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Sure, you can try to fix it during data processing, but you're usually better off fixing the acquisition!

Friday, July 6, 2012

Siemens slice ordering

I've heard on the wind that there is still confusion or even a total lack of awareness of the change in slice ordering for interleaved slices when going from an odd number to an even number of slices, or vice versa. It makes a big difference for slice timing correction. So I though I'd post below a section from my user training guide/FAQ as a ready reference. Note that as far as I know this change in slice ordering is only an issue for Siemens scanners running VB15 or VB17 software, I can't comment on VD11 or other versions, and I haven't actually tested any scanner platform except a TIM Trio. Furthermore, it's only an issue if you're using interleaved slices. If anyone has additional information, especially if it conflicts with the situation posted here, then the field would probably appreciate a comment!


In what order does the scanner acquire EPI slices?

There are three options for slice ordering for EPI. To understand the ordering you first need to know the Siemens reference frame for the slice axis: the negative direction is [Right, Anterior, Foot] and the positive direction is [Left, Posterior, Head]. The modes are then:
  • Ascending - In this mode, slices are acquired from the negative direction to the positive direction.
  • Descending - In this mode, slices are acquired from the positive direction to the negative direction.
  • Interleaved - In this mode, the order of acquisition depends on the number of slices acquired:
    • If there is an odd number of slices, say 27, the slices will be collected as:
1 3 5 7 9 11 13 15 17 19 21 23 25 27 2 4 6 8 10 12 14 16 18 20 22 24 26.
    • If there is an even number of slices (say 28) the slices will be collected as:
2 4 6 8 10 12 14 16 18 20 22 24 26 28 1 3 5 7 9 11 13 15 17 19 21 23 25 27.

Interleaved always goes in the negative to positive direction, e.g. foot-to-head for transverse slices.

So, if you are doing 28 interleaved axial slices the order will be evens then odds in the foot-to-head direction. 27 interleaved axial slices would also be acquired in the foot-to-head direction but would be in the order odds then evens. If you switch to 28 descending axial slices the acquisition order will become 1,2,3,4,5…28 and the direction will swap to being head-to-foot.


  1. I'm working on fMRI data acquired with a "Siemens AVANTO 1.5T" with software version "Syngo MR B17".
    Should I consider such version equivalent to the VB17 you cited above and so affected by the same issue?
    I'm concerned because my data are interleaved acquisitions of 32 slices and because of the MOSAIC standard I see no way of finding out whether their order is odd-even or even-odd.
    kind regards

    1. Hi Orso, it is my understanding that the software will perform the same regardless of the scanner type or field strength. I can't seem to locate that part of the Siemens manuals from which I took the information in my post, but it looks as if the coordinate convention began with Syngo MR (i.e. all released from VB13 and on) and was adopted to match the DICOM convention, with the Left, Posterior and Head directions being designated as positive slice offsets.

      If there is any residual concern then a long TR experiment with intentional movement will quickly show you what you have: