Checking orientation and phase encoding direction

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1

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?

2

Hi,

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)
  • …
3

Opening in FSLeyes and overlaying the information worked for me.