?
The only processing steps applied here are dicom conversion(to3d), slice timing correction (3dTshift) and motion correction (3dvolreg).

Many thanks,
Jasper

3dinfo -slice_timing run_1+orig 
0.000000|1.032500|0.085000|1.117500|0.170000|1.205000|0.257500|1.290000|0.342500|1.375000|0.430000|1.462500|0.515000|1.547500|0.602500|1.635000|0.687500|1.720000|0.772500|1.807500|0.860000|1.892500|0.945000|0.000000|1.032500|0.085000|1.117500|0.170000|1.205000|0.257500|1.290000|0.342500|1.375000|0.430000|1.462500|0.515000|1.547500|0.602500|1.635000|0.687500|1.720000|0.772500|1.807500|0.860000|1.892500|0.945000

3dinfo run_1+orig

Dataset File:    run_1+orig
Identifier Code: XYZ_slYlY6IdWOhPNmi1MkO47Q  Creation Date: Fri Jun 23 14:02:50 2017
Template Space:  ORIG
Dataset Type:    Echo Planar (-epan)
Byte Order:      LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode:    BRIK
Storage Space:   328,373,760 (328 million [mega]) bytes
Geometry String: "MATRIX(2,0,0,-102.5542,0,1.978032,-0.295619,-102.305,0,0.295619,1.978032,-66.97668):104,104,46"
Data Axes Tilt:  Oblique (8.500 deg. from plumb)
Data Axes Approximate Orientation:
  first  (x) = Right-to-Left
  second (y) = Anterior-to-Posterior
  third  (z) = Inferior-to-Superior   [-orient RAI]
R-to-L extent:  -102.554 [R] -to-   103.446 [L] -step-     2.000 mm [104 voxels]
A-to-P extent:   -95.451 [A] -to-   110.549 [P] -step-     2.000 mm [104 voxels]
I-to-S extent:   -51.605  -to-    38.395 [S] -step-     2.000 mm [ 46 voxels]
Number of time steps = 165  Time step = 2.00000s  Origin = 0.00000s  Number time-offset slices = 46  Thickness = 2.000
  -- At sub-brick #0 '#0' datum type is float:            0 to         39112
  -- At sub-brick #1 '#1' datum type is float:            0 to         38725
  -- At sub-brick #2 '#2' datum type is float:            0 to         42286
** For info on all 165 sub-bricks, use '3dinfo -verb' **

----- HISTORY -----
[spock-login.pni.princeton.edu: Fri Jun 23 14:02:50 2017] to3d -prefix run_1 -ushort2float -time:zt 46 165 2000 FROM_IMAGE 11-100-1.dcm 11-101-1.dcm 11-10-1.dcm ... 11-98-1.dcm 11-99-1.dcm