questions > Unable to equalize slice distances: slice order not consistently ascending.
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Nov 13, 2024  02:11 PM | cathy lei
Unable to equalize slice distances: slice order not consistently ascending.

Hello. 


I am working on processing PET images and encountered an issue when converting DICOM files to NIFTI files. I get the following from dcm2niix:


Chris Rorden's dcm2niiX version v1.0.20220720  GCC10.4.0 x86-64 (64-bit Linux)
Found 255 DICOM file(s)
Warning: Reordering volumes based on FrameReferenceTime (0054,1300; issue 577)
Warning: Interslice distance varies in this volume (incompatible with NIfTI format).
Warning: Reordering volumes based on FrameReferenceTime (0054,1300; issue 577)
Unable to equalize slice distances: slice order not consistently ascending.
First spatial position repeated 1 times
Error:  Recompiling with '-DmyInstanceNumberOrderIsNotSpatial' might help.


Would you have any suggestions on what to do?


Many thanks,
Cathy

Nov 13, 2024  04:11 PM | Chris Rorden
RE: Unable to equalize slice distances: slice order not consistently ascending.

The version of dcm2niix you were using is from 2022, before the PET BIDS specification existed. I would urge you to use the latest stable release


  https://github.com/rordenlab/dcm2niix/re...


typically, the DICOM images do not contain all the information required for subsequent processing, so you may want to use the PET2BIDS wrapper for dcm2niix

  https://github.com/openneuropet/PET2BIDS


The variable slice issue either reflects your data was acquired with variable distance between slices (common in CT, virtually unknown in MR) or that some slices are missing. Visual inspection should help you distinguish between these. I would check the provenance of your images and ensure that you have all the DICOM files, as missing files will cause issues.