Gaurav-
Our scanner also does not put the slice timing information into the DICOM and resulting NIFTI files (converted with either dcm2nii or Dimon/to3d). One solution is to add the following line to your afni_proc.py scripts. In our case, the slices are alternating starting at 1 instead of 0 - substitute whatever your slice sequence is for alt+z2.
-tshift_opts_ts -tpattern alt+z2
Two other options are 1) use nifti_tool to change the slice info (see: [
nifti.nimh.nih.gov]). Or 2) use a different DICOM to NIFTI converter, such as
dcmstack, which encodes the slice order based on the acquisition time.
