Checking orientation and phase encoding direction

I noticed some possible discrepancies in the phase encoding directions of my EPI scans.

I read that the phase encoding direction depends on the orientation (e.g., LPI, RAS, LAS, etc.).

Where in the .json file or header can I find the orientation of my scans before and after running fmriprep?


You can find information about the orientation in the header of the NIFTI files.

To look at this information, you can use:

  • fslhd (FSL)
  • 3dinfo (AFNI)
  • mri_info (FreeSurfer)
  • mrinfo (MRtrix3)

Opening in FSLeyes and overlaying the information worked for me.