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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:

  2. Hi, my fRMI data was acquired in descending order (32 axial slices) on a 3T Siemens TIM Trio
    System. Following your line, the slice order should be 1,2,3...32, right? and the next question is which one should be the reference slice, 16 or 17? maybe either is ok? Any suggestion would be appreciated!

    1. Hi Zhiwei, by reference slice do you mean for a temporal reference as you would use for slice timing correction? I don't know what the convention is, but the middle slice makes sense to me. I'd suggest asking the same question to an FLS or SPM help list because the answer isn't specific to Siemens!


    2. yes, it will be used for slice timing correction.
      and it seems that the slice order is 1,2,3..32 for both Ascending and Descending order (say 32 slices). I almost thought that the order for Descending slices should be 32,31,30...1 before o(╯□╰)o
      Thanks for your suggestion.

  3. Thank you very much for this article. I saw it when I started working on fMRI and did not give much of a thought, but now that I know more about the nuts and bolts of fmri acquisition, this issue is one of the first I check systematically!

    I updated the Wikibook entry to add more info on slice order, maybe this can be useful to others:

    In particular it is possible to check the slice order acquisition time from DICOM files and the patient orientation in the machine, this can be very useful to double check. Also there are a few parameters that are important to consider such as Tranversal H >> F which would reverse the order (from ascending to descending, even if interleaved is selected!). Also more details from Siemens directly can be found in this white paper:

  4. lrq3000 - your notes and edits are very helpful. However, there is one inaccuracy: changing the Image Numbering from F >> H to H >> F changes how the images are displayed in mosaics but does not change how they are acquired. Siemens Interleaved and Ascending sequences are acquired in Ascending order regardless of the image numbering setting. I provide sample images from the Siemens Product as well as CMRR Sequences that demonstrate this on my web page

    1. Thank you very much for your reply Chris, indeed I later found the info on your web page, this is highly useful and not detailed in their documentation. However, your test was done on 40 slices, an even number, but the odd number case is more debatable, as your finding (that it does not change the acquisition but only the display/storage in mosaics) contradicts the Siemens documentation I linked above: if your finding is correct also for odd number, then the first volume in mosaic should be even, but according to Siemens it will still be odd!

    2. This comment has been removed by the author.

    3. I found my answer in another work by a team from the University of Gent, which clarifies a bit: both the Siemens documentation and your observation are correct and applicable about the reverse mosaic order (H >> F) of interleaved with an odd number of slices, it will also be odd-first, just as with an even number of slices.

      Also, and more importantly, H >> F does NOT change the slice order at all, so it only changes the display, not the slice storage! (nor acquisition as you said). Hence, contrary to Siemens documentation (or at least this was not clear), one should use the same slice order, whether F >> H or H >> F.

      For reference, here is the Ugent work (and I also updated the SPM Slice Timing wikibooks entry accordingly):
      Descamps, B., Roggeman, C., Vandemaele, P., & Achten, E. (2007), "Image Aquisition Order and Input Order of BOLD-fMRI Data for Slice Time Correction in fMRI Data Processing Tools", in First Benelux In Vivo MR Methods Symposium 2007 PROGRAM BOOK, doi:1854/10927