How to verify slice acquisition order

Every time the question of – what slice acquisition order was used/what is the slice timing – comes up, I feel like a whole bunch of us spend forever trying to figure it out. What is the way to found out the slice acquisition order when

  • the image is not acquired on a Siemens scanner (where the slice timing is stored in the DICOM header)
  • we don’t have the DICOM image
  • there’s no MR technician who knows to ask

A followup question is – how do you know if you have botched up the slice timing information during slice timing correction, or in general how do you verify incorrect slice timing correction?

Many thanks,

As a general answer:

Since you state that you do not have access to the DICOM data, nor have access to a MRI technologist, your options are more limited. One option is to look at your 4D dataset using MRIcroGL or FSLeyes, and scan for a volume where head motion occurred. You can use visual inspection as I describe here. Head motion will cause characteristic zebra-stripes due to head motion for interleaved sequences relative to sequential scans.

Awesome – thank you, Chris! So if you didn’t have the DICOM or access to the original sequence protocol/MRi tech person, you wouldn’t necessarily be able to know if you have ascending vs. descending? Would you relink to where you describe how to visually inspect the images (the link now seems to just go back to this message). THANK YOU!

The method for visually determining slice order is illustrated here. You can practice on this dataset. However, these sample datasets have dramatic, intentional head movements designed to confirm slice order. The effects are much more subtle in scans where the participant is trying to keep their head still. Good luck.